100 results on '"Xiaoyuan Song"'
Search Results
52. The Sperm Proteome of the Oyster Crassostrea hongkongensis
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Duo Zhang, Yanjie Zhang, Yang Zhang, Huawei Mu, Shengwei Ke, Ziniu Yu, Jian-Wen Qiu, and Xiaoyuan Song
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Male ,Proteomics ,Oyster ,Proteome ,Sequence alignment ,Biochemistry ,03 medical and health sciences ,Human fertilization ,Tandem Mass Spectrometry ,biology.animal ,Animals ,Crassostrea ,Molecular Biology ,reproductive and urinary physiology ,030304 developmental biology ,0303 health sciences ,biology ,urogenital system ,fungi ,030302 biochemistry & molecular biology ,Marine invertebrates ,biology.organism_classification ,Sperm ,Spermatozoa ,Chromatography, Liquid - Abstract
Sperm proteins play vital roles in fertilization, but little is known about their identities in free-spawning marine invertebrates. Here, 286 sperm proteins are reported from the Hong Kong oyster Crassostrea hongkongensis using label-free and semi-quantitative proteomics. Proteins extracted from three sperm samples are separated by SDS-PAGE, analyzed by LC-MS/MS, and identified using Mascot. Functional classification of the sperm proteome reveals energy metabolism (33%), signaling and binding (23%), and protein synthesis and degradation (12%) as the top functional categories. Comparison of orthologous sperm proteins between C. hongkongensis, Crassostrea gigas, Mytilus edulis, and M. galloprovincialis suggests that energy metabolism (48%) is the most conserved functional group. Sequence alignment of the C. hongkongensis bindin, an acrosomal protein that binds the sperm and the egg, with those of three other Crassostrea species, reveals several conserved motifs. The study has enriched the data of invertebrate sperm proteins and may contribute to studies of mechanisms of fertilization in free-spawning invertebrates. The proteomic data are available in ProteomeXchange with the identifier PXD018255.
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- 2020
53. Reorganized 3D Genome Structures Support Transcriptional Regulation in Mouse Spermatogenesis
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X Wang, Xiaowen Gong, C. Yan Cheng, Zhengyu Luo, Michael G. Rosenfeld, Fei Sun, Yusheng Chen, Xiaoyuan Song, Jian Chen, Qianlan Xu, Ji Wu, Ruoyu Wang, Yun-Gui Yang, Jun Cao, Wenbo Li, Hong Jiang, and Chunsheng Han
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0301 basic medicine ,Regulation of gene expression ,Multidisciplinary ,Cohesin ,Male Reproductive Endocrinology ,02 engineering and technology ,Genomics ,Compartmentalization (psychology) ,Biology ,021001 nanoscience & nanotechnology ,Genome ,Article ,Cell biology ,Chromatin ,03 medical and health sciences ,030104 developmental biology ,Meiosis ,CTCF ,Transcriptional regulation ,lcsh:Q ,0210 nano-technology ,Transcriptomics ,lcsh:Science - Abstract
Summary Three-dimensional chromatin structures undergo dynamic reorganization during mammalian spermatogenesis; however, their impacts on gene regulation remain unclear. Here, we focused on understanding the structure-function regulation of meiotic chromosomes by Hi-C and other omics techniques in mouse spermatogenesis across five stages. Beyond confirming recent reports regarding changes in compartmentalization and reorganization of topologically associating domains (TADs), we further demonstrated that chromatin loops are present prior to and after, but not at, the pachytene stage. By integrating Hi-C and RNA-seq data, we showed that the switching of A/B compartments between spermatogenic stages is tightly associated with meiosis-specific mRNAs and piRNAs expression. Moreover, our ATAC-seq data indicated that chromatin accessibility per se is not responsible for the TAD and loop diminishment at pachytene. Additionally, our ChIP-seq data demonstrated that CTCF and cohesin remain bound at TAD boundary regions throughout meiosis, suggesting that dynamic reorganization of TADs does not require CTCF and cohesin clearance., Graphical Abstract, Highlights • Chromatin loops are reorganized during mouse spermatogenesis, being absent in pacSC • CTCF and cohesin remain bound to pacSC chromatin while TADs and loops are lost • Chromatin accessibility per se is not involved in the loss of TADs or loops in pacSC • A/B compartments switching is related to meiosis-specific mRNAs and piRNAs expression, Male Reproductive Endocrinology; Genomics; Transcriptomics
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- 2020
54. Senescence-associated genes and non-coding RNAs function in pancreatic cancer progression
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Qingyu Cheng, Xuan Ouyang, Xiaoyuan Song, Lianbang Zhu, and Ran Zhang
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Senescence ,Aging ,Biology ,03 medical and health sciences ,0302 clinical medicine ,Senescence associated genes ,Gene Modules ,Pancreatic cancer ,medicine ,Biomarkers, Tumor ,Humans ,Gene Regulatory Networks ,Molecular Biology ,030304 developmental biology ,Cell Proliferation ,0303 health sciences ,Gene Expression Profiling ,Computational Biology ,Cell Biology ,Non-coding RNA ,medicine.disease ,Gene Expression Regulation, Neoplastic ,Pancreatic Neoplasms ,030220 oncology & carcinogenesis ,Cancer research ,Disease Progression ,RNA, Long Noncoding ,Function (biology) ,Transcription Factors ,Research Paper - Abstract
Pancreatic cancer is a major cause of mortality with a poor diagnosis and prognosis that most often occurs in elderly patients. Few studies, however, focus on the interplay of age and pancreatic cancer at the transcriptional level. Here we evaluated the possible roles of age-dependent, differentially expressed genes (DEGs) in pancreatic cancer. These DEGs were used to construct a correlation network and clustered in six gene modules, among which two modules were highly correlated with patients’ survival time. Integrating different datasets, including ATAC-Seq and ChIP-Seq, we performed multi-parallel analyses and identified eight age-dependent protein coding genes and two non-coding RNAs as potential candidates. These candidates, together with KLF5, a potent functional transcription factor in pancreatic cancer, are likely to be key elements linking cellular senescence and pancreatic cancer, providing insights on the balance between them, as well as on diagnosis and subsequent prognosis of pancreatic cancer.
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- 2020
55. A chemical screening method for menaquinone-producing strains based on HPLC-UV technology
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Weiping Chen, Sheng Cao, Ganjun Yuan, Pingyi Li, Xia Du, Shanjun Chen, Xiaoyuan Song, and Bingdi Kuang
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Microbiology (medical) ,Bacillus amyloliquefaciens ,Bacillus ,Bacillus subtilis ,Microbiology ,03 medical and health sciences ,Bacillus isolates ,Screening method ,Mass Screening ,Molecular Biology ,Chromatography, High Pressure Liquid ,030304 developmental biology ,Bacillus (shape) ,0303 health sciences ,biology ,Strain (chemistry) ,030306 microbiology ,Chemistry ,Vitamin K 2 ,biology.organism_classification ,Chemical screening ,Biochemistry ,Fermentation ,Soybeans ,Fermented Foods - Abstract
Despite menaquinones (MKs)-4 and − 7 being known to have extensive biological activities and applications, less attention has been paid to the other MKs. Thus, to obtain a range of MKs to further explore their pharmacological activities, structure-activity relationships, and applications, a chemical screening method for MK-producing strains was established based on high-performance liquid chromatography-ultraviolet (HPLC-UV) technology. Considering that Bacillus strains have proven to be an important MK-producing bioresource, twenty-nine putative Bacillus isolates previously sought from a fermented soybean sample were used for the validation of the chemical screening method, which ultimately led to the discovery of sixteen MK-producing strains. Among them, Bacillus subtilis DC-1 presented excellent ability to produce MKs. Another, a purchased strain of B. amyloliquefaciens was discovered to be an MK-producing strain. These results indicated this screening method was simple and highly efficient for the discovery of MK-producing strains, especially those producing a range of MK structures.
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- 2019
56. Cryogenic Characteristics and Relaxation Polarization Mechanism of NaCl Aqueous Solutions
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Jiaxi He, Jinghui Gao, Xiaoyuan Song, Lisheng Zhong, Minchen Qiu, and Qinxue Yu
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Aqueous solution ,Materials science ,Hydrogen ,Relaxation (NMR) ,Analytical chemistry ,chemistry.chemical_element ,Dielectric ,Activation energy ,law.invention ,Differential scanning calorimetry ,chemistry ,law ,Amorphous ice ,Physics::Chemical Physics ,Crystallization ,Physics::Atmospheric and Oceanic Physics - Abstract
In this paper, the crystallization and relaxation of NaCl aqueous solutions at low temperatures were studied by differential scanning calorimetry (DSC) analysis and dielectric analysis. From DSC analysis, the three-phase composite ice structural model consisting of pure ice, salty ice, and amorphous ice after the liquid-solid phase transition of NaCl aqueous solution under low temperature is established. The conversion rate of pure ice decreases monotonically with the increase of solution concentration. From dielectric analysis, the relaxation time of water molecules in composite ice decreases significantly at first and then increases slightly with increasing concentration, while the relaxation activation energy increases significantly at first and then decreases slightly. This is due to the damaging effect of ions on hydrogen bonds between water molecules and the interaction between anions and cations. This study can provide theoretical support and experimental basis for cryopreservation technology of biomaterials controlled by electromagnetic field.
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- 2019
57. DC breakdown properties in large oil gaps with and without pressboard interface
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Baofeng Xi, Linfeng Xia, Lisheng Zhong, Mingbang Guo, Xiaoyuan Song, Songlin Jiang, Qinxue Yu, and Xin Yue
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Pressboard ,Materials science ,Dielectric strength ,Electrode ,Direct current ,medicine ,Breakdown voltage ,Composite material ,Mineral oil ,medicine.drug - Abstract
Dielectric breakdown values were measured in 15-100mm gaps in mineral oil and two types of natural esters. The test included breakdown properties in oils and creeping discharge over pressboard immersed in oils under negative and positive direct current with a boost speed of 2kV/s. The test used point-plane electrode system. It has been found that except the positive breakdown voltage at small gaps under the experimental gap, the insulating properties of mineral oils are superior to the two natural esters. The DC properties of the two natural esters are almost the same, and each has its own advantages.
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- 2019
58. An electrically switched ion exchange system with self-electrical-energy recuperation for efficient and selective LiCl separation from brine lakes
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Zhongde Wang, Guoqing Guan, Wangwang Ji, Wenjun Yan, Junjian Niu, Xiaogang Hao, and Xiaoyuan Song
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Materials science ,Ion exchange ,Electric potential energy ,Inorganic chemistry ,chemistry.chemical_element ,Filtration and Separation ,02 engineering and technology ,021001 nanoscience & nanotechnology ,Electrochemistry ,Analytical Chemistry ,Ion ,Brine ,020401 chemical engineering ,chemistry ,Desorption ,Electrode ,Lithium ,0204 chemical engineering ,0210 nano-technology - Abstract
Various electrochemical separation methods have been investigated for the recovery of lithium to satisfy the global demand for lithium. However, most of them are still greatly limited by high energy consumption and deficient selectivity. To overcome these issues, in this study, an electrically switched ion exchange (ESIX) system for efficient and selective LiCl separation from brine lakes was developed based on a strategy of self-electrical-energy recuperation, in which the electric energy generated in the process of LiCl uptake was proposed to compensate the energy consumed for the desorption of ions as well as the regeneration of electrodes. λ-MnO2 film coated electrode and BiOCl@PPy film coated electrode were fabricated to capture Li+ and Cl- ions in the brine lake, respectively. In the ion uptake process, the inherent potential difference between the two electrodes was balanced due to the embeddedness of Li+ and Cl- ions, which simultaneously triggered the generation of electric energy. This generated electric energy was automatically stored and provided for the desorption of the Li+ and Cl- ions from the electrodes in the ion releasing process. As a result, this ESIX system featured with extremely low energy consumption (1.007 Wh for separating per mole of LiCl) and excellent selectivity with a LiCl recovery capacity of 10.88 mg/g. It is expected that such an ESIX system with self-electrical-energy recuperation could be a promising alternative to those current electrochemical techniques for the recovery of LiCl from brine lakes.
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- 2021
59. Author Correction: The genome of Nautilus pompilius illuminates eye evolution and biomineralization
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He Dai, Lvping Zhang, Fan Mao, Ziwei Zhang, Yuanyan Xiong, Haitao Ma, Hongkun Zheng, Minwei Huang, Lili Wang, Huawei Mu, Xiaoyuan Song, Nai-Kei Wong, Xiyu Mu, Yang Zhang, Yongbo Bao, Mingli Ma, Shu Xiao, Oleg Simakov, Ziniu Yu, Yuehuan Zhang, Zhiming Xiang, Jun Li, and Fan Wang
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2019-20 coronavirus outbreak ,Evolution of the eye ,Ecology ,biology ,Coronavirus disease 2019 (COVID-19) ,Evolutionary biology ,Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) ,Nautilus ,biology.organism_classification ,Genome ,Ecology, Evolution, Behavior and Systematics - Published
- 2021
60. Shining the Light on Senescence Associated LncRNAs
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Qingyu Cheng, Muhammad Azhar, Xiaoyuan Song, Qianlan Xu, Shengwei Ke, and A. R. Ghanam
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0301 basic medicine ,Senescence ,Cell cycle checkpoint ,Cell ,lncRNAs ,Cellular senescence ,biomarkers ,Cell Biology ,Review ,Biology ,Phenotype ,In vitro ,Pathology and Forensic Medicine ,Cell biology ,03 medical and health sciences ,030104 developmental biology ,medicine.anatomical_structure ,Cell culture ,Tumor progression ,medicine ,cellular senescence ,Neurology (clinical) ,Geriatrics and Gerontology - Abstract
Cellular senescence can be described as a complex stress response that leads to irreversible cell cycle arrest. This process was originally described as an event that primary cells go through after many passages of cells during cell culture. More recently, cellular senescence is viewed as a programmed process by which the cell displays a senescence phenotype when exposed to a variety of stresses. Cellular senescence has been implicated in tumor suppression and aging such that senescence may contribute to both tumor progression and normal tissue repair. Here, we review different forms of cellular senescence, as well as current biomarkers used to identify senescent cells in vitro and in vivo. Additionally, we highlight the role of senescence-associated long noncoding RNAs (lncRNAs).
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- 2017
61. Mechanisms of three-dimensional transcriptional regulation in cell senescence
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Qi Peng, Qingyu Cheng, Jun Cao, Xiaoyuan Song, Zhengyu Luo, and Yan Wu
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Regulation of gene expression ,Genetics ,Histone ,biology ,Cellular differentiation ,DNA methylation ,biology.protein ,Transcriptional regulation ,Pharmacology (medical) ,Epigenetics ,Chromatin ,Epigenomics ,Cell biology - Abstract
Precise regulation of gene expression is a prerequisite for cell differentiation, development, and maintenance of normal activity and function. Many studies have shown that activation or inhibition of gene transcription is not only affected by histone modifications, DNA methylation, and other epigenetic modifications but is also highly dependent on chromatin conformation. In addition, in the process of cellular senescence, long noncoding RNAs (lncRNAs) also play a significant role in gene transcriptional regulation. Here, we highlight recent studies of the mechanism of function of lncRNAs in cellular senescence. In particular, we focus on gene transcription regulation mediated by lncRNAs participating in the formation of the three-dimensional conformation of chromatin.
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- 2017
62. Synthesis and Antibacterial Activity of Ursolic Acid Derivatives
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Junfang Li, Wang Yimin, Ganjun Yuan, Houqin Yi, Shan Lai, Pingyi Li, and Xiaoyuan Song
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Mtt ,Chemistry ,Broth microdilution ,Antimicrobial ,medicine.disease_cause ,Antibacterial Activity ,chemistry.chemical_compound ,Synthesis ,Ursolic acid ,Staphylococcus aureus ,Toxicity ,medicine ,Ursolic Acid ,Structural Modification ,Mic ,Antibacterial activity ,Cytotoxicity ,IC50 ,Nuclear chemistry - Abstract
To obtained natural products with remarkable antibacterial activities, three 3-amino substituted (UA) derivatives 2, 3 and 4 were designed and synthesized, and their antibacterial activity were assayed using broth microdilution method. Compared to UA, there three derivatives present higher antimicrobial activities against methicillin-resistant Staphylococcus aureus (MRSA) with the minimum inhibitory concentrations of 16 to 32 μg/mL. Furthermore, their cytotoxicities to human hepatoma cell (BEL-7402) were evaluated using MTT method, and the results indicated that their derivatives had no toxicity (IC50 value was larger than 10 μM), while UA presented a certain cytotoxicity.Read Complete Article at ijSciences: V82019082169 AND DOI: http://dx.doi.org/10.18483/ijSci.2169
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- 2019
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63. Three-dimensional genome reorganization during mouse spermatogenesis
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Feifei Sun, Xiaowen Gong, Zhengyu Luo, Yunqiang Yang, Chen Y, Chen J, Xiaoyuan Song, Chao Han, Qianlan Xu, Jun Cao, X Wang, Jiaoxiang Wu, Wenbo Li, and Ruiping Wang
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CTCF ,Transcriptional regulation ,Promoter ,Biology ,Enhancer ,Genome ,X chromosome ,Chromatin ,Cell biology ,Genomic organization - Abstract
Three-dimensional genome organization plays an important role in many biological processes. Yet, how the genome is packaged at the molecular level during mammalian spermatogenesis remains unclear. Here, we performed Hi-C in seven sequential stages during mouse spermatogenesis. We found that topological associating domains (TADs) and chromatin loops underwent highly dynamic reorganization. They displayed clear existence in primitive type A spermatogonia, disappearance at pachytene stage, and reestablishment in spermatozoa. Surprisingly, even in the absence of TADs and chromatin loops at pachytene stage, CTCF remained bound at TAD boundary regions (identified in primitive type A spermatogonia). Additionally, many enhancers and promoters exhibited features of open chromatin and transcription remained active at pachytene stage. A/B compartmentalization and segmentation ratio were conserved in different stages of spermatogenesis in autosomes, although there were A/B compartment switching events correlated with gene activity changes. Intriguingly, A/B compartment structure on the X chromosome disappeared during pacSC, rST and eST stages. Together, our work uncovered a dynamic three-dimensional chromatin organization during mouse spermatogenesis and suggested that transcriptional regulation could be independent of TADs and chromatin loops at specific developmental stages.
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- 2019
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64. Front Cover: The Sperm Proteome of the Oyster Crassostrea hongkongensis
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Yanjie Zhang, Duo Zhang, Jian-Wen Qiu, Huawei Mu, Yang Zhang, Xiaoyuan Song, Shengwei Ke, and Ziniu Yu
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Crassostrea hongkongensis ,Oyster ,Front cover ,biology.animal ,Proteome ,Zoology ,Biology ,Molecular Biology ,Biochemistry ,Sperm - Published
- 2020
65. Crystal Structure and Substrate Specificity of PTPN12
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Xiaoyun Ma, Wenjun Wang, Peng Xiao, Fu-ai Cui, Xiaoyuan Song, Fan Yi, Zong-Lai Liang, Jin-Peng Sun, Zhigang Xu, Dongfang He, Wei Zhang, Yunfei Xu, Hong-Mei Wang, Chun-Hua Liu, Chuan Liu, Wenshuai Zheng, Hui Li, Xiao Yu, and Fan Yang
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Models, Molecular ,0301 basic medicine ,Protein Tyrosine Phosphatase, Non-Receptor Type 12 ,Protein tyrosine phosphatase ,Crystal structure ,Crystallography, X-Ray ,Protein Structure, Secondary ,General Biochemistry, Genetics and Molecular Biology ,Substrate Specificity ,Phosphoserine ,03 medical and health sciences ,Protein structure ,Catalytic Domain ,Hydrolase ,Humans ,Amino Acid Sequence ,Phosphorylation ,lcsh:QH301-705.5 ,Peptide sequence ,biology ,Cyclin-Dependent Kinase 2 ,Cyclin-dependent kinase 2 ,Kinetics ,030104 developmental biology ,lcsh:Biology (General) ,Biochemistry ,biology.protein ,Substrate specificity ,Peptides - Abstract
SummaryPTPN12 is an important tumor suppressor that plays critical roles in various physiological processes. However, the molecular basis underlying the substrate specificity of PTPN12 remains uncertain. Here, enzymological and crystallographic studies have enabled us to identify two distinct structural features that are crucial determinants of PTPN12 substrate specificity: the pY+1 site binding pocket and specific basic charged residues along its surface loops. Key structurally plastic regions and specific residues in PTPN12 enabled recognition of different HER2 phosphorylation sites and regulated specific PTPN12 functions. In addition, the structure of PTPN12 revealed a CDK2 phosphorylation site in a specific PTPN12 loop. Taken together, our results not only provide the working mechanisms of PTPN12 for desphosphorylation of its substrates but will also help in designing specific inhibitors of PTPN12.
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- 2016
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66. The key role of CYC2 during meiosis in Tetrahymena thermophila
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Guanxiong Yan, Qianlan Xu, Xiaoyuan Song, A. R. Ghanam, Ruoyu Wang, and Wei Miao
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0301 basic medicine ,Spo11 ,DNA repair ,lcsh:Animal biochemistry ,homologous recombination ,Biology ,Biochemistry ,Genetic recombination ,Tetrahymena thermophila ,03 medical and health sciences ,0302 clinical medicine ,cyclin ,Meiosis ,Drug Discovery ,meiosis ,RNA-Seq ,lcsh:QH573-671 ,lcsh:QP501-801 ,Gene ,Genetics ,lcsh:Cytology ,fungi ,Tetrahymena ,Cell Biology ,biology.organism_classification ,030104 developmental biology ,biology.protein ,DNA mismatch repair ,Homologous recombination ,030217 neurology & neurosurgery ,Biotechnology - Abstract
Meiotic recombination is carried out through a specialized pathway for the formation and repair of DNA double-strand breaks (DSBs) made by the Spo11 protein. The present study shed light on the functional role of cyclin, CYC2, in Tetrahymena thermophila which has transcriptionally high expression level during meiosis process. Knocking out the CYC2 gene results in arrest of meiotic conjugation process at 2.5–3.5 h after conjugation initiation, before the meiosis division starts, and in company with the absence of DSBs. To investigate the underlying mechanism of this phenomenon, a complete transcriptome profile was performed between wild-type strain and CYC2 knock-out strain. Functional analysis of RNA-Seq results identifies related differentially expressed genes (DEGs) including SPO11 and these DEGs are enriched in DNA repair/mismatch repair (MMR) terms in homologous recombination (HR), which indicates that CYC2 could play a crucial role in meiosis by regulating SPO11 and participating in HR.
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- 2016
67. Identification ofpara-Substituted Benzoic Acid Derivatives as Potent Inhibitors of the Protein Phosphatase Slingshot
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Hao Fang, Peng Xiao, Jin-Peng Sun, Duxiao Yang, Kangshuai Li, Xu Chen, Xiaoyuan Song, Xuben Hou, Dongfang He, Hongda Liu, Xiao Yu, Daolai Zhang, Lin Ge, and Ke-rui Han
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Rhodanine ,Phosphatase ,Benzoates ,PC12 Cells ,Biochemistry ,Dephosphorylation ,Inhibitory Concentration 50 ,Structure-Activity Relationship ,Cell Movement ,Nerve Growth Factor ,Drug Discovery ,Phosphoprotein Phosphatases ,Animals ,Structure–activity relationship ,Enzyme Inhibitors ,Phosphorylation ,General Pharmacology, Toxicology and Pharmaceutics ,Pharmacology ,Slingshot ,Chemistry ,Kinase ,Organic Chemistry ,Lim Kinases ,Benzoic Acid ,Cofilin ,Angiotensin II ,Molecular biology ,Rats ,Kinetics ,Molecular Medicine ,Protein Binding - Abstract
Slingshot proteins form a small group of dual-specific phosphatases that modulate cytoskeleton dynamics through dephosphorylation of cofilin and Lim kinases (LIMK). Small chemical compounds with Slingshot-inhibiting activities have therapeutic potential against cancers or infectious diseases. However, only a few Slingshot inhibitors have been investigated and reported, and their cellular activities have not been examined. In this study, we identified two rhodanine-scaffold-based para-substituted benzoic acid derivatives as competitive Slingshot inhibitors. The top compound, (Z)-4-((4-((4-oxo-2-thioxo-3-(o-tolyl)thiazolidin-5-ylidene)methyl)phenoxy)methyl)benzoic acid (D3) had an inhibition constant (Ki) of around 4 μm and displayed selectivity over a panel of other phosphatases. Moreover, compound D3 inhibited cell migration and cofilin dephosphorylation after nerve growth factor (NGF) or angiotensin II stimulation. Therefore, our newly identified Slingshot inhibitors provide a starting point for developing Slingshot-targeted therapies.
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- 2015
68. piRDisease v1.0: a manually curated database for piRNA associated diseases
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Xiaoyuan Song, Hong Jiang, Azhar Muhammad, Ramay Waheed, and Nauman Ali Khan
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Treatment response ,endocrine system ,Data curation ,Database ,Computer science ,urogenital system ,Association (object-oriented programming) ,Piwi-interacting RNA ,computer.software_genre ,General Biochemistry, Genetics and Molecular Biology ,Database Tool ,Humans ,Disease ,RNA, Small Interfering ,General Agricultural and Biological Sciences ,Databases, Nucleic Acid ,computer ,Data Curation ,Information Systems ,Reference genome - Abstract
In recent years, researches focusing on PIWI-interacting RNAs (piRNAs) have increased rapidly. It has been revealed that piRNAs have strong association with a wide range of diseases; thus, it becomes very important to understand piRNAs’ role(s) in disease diagnosis, prognosis and assessment of treatment response. We searched more than 2500 articles using keywords, such as `PIWI-interacting RNAs’ and `piRNAs’, and further scrutinized the articles to collect piRNAs-disease association data. These data are highly complex and heterogeneous due to various types of piRNA idnetifiers (IDs) and different reference genome versions. We put considerable efforts into removing redundancy and anomalies and thus homogenized the data. Finally, we developed the piRDisease database, which incorporates experimentally supported data for piRNAs’ relationship with wide range of diseases. The piRDisease (piRDisease v1.0) is a novel, comprehensive and exclusive database resource, which provides 7939 manually curated associations of experimentally supported 4796 piRNAs involved in 28 diseases. piRDisease facilitates users by providing detailed information of the piRNA in respective disease, explored by experimental support, brief description, sequence and location information. Considering piRNAs’ role(s) in wide range of diseases, it is anticipated that huge amount of data would be produced in the near future. We thus offer a submitting page, on which users or researches can contribute in to update our piRDisease database.
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- 2018
69. Azalomycin F
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Ganjun, Yuan, Li, Xu, Xuejie, Xu, Peibo, Li, Qiwang, Zhong, Hailin, Xia, Yamei, Hu, Pingyi, Li, Xiaoyuan, Song, Junfang, Li, and Qianru, Liu
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Lipopolysaccharides ,Methicillin-Resistant Staphylococcus aureus ,Teichoic Acids ,Cell Membrane Permeability ,Cell Membrane ,Macrolides ,Molecular Dynamics Simulation ,Phospholipids ,Anti-Bacterial Agents - Abstract
Azalomycin F
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- 2018
70. Rearrangement of macronucleus chromosomes correspond to TAD-like structures of micronucleus chromosomes in
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Zhengyu, Luo, Tengfei, Hu, Hong, Jiang, Ruoyu, Wang, Qianlan, Xu, Simo, Zhang, Jun, Cao, and Xiaoyuan, Song
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Meiosis ,Macronucleus ,Research ,Centromere ,Micronucleus, Germline ,Chromatin ,Chromosomes ,Tetrahymena thermophila - Abstract
The somatic macronucleus (MAC) and germline micronucleus (MIC) of Tetrahymena thermophila differ in chromosome numbers, sizes, functions, transcriptional activities, and cohesin complex location. However, the higher-order chromatin organization in T. thermophila is still largely unknown. Here, we explored the higher-order chromatin organization in the two distinct nuclei of T. thermophila using the Hi-C and HiChIP methods. We found that the meiotic crescent MIC has a specific chromosome interaction pattern, with all the telomeres or centromeres on the five MIC chromosomes clustering together, respectively, which is also helpful to identify the midpoints of centromeres in the MIC. We revealed that the MAC chromosomes lack A/B compartments, topologically associating domains (TADs), and chromatin loops. The MIC chromosomes have TAD-like structures but not A/B compartments and chromatin loops. The boundaries of the TAD-like structures in the MIC are highly consistent with the chromatin breakage sequence (CBS) sites, suggesting that each TAD-like structure of the MIC chromosomes develops into one MAC chromosome during MAC development, which provides a mechanism of the formation of MAC chromosomes during conjugation. Overall, we demonstrated the distinct higher-order chromatin organization in the two nuclei of the T. thermophila and suggest that the higher-order chromatin structures may play important roles during the development of the MAC chromosomes.
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- 2018
71. Excessive nerve growth factor impairs bidirectional communication between the oocyte and cumulus cells resulting in reduced oocyte competence
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Yong Wang, Xiaoyuan Song, Yiwen Zhai, Guidong Yao, Faiza Rao, and Fei Sun
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0301 basic medicine ,Adult ,endocrine system ,China ,lcsh:QH471-489 ,In Vitro Oocyte Maturation Techniques ,Bidirectional communication ,Cell Communication ,Biology ,lcsh:Gynecology and obstetrics ,Andrology ,03 medical and health sciences ,Mice ,Endocrinology ,Nerve Growth Factor ,medicine ,lcsh:Reproduction ,Animals ,Humans ,RNA, Messenger ,Receptor, trkA ,Receptor ,lcsh:RG1-991 ,Polycystic ovary syndrome ,Cells, Cultured ,NGF ,Mice, Inbred ICR ,Cumulus Cells ,Oocyte-derived paracrine factors ,Dose-Response Relationship, Drug ,Research ,fungi ,Obstetrics and Gynecology ,Oocyte ,Polycystic ovary ,Follicular fluid ,Follicular Fluid ,Meiosis ,030104 developmental biology ,medicine.anatomical_structure ,Real-time polymerase chain reaction ,Nerve growth factor ,Reproductive Medicine ,PFKP ,Oocytes ,Female ,Glycolysis ,Developmental Biology - Abstract
Background Excessive nerve growth factor (NGF) is commonly found in the follicular fluid of patients with polycystic ovary syndrome (PCOS). Furthermore, oocytes from PCOS patients exhibit lower developmental competence. The purpose of this study was to explore the association between excessive NGF and low oocyte competence in vitro. Methods Excessive NGF was added to mouse cumulus oocyte complexes (COCs) cultured in vitro to investigate meiotic maturation of the oocyte. After culture, mRNA expression levels of Pfkp and Ldha genes in cumulus cells (CCs) and Gdf9, Bmp15 and Fgf8 genes in oocytes, were determined by real-time quantitative polymerase chain reaction (qPCR). We also investigated the mRNA content of Pfkp and Ldha in CCs from PCOS and non-PCOS patients. Results Excessive NGF significantly inhibited oocyte meiotic maturation. The inhibitory effect was mediated by the NGF high-affinity receptor, NTRK1. mRNA content of Pfkp and Ldha genes in CCs was significantly reduced by excessive NGF stimulation. Moreover, the expression levels of Gdf9, Bmp15 and Fgf8 were also decreased in oocytes, and was induced by excessive NGF-stimulated CCs. In addition, lower expression levels of Pfkp and Ldha in CCs were identified in Chinese PCOS patients with excessive NGF (PCOS, 22 ± 2.63 ng/ml, n = 13; non-PCOS, 7.18 ± 2.42 ng/ml, n = 9; p
- Published
- 2018
72. Hepatocellular Carcinoma-propagating Cells are Detectable by Side Population Analysis and Possess an Expression Profile Reflective of a Primitive Origin
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Wei-Hua Ren, Wei-Dong Jia, Honghai Xia, Qingyu Cheng, Geliang Xu, Xiaoyuan Song, Yang Lv, Jun Cao, and Qing Li
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0301 basic medicine ,Pathology ,medicine.medical_specialty ,Carcinoma, Hepatocellular ,Kruppel-Like Transcription Factors ,Mice, SCID ,Biology ,Stem cell marker ,Article ,Transcriptome ,Kruppel-Like Factor 4 ,Mice ,03 medical and health sciences ,Side population ,Cancer stem cell ,SALL4 ,medicine ,Animals ,Humans ,Side-Population Cells ,Cell Proliferation ,Multidisciplinary ,Microarray analysis techniques ,HMGA2 Protein ,Liver Neoplasms ,Hep G2 Cells ,Molecular biology ,digestive system diseases ,Gene Expression Regulation, Neoplastic ,030104 developmental biology ,CCAAT-Binding Factor ,KLF4 ,Neoplastic Stem Cells ,Heterografts ,Stem cell ,Transcription Factors - Abstract
The recent identification of “Side Population” (SP) cells in a number of unrelated human cancers has renewed interests in the hypothesis of cancer stem cells. Here we isolated SP cells from HepG2 cells and 18 of the 21 fresh hepatocellular carcinoma (HCC) tissue samples. These SP cells have higher abilities of forming spheroids, invasion and migration. Tumors could generate only from SP, not non-SP (NSP), cells in a low dose of subcutaneous injection to the NOD/SCID mice (5 × 102 cells/mouse). The mRNA microarray analysis of the SP vs. NSP cells isolated from HepG2 cells revealed that the SP cells express higher levels of pluripotency- and stem cell-associated transcription factors including Klf4, NF-Ya, SALL4 and HMGA2. Some of the known hepatobiliary progenitor/stem cell markers, such as Sox9 was also up-regulated. RT-qPCR analysis of the gene expression between SP cells and NSP cells isolated from both HepG2 cells and HCC tissue samples showed that most of the tested mRNAs’ changes were in consistent with the microarray data, including the general progenitor/stem cells markers such as Klf4, NF-Ya, SALL4 and HMGA2, which were up-regulated in SP cells. Our data indicates that HCC cancer stem cells exist in HepG2 and HCC fresh tissue samples and can be isolated by SP assay.
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- 2016
- Full Text
- View/download PDF
73. The nonhistone, N-terminal tail of an essential, chimeric H2A variant regulates mitotic H3-S10 dephosphorylation
- Author
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Xiaoyuan Song, Josephine Bowen, Wei Miao, Martin A. Gorovsky, and Yifan Liu
- Subjects
DNA Replication ,Saccharomyces cerevisiae Proteins ,animal structures ,Molecular Sequence Data ,Mutant Chimeric Proteins ,Mitosis ,Chimeric gene ,medicine.disease_cause ,Tetrahymena thermophila ,Histones ,Dephosphorylation ,Gene Knockout Techniques ,Protein Phosphatase 1 ,Genetics ,medicine ,Nucleosome ,Amino Acid Sequence ,Phosphorylation ,Phylogeny ,Mutation ,biology ,Tetrahymena ,biology.organism_classification ,Molecular biology ,Nucleosomes ,Protein Structure, Tertiary ,Histone ,embryonic structures ,ras Proteins ,biology.protein ,Protein Processing, Post-Translational ,Research Paper ,Developmental Biology - Abstract
H2A.Y is an essential, divergent Tetrahymena thermophila histone variant. It has a long nonhistone N terminus that contains leucine-rich repeats (LRR) and an LRR cap domain with similarity to Sds22p, a regulator of yeast protein phosphatase 1 (PP1) activity in the nucleus. In growing cells, H2A.Y is incorporated into micronuclei only during S phase, which occurs immediately after micronuclear mitosis. Depletion of H2A.Y causes prolonged retention of mitosis-associated histone H3-S10 phosphorylation and mitotic abnormalities that mimic S10E mutation. In cells where H2A.Y is depleted, an inducible chimeric gene, in which the H2A.Y N terminus is attached to H2A.X, is shown to regulate micronuclear H3-S10 phosphorylation. H2A.Y can also be specifically coimmunoprecipitated with a Tetrahymena PP1 ortholog (Ppo1p). Taken together, these results argue that the N terminus of H2A.Y functions to regulate H3-S10 dephosphorylation. This striking in vivo case of “cross-talk” between a H2A variant and a specific post-translational modification of another histone demonstrates a novel function for a histone variant.
- Published
- 2012
74. 9p21 DNA variants associated with Coronary Artery Disease impair IFNγ signaling response
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Kelly A. Frazer, Bogdan Tanasa, Dimple Notani, Xiaoyuan Song, Nazli G. Rahim, Eric J. Topol, Olivier Harismendy, Bing Ren, Nathaniel D. Heintzman, Xiang-Dong Fu, and Michael G. Rosenfeld
- Subjects
Male ,Single-nucleotide polymorphism ,Locus (genetics) ,Genome-wide association study ,Coronary Artery Disease ,030204 cardiovascular system & hematology ,Biology ,Polymorphism, Single Nucleotide ,Linkage Disequilibrium ,White People ,Article ,Cell Line ,Interferon-gamma ,03 medical and health sciences ,0302 clinical medicine ,Humans ,Genetic Predisposition to Disease ,Allele ,Enhancer ,Gene ,Alleles ,Conserved Sequence ,Cyclin-Dependent Kinase Inhibitor p15 ,030304 developmental biology ,Regulation of gene expression ,Genetics ,0303 health sciences ,Multidisciplinary ,CDKN2BAS ,Endothelial Cells ,Genetic Variation ,Interferon-alpha ,Chromatin ,Enhancer Elements, Genetic ,STAT1 Transcription Factor ,Diabetes Mellitus, Type 2 ,Gene Expression Regulation ,Haplotypes ,Purine-Nucleoside Phosphorylase ,Gene Knockdown Techniques ,Chromosomes, Human, Pair 9 ,Genome-Wide Association Study ,HeLa Cells ,Protein Binding ,Signal Transduction - Abstract
Genome-wide association studies have identified single nucleotide polymorphisms (SNPs) in the 9p21 gene desert associated with coronary artery disease (CAD) and type 2 diabetes. Despite evidence for a role of the associated interval in neighbouring gene regulation, the biological underpinnings of these genetic associations with CAD or type 2 diabetes have not yet been explained. Here we identify 33 enhancers in 9p21; the interval is the second densest gene desert for predicted enhancers and six times denser than the whole genome (P < 6.55 × 10(-33)). The CAD risk alleles of SNPs rs10811656 and rs10757278 are located in one of these enhancers and disrupt a binding site for STAT1. Lymphoblastoid cell lines homozygous for the CAD risk haplotype show no binding of STAT1, and in lymphoblastoid cell lines homozygous for the CAD non-risk haplotype, binding of STAT1 inhibits CDKN2BAS (also known as CDKN2B-AS1) expression, which is reversed by short interfering RNA knockdown of STAT1. Using a new, open-ended approach to detect long-distance interactions, we find that in human vascular endothelial cells the enhancer interval containing the CAD locus physically interacts with the CDKN2A/B locus, the MTAP gene and an interval downstream of IFNA21. In human vascular endothelial cells, interferon-γ activation strongly affects the structure of the chromatin and the transcriptional regulation in the 9p21 locus, including STAT1-binding, long-range enhancer interactions and altered expression of neighbouring genes. Our findings establish a link between CAD genetic susceptibility and the response to inflammatory signalling in a vascular cell type and thus demonstrate the utility of genome-wide association study findings in directing studies to novel genomic loci and biological processes important for disease aetiology.
- Published
- 2011
75. Moderate UV Exposure Enhances Learning and Memory by Promoting a Novel Glutamate Biosynthetic Pathway in the Brain
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Yan Xu, Guangming Huang, Junchao Qian, Sijia Fan, Lei Yao, Yiwen Hou, Qi Chen, Xiaoyuan Song, Xin Zuo, Jiali Li, Qiaoyun Zhao, Hongying Zhu, Weiwei Guo, Tian Xue, Ning Wang, Feng Du, Siling Liu, Wei Xiong, Yujun Guo, Ran Zhang, and Kai Zhong
- Subjects
Male ,0301 basic medicine ,Patch-Clamp Techniques ,Ultraviolet Rays ,Glutamic Acid ,Hippocampus ,Biology ,Synaptic vesicle ,General Biochemistry, Genetics and Molecular Biology ,Small hairpin RNA ,Mice ,03 medical and health sciences ,Glutamatergic ,chemistry.chemical_compound ,0302 clinical medicine ,Memory ,Tandem Mass Spectrometry ,Animals ,Learning ,RNA, Small Interfering ,Chromatography, High Pressure Liquid ,Neurons ,Urocanate Hydratase ,Urocanic Acid ,Glutamate receptor ,Brain ,Glutamic acid ,Magnetic Resonance Imaging ,Cell biology ,Mice, Inbred C57BL ,Metabolic pathway ,Urocanic acid ,030104 developmental biology ,chemistry ,RNA Interference ,030217 neurology & neurosurgery - Abstract
Sunlight exposure is known to affect mood, learning, and cognition. However, the molecular and cellular mechanisms remain elusive. Here, we show that moderate UV exposure elevated blood urocanic acid (UCA), which then crossed the blood-brain barrier. Single-cell mass spectrometry and isotopic labeling revealed a novel intra-neuronal metabolic pathway converting UCA to glutamate (GLU) after UV exposure. This UV-triggered GLU synthesis promoted its packaging into synaptic vesicles and its release at glutamatergic terminals in the motor cortex and hippocampus. Related behaviors, like rotarod learning and object recognition memory, were enhanced after UV exposure. All UV-induced metabolic, electrophysiological, and behavioral effects could be reproduced by the intravenous injection of UCA and diminished by the application of inhibitor or short hairpin RNA (shRNA) against urocanase, an enzyme critical for the conversion of UCA to GLU. These findings reveal a new GLU biosynthetic pathway, which could contribute to some of the sunlight-induced neurobehavioral changes.
- Published
- 2018
76. Correction to: The key role of CYC2 during meiosis in Tetrahymena Thermophila
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Xiaoyuan Song, Wei Miao, Ruoyu Wang, A. R. Ghanam, Qianlan Xu, and Guanxiong Yan
- Subjects
DNA Repair ,Protozoan Proteins ,lcsh:Animal biochemistry ,Library science ,homologous recombination ,Real-Time Polymerase Chain Reaction ,DNA Mismatch Repair ,Biochemistry ,Tetrahymena thermophila ,cyclin ,Cyclins ,Political science ,Drug Discovery ,meiosis ,DNA Breaks, Double-Stranded ,RNA-Seq ,lcsh:QH573-671 ,China ,lcsh:QP501-801 ,Endodeoxyribonucleases ,biology ,Sequence Analysis, RNA ,lcsh:Cytology ,fungi ,Tetrahymena ,Correction ,Cell Cycle Checkpoints ,Cell Biology ,biology.organism_classification ,Phenotype ,Microscopy, Fluorescence ,Work (electrical) ,Key (cryptography) ,Christian ministry ,Transcriptome ,Research Article ,Biotechnology - Abstract
Meiotic recombination is carried out through a specialized pathway for the formation and repair of DNA double-strand breaks (DSBs) made by the Spo11 protein. The present study shed light on the functional role of cyclin, CYC2, in Tetrahymena thermophila which has transcriptionally high expression level during meiosis process. Knocking out the CYC2 gene results in arrest of meiotic conjugation process at 2.5–3.5 h after conjugation initiation, before the meiosis division starts, and in company with the absence of DSBs. To investigate the underlying mechanism of this phenomenon, a complete transcriptome profile was performed between wild-type strain and CYC2 knock-out strain. Functional analysis of RNA-Seq results identifies related differentially expressed genes (DEGs) including SPO11 and these DEGs are enriched in DNA repair/mismatch repair (MMR) terms in homologous recombination (HR), which indicates that CYC2 could play a crucial role in meiosis by regulating SPO11 and participating in HR. Electronic supplementary material The online version of this article (doi:10.1007/s13238-016-0254-9) contains supplementary material, which is available to authorized users.
- Published
- 2018
77. Induced ncRNAs Allosterically Modify RNA Binding Proteins in cis to Inhibit Transcription
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Xiangting Wang, Riki Kurokawa, Kun Du, Paul Tempst, Xiaoyuan Song, Gabriel Pascual, Shigeki Arai, Donna Reichart, Michael G. Rosenfeld, and Christopher K. Glass
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RNA, Untranslated ,Transcription, Genetic ,Oligonucleotides ,Down-Regulation ,RNA-binding protein ,Article ,Cell Line ,03 medical and health sciences ,0302 clinical medicine ,Allosteric Regulation ,Transcription (biology) ,Consensus Sequence ,Humans ,Cyclin D1 ,CREB-binding protein ,Promoter Regions, Genetic ,Gene ,030304 developmental biology ,Histone Acetyltransferases ,Genetics ,0303 health sciences ,Multidisciplinary ,biology ,RNA ,Non-coding RNA ,CREB-Binding Protein ,Cell biology ,Regulatory sequence ,biology.protein ,RNA-Binding Protein FUS ,Functional genomics ,030217 neurology & neurosurgery ,DNA Damage ,HeLa Cells - Abstract
With the recent recognition of non-coding RNAs (ncRNAs) flanking many genes, a central issue is to obtain a full understanding of their potential roles in regulated gene transcription programmes, possibly through different mechanisms. Here we show that an RNA-binding protein, TLS (for translocated in liposarcoma), serves as a key transcriptional regulatory sensor of DNA damage signals that, on the basis of its allosteric modulation by RNA, specifically binds to and inhibits CREB-binding protein (CBP) and p300 histone acetyltransferase activities on a repressed gene target, cyclin D1 (CCND1) in human cell lines. Recruitment of TLS to the CCND1 promoter to cause gene-specific repression is directed by single-stranded, low-copy-number ncRNA transcripts tethered to the 5' regulatory regions of CCND1 that are induced in response to DNA damage signals. Our data suggest that signal-induced ncRNAs localized to regulatory regions of transcription units can act cooperatively as selective ligands, recruiting and modulating the activities of distinct classes of RNA-binding co-regulators in response to specific signals, providing an unexpected ncRNA/RNA-binding protein-based strategy to integrate transcriptional programmes.
- Published
- 2008
78. Effects of 1.8GHz electromagnetic radiation on dielectric properties of SD Rat's typical tissues
- Author
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Minchen, Qiu, primary, Lisheng, Zhong, additional, Xiaoyuan, Song, additional, Jiaxi, He, additional, Jinghui, Gao, additional, and Qinxue, Yu, additional
- Published
- 2017
- Full Text
- View/download PDF
79. Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation
- Author
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Daria Merkurjev, Wenbo Li, Xiang Zhou, Qi Ma, Michael G. Rosenfeld, Jie Zhang, Soohwan Oh, Yiren Hu, Aaron Yun Chen, Xiaoyuan Song, Kenny Ohgi, Bogdan Tanasa, Wen Liu, Zhijie Liu, and Xin He
- Subjects
Condensin ,Enhancer RNAs ,Medical and Health Sciences ,Models ,2.1 Biological and endogenous factors ,RNA, Neoplasm ,Aetiology ,Promoter Regions, Genetic ,Cancer ,Regulation of gene expression ,Adenosine Triphosphatases ,biology ,Estradiol ,Adaptor Proteins ,Nuclear Proteins ,DNA, Neoplasm ,Biological Sciences ,Chromatin ,Ubiquitin ligase ,Cell biology ,Nuclear Receptor Interacting Protein 1 ,DNA-Binding Proteins ,Enhancer Elements, Genetic ,Gene Knockdown Techniques ,MCF-7 Cells ,Female ,Protein Binding ,Enhancer Elements ,Ubiquitin-Protein Ligases ,1.1 Normal biological development and functioning ,Molecular Sequence Data ,Breast Neoplasms ,macromolecular substances ,Models, Biological ,Article ,Promoter Regions ,Condensin complex ,Genetic ,Underpinning research ,Breast Cancer ,Genetics ,Humans ,Enhancer ,Molecular Biology ,Interphase ,Adaptor Proteins, Signal Transducing ,Binding Sites ,Base Sequence ,Signal Transducing ,Estrogen Receptor alpha ,Ubiquitination ,Cell Biology ,DNA ,Biological ,Molecular biology ,Estrogen ,Multiprotein Complexes ,biology.protein ,Neoplasm ,RNA ,Generic health relevance ,Estrogen receptor alpha ,Developmental Biology - Abstract
Enhancers instruct spatio-temporally specific gene expression in a manner tightly linked to higher-order chromatin architecture. Critical chromatin architectural regulators condensin I and condensin II play non-redundant roles controlling mitotic chromosomes. But the chromosomal locations of condensins and their functional roles in interphase are poorly understood. Here we report that both condensin complexes exhibit an unexpected, dramatic estrogen-induced recruitment to estrogen receptor α (ER-α)-bound eRNA(+) active enhancers in interphase breast cancer cells, exhibiting non-canonical interaction with ER-α via its DNA-binding domain (DBD). Condensins positively regulate ligand-dependent enhancer activation at least in part by recruiting an E3 ubiquitin ligase, HECTD1, to modulate the binding of enhancer-associated coactivators/corepressors, including p300 and RIP140, permitting full eRNA transcription, formation of enhancer:promoter looping, and the resultant coding gene activation. Collectively, our results reveal an important, unanticipated transcriptional role of interphase condensins in modulating estrogen-regulated enhancer activation and coding gene transcriptional program.
- Published
- 2015
80. Study on temperature dependent broadband frequency dielectric spectrum of SD rat muscle tissues
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Lisheng Zhong, Xiaoyuan Song, Shaopeng Li, Yan Wang, Qinxue Yu, Jinghui Gao, Minchen Qiu, and Jiaxi He
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Muscle tissue ,Permittivity ,Arrhenius equation ,Materials science ,Quantitative Biology::Tissues and Organs ,Physics::Medical Physics ,Activation energy ,Dielectric ,Molecular physics ,Electromagnetic radiation ,Dielectric spectroscopy ,symbols.namesake ,medicine.anatomical_structure ,Nuclear magnetic resonance ,medicine ,symbols ,Relaxation (physics) - Abstract
With the increasing recognition of threat of electromagnetic radiation to human health and environment, the study of electromagnetic biological effect has received wide attention. And the studies on dielectric properties of biological tissues play a key role on the electromagnetic biological effect to bio-dielectrics. In this work, the muscle tissues of SD rat have been studied by using the broadband dielectric spectrum in-vitro between the temperatures of 9°C–42°C at the frequency range of 1MHz–2GHz. We also do the dehydration rate experiment of muscle tissue in vitro, in order to explain the activity during testing time. The results indicate that all the measured muscle tissues show a single dielectric relaxation in the testing frequency range; as increasing the temperature for muscle tissues, the values of dielectric constant (real part) increase, and the peaks of dielectric constant (imaginary part) shift to higher frequency. According the Arrhenius formula and using piecewise fitting, we can obtain the activation energy for muscle tissue at multiple temperature ranges, and the relationship between the dielectric properties and biological activity is discussed. Meanwhile, it is shown that the results of dielectric constant at different frequencies and temperatures can provide necessary database for the study on the biological electromagnetic radiation effect.
- Published
- 2015
81. Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program
- Author
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Feng Zhang, Kenneth A. Ohgi, Anna Krones, Daria Merkurjev, Bogdan Tanasa, Wenbo Li, Michael G. Rosenfeld, Chijen Lin, Zhijie Liu, Jie Zhang, Yuliang Tan, Dorota Skowronska-Krawczyk, and Xiaoyuan Song
- Subjects
Enhancer Elements ,Knockout ,LDB1 ,1.1 Normal biological development and functioning ,Stem Cell Research - Embryonic - Non-Human ,Enhancer RNAs ,Biology ,DNA-binding protein ,Cell Line ,Promoter Regions ,Mice ,Genetic ,Transcription (biology) ,Underpinning research ,Genetics ,Enhancer trap ,Animals ,Enhancer ,Promoter Regions, Genetic ,Psychological repression ,Corticotrophs ,Mice, Knockout ,Multidisciplinary ,ASCL1 ,Promoter ,Biological Sciences ,LIM Domain Proteins ,Stem Cell Research ,DNA-Binding Proteins ,Enhancer Elements, Genetic ,MTA2 ,looping ,enhancer ,Biotechnology - Abstract
Substantial evidence supports the hypothesis that enhancers are critical regulators of cell-type determination, orchestrating both positive and negative transcriptional programs; however, the basic mechanisms by which enhancers orchestrate interactions with cognate promoters during activation and repression events remain incompletely understood. Here we report the required actions of LIM domain-binding protein 1 (LDB1)/cofactor of LIM homeodomain protein 2/nuclear LIM interactor, interacting with the enhancer-binding protein achaete-scute complex homolog 1, to mediate looping to target gene promoters and target gene regulation in corticotrope cells. LDB1-mediated enhancer:promoter looping appears to be required for both activation and repression of these target genes. Although LDB1-dependent activated genes are regulated at the level of transcriptional initiation, the LDB1-dependent repressed transcription units appear to be regulated primarily at the level of promoter pausing, with LDB1 regulating recruitment of metastasis-associated 1 family, member 2, a component of the nucleosome remodeling deacetylase complex, on these negative enhancers, required for the repressive enhancer function. These results indicate that LDB1-dependent looping events can deliver repressive cargo to cognate promoters to mediate promoter pausing events in a pituitary cell type.
- Published
- 2015
82. Elimination of Foreign DNA during Somatic Differentiation in Tetrahymena thermophila Shows Position Effect and Is Dosage Dependent
- Author
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Kathleen M. Karrer, Martin A. Gorovsky, Yifan Liu, and Xiaoyuan Song
- Subjects
Transposable element ,Genetics ,biology ,Macronucleus ,Somatic cell ,Tetrahymena ,Cell Differentiation ,Articles ,General Medicine ,DNA, Protozoan ,biology.organism_classification ,Microbiology ,Genome ,Tetrahymena thermophila ,chemistry.chemical_compound ,Position effect ,chemistry ,Animals ,Gene Silencing ,Micronucleus, Germline ,Molecular Biology ,Gene ,DNA ,Repetitive Sequences, Nucleic Acid - Abstract
In the ciliate Tetrahymena thermophila , approximately 15% of the germ line micronuclear DNA sequences are eliminated during formation of the somatic macronucleus. The vast majority of the internal eliminated sequences (IESs) are repeated in the micronuclear genome, and several of them resemble transposable elements. Thus, it has been suggested that DNA elimination evolved as a means for removing invading DNAs. In the present study, bacterial neo genes introduced into the germ line micronuclei were eliminated from the somatic genome. The efficiency of elimination from two different loci increased dramatically with the copy number of the neo genes in the micronuclei. The timing of neo elimination is similar to that of endogenous IESs, and they both produce bidirectional transcripts of the eliminated element, suggesting that the deletion of neo occurred by the same mechanism as elimination of endogenous IESs. These results indicate that repetition of an element in the micronucleus enhances the efficiency of its elimination from the newly formed somatic genome of Tetrahymena thermophila . The implications of these data in relation to the function and mechanism of IES elimination are discussed.
- Published
- 2005
83. A robust inducible-repressible promoter greatly facilitates gene knockouts, conditional expression, and overexpression of homologous and heterologous genes in Tetrahymena thermophila
- Author
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Yan Gao, Yuhua Shang, Jacek Gaertig, Robert Corstanje, Josephine Bowen, Xiaoyuan Song, and Martin A. Gorovsky
- Subjects
Genes, Protozoan ,Molecular Sequence Data ,Mutant ,Down-Regulation ,Antigens, Protozoan ,Chimeric gene ,Biology ,Gene dosage ,Tetrahymena thermophila ,Histones ,Gene Frequency ,Genes, Reporter ,Tubulin ,Gene cluster ,Animals ,RNA, Messenger ,Transgenes ,Promoter Regions, Genetic ,Gene ,Germ-Line Mutation ,Gene knockout ,Regulation of gene expression ,Genes, Essential ,Multidisciplinary ,Tetrahymena ,Neomycin ,Biological Sciences ,biology.organism_classification ,Molecular biology ,Up-Regulation ,Mutagenesis, Insertional ,Gene Expression Regulation ,Genes, Lethal ,Metallothionein ,Gene Deletion ,RNA, Protozoan ,Cadmium - Abstract
The Cd 2+ -inducible metallothionein ( MTT1 ) gene was cloned from Tetrahymena thermophila . Northern blot analysis showed that MTT1 mRNA is not detectable in the absence of Cd 2+ , is induced within 10 min of its addition, is expressed in proportion to its concentration, and rapidly disappears upon its withdrawal. Similarly, when the neo1 gene coding region flanked by the MTT1 gene noncoding sequences was used to disrupt the MTT1 locus, no transformants were observed in the absence of Cd 2+ , and the number of transformants was proportional to increased Cd 2+ concentration. The neo3 cassette, in which the MTT1 promoter replaced the histone gene HHF1 promoter of the previously used neo2 cassette , transformed cells at much higher frequencies than neo2 and produced germ-line knockouts where neo2 had failed. Rescuing the progeny of a mating of γ-tubulin gene, GTU1, knockout heterokaryons with a GTU1 gene inserted into the MTT1 locus yielded >75 times more transformants than rescuing with the wild-type GTU1 gene itself. When cells rescued with the MTT1-GTU1 chimeric gene were transferred to medium lacking Cd 2+ , they stopped growing and had phenotypic changes indistinguishable from cells containing only disrupted GTU1 genes. Thus, it is now possible to create conditional lethal mutants and study the terminal phenotypes of null mutations for essential genes by replacing the endogenous gene with one under the control of the MTT1 promoter. The MTT1 promoter also resulted in ≈30 times more overexpression of the IAG48[G1] surface antigen gene of the ciliate fish parasite Ichthyophthirius multifiliis than the highly expressed BTU1 promoter, accounting for ≈1% of the total cell protein. Thus, the MTT1 promoter should enable routine over-expression of endogenous and foreign genes in Tetrahymena .
- Published
- 2002
84. EEG-based emotion recognition using wavelet features
- Author
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Huiping Jiang, Zhengjie Zhou, and Xiaoyuan Song
- Subjects
medicine.diagnostic_test ,Computer science ,business.industry ,Speech recognition ,Feature extraction ,Pattern recognition ,Electroencephalography ,Support vector machine ,Kernel (linear algebra) ,ComputingMethodologies_PATTERNRECOGNITION ,Wavelet ,Kernel (statistics) ,medicine ,Emotion recognition ,Artificial intelligence ,business - Abstract
This paper described a research project conducted to recognize to finding the relationship between EEG signals and Human emotions. EEG signals are used to classify three kinds of emotions, positive, neuter and negative. Firstly, literature research has been performed to establish a suitable approach for emotion recognition. Secondly, we extracted features from original EEG data using 4-order wavelet and put them in SVM classifier with different kernel functions. The result shows that an SVM with linear kernel has higher average test accuracy than other kernel function.
- Published
- 2014
85. Emotion recognition system based on MAPL
- Author
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Zhengjie Zhou, Huiping Jiang, and Xiaoyuan Song
- Subjects
Support vector machine ,Statistical classification ,Computer science ,business.industry ,Speech recognition ,SIGNAL (programming language) ,Feature extraction ,Feature (machine learning) ,Pattern recognition ,Artificial intelligence ,Emotion recognition ,business - Abstract
A EEG signal-based emotion recognition system was designed. The system was developed to operate as a user-independent system, based on MAPL (minority affective picture library), EEG-signal database obtained from multiple ethnic objections. The system consisted of preprocessing, feature extraction and pattern classification stages. Preprocessing and feature extraction methods were devised so that emotion-specific characteristics could be extracted. a simple experiment was carried out, and the classification result is about 56.4%, which indicated that minorities emotion problems can be studied based MPAL emotion recognition system.
- Published
- 2014
86. Enhancer activation requires trans-recruitment of a mega transcription factor complex
- Author
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Daria Merkurjev, Wenbo Li, Kenneth A. Ohgi, Anna Krones, Feng Zhang, Meyer J. Friedman, Soohwan Oh, Michael G. Rosenfeld, Xiaoyuan Song, Feng Yang, Zhijie Liu, and Qi Ma
- Subjects
Hepatocyte Nuclear Factor 3-alpha ,Enhancer Elements ,1.1 Normal biological development and functioning ,Transcription factor complex ,Enhancer RNAs ,GATA3 Transcription Factor ,Biology ,Medical and Health Sciences ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,Genetic ,Transcription (biology) ,Underpinning research ,Genetics ,Humans ,Enhancer ,Transcription factor ,030304 developmental biology ,Regulation of gene expression ,0303 health sciences ,Biochemistry, Genetics and Molecular Biology(all) ,Activator (genetics) ,Human Genome ,Estrogen Receptor alpha ,Estrogens ,Biological Sciences ,Cell biology ,Enhancer Elements, Genetic ,Gene Expression Regulation ,030220 oncology & carcinogenesis ,Multiprotein Complexes ,Trans-acting ,Generic health relevance ,Developmental Biology ,Transcription Factors - Abstract
SummaryEnhancers provide critical information directing cell-type-specific transcriptional programs, regulated by binding of signal-dependent transcription factors and their associated cofactors. Here, we report that the most strongly activated estrogen (E2)-responsive enhancers are characterized by trans-recruitment and in situ assembly of a large 1–2 MDa complex of diverse DNA-binding transcription factors by ERα at ERE-containing enhancers. We refer to enhancers recruiting these factors as mega transcription factor-bound in trans (MegaTrans) enhancers. The MegaTrans complex is a signature of the most potent functional enhancers and is required for activation of enhancer RNA transcription and recruitment of coactivators, including p300 and Med1. The MegaTrans complex functions, in part, by recruiting specific enzymatic machinery, exemplified by DNA-dependent protein kinase. Thus, MegaTrans-containing enhancers represent a cohort of functional enhancers that mediate a broad and important transcriptional program and provide a molecular explanation for transcription factor clustering and hotspots noted in the genome.
- Published
- 2014
87. Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation
- Author
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Daria Merkurjev, Wenbo Li, Xiaoyuan Song, Qi Ma, Soohwan Oh, Christopher K. Glass, Dimple Notani, Bogdan Tanasa, Hong-Sook Kim, Michael G. Rosenfeld, Jie Zhang, Aaron Yun Chen, Kenneth A. Ohgi, and Esperanza Nunez
- Subjects
Transcriptional Activation ,RNA, Untranslated ,Transcription, Genetic ,Chromosomal Proteins, Non-Histone ,Enhancer RNAs ,Cell Cycle Proteins ,Biology ,Ligands ,Article ,Transcription (biology) ,Gene expression ,Humans ,Enhancer ,Promoter Regions, Genetic ,Gene ,Genetics ,Regulation of gene expression ,Multidisciplinary ,Estradiol ,Estrogen Receptor alpha ,RNA ,Estrogens ,Research Highlight ,Enhancer Elements, Genetic ,MCF-7 Cells ,Nucleic Acid Conformation ,Estrogen receptor alpha - Abstract
The functional importance of gene enhancers in regulated gene expression is well established. In addition to widespread transcription of long non-coding RNAs (lncRNAs) in mammalian cells, bidirectional ncRNAs are transcribed on enhancers, and are thus referred to as enhancer RNAs (eRNAs). However, it has remained unclear whether these eRNAs are functional or merely a reflection of enhancer activation. Here we report that in human breast cancer cells 17β-oestradiol (E2)-bound oestrogen receptor α (ER-α) causes a global increase in eRNA transcription on enhancers adjacent to E2-upregulated coding genes. These induced eRNAs, as functional transcripts, seem to exert important roles for the observed ligand-dependent induction of target coding genes, increasing the strength of specific enhancer-promoter looping initiated by ER-α binding. Cohesin, present on many ER-α-regulated enhancers even before ligand treatment, apparently contributes to E2-dependent gene activation, at least in part by stabilizing E2/ER-α/eRNA-induced enhancer-promoter looping. Our data indicate that eRNAs are likely to have important functions in many regulated programs of gene transcription.
- Published
- 2012
88. Downregulation of miR-320a/383-sponge-like long non-coding RNA NLC1-C (narcolepsy candidate-region 1 genes) is associated with male infertility and promotes testicular embryonal carcinoma cell proliferation
- Author
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Cao Yx, Min Lu, Ping P, Xiaoyuan Song, Hui Tian, He X, He-Feng Huang, Liangyi Chen, and Fei Sun
- Subjects
Adult ,Male ,Cancer Research ,Embryonal Carcinoma Stem Cells ,Immunology ,Down-Regulation ,RNA-binding protein ,Biology ,Cellular and Molecular Neuroscience ,Young Adult ,Downregulation and upregulation ,Testicular Neoplasms ,Carcinoma, Embryonal ,microRNA ,Humans ,Gene ,Infertility, Male ,Cell Proliferation ,Genetics ,RNA ,RNA-Binding Proteins ,Cell Biology ,Middle Aged ,Neoplasms, Germ Cell and Embryonal ,Phosphoproteins ,Long non-coding RNA ,Cell biology ,Testicular Embryonal Carcinoma ,MicroRNAs ,Case-Control Studies ,Original Article ,RNA, Long Noncoding ,Nucleolin - Abstract
Long non-coding RNAs (lncRNAs), which are extensively transcribed from the genome, have been proposed to be key regulators of diverse biological processes. However, little is known about the role of lncRNAs in regulating spermatogenesis in human males. Here, using microarray technology, we show altered expression of lncRNAs in the testes of infertile men with maturation arrest (MA) or hypospermatogenesis (Hypo), with 757 and 2370 differentially down-regulated and 475 and 163 up-regulated lncRNAs in MA and Hypo, respectively. These findings were confirmed by quantitative real-time PCR (qRT-PCR) assays on select lncRNAs, including HOTTIP, imsrna320, imsrna292 and NLC1-C (narcolepsy candidate-region 1 genes). Interestingly, NLC1-C, also known as long intergenic non-protein-coding RNA162 (LINC00162), was down-regulated in the cytoplasm and accumulated in the nucleus of spermatogonia and primary spermatocytes in the testes of infertile men with mixed patterns of MA compared with normal control. The accumulation of NLC1-C in the nucleus repressed miR-320a and miR-383 transcript and promoted testicular embryonal carcinoma cell proliferation by binding to Nucleolin. Here, we define a novel mechanism by which lncRNAs modulate miRNA expression at the transcriptional level by binding to RNA-binding proteins to regulate human spermatogenesis.
- Published
- 2015
89. Promoter-associated noncoding RNA from the CCND1 promoter
- Author
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Xiaoyuan, Song, Xiangting, Wang, Shigeki, Arai, and Riki, Kurokawa
- Subjects
Chromatin Immunoprecipitation ,RNA, Untranslated ,Humans ,Cyclin D1 ,Blotting, Northern ,Promoter Regions, Genetic ,Real-Time Polymerase Chain Reaction - Abstract
More than 90% of the human genome have been found to be transcribed and most of the transcripts are noncoding (nc) RNAs (Willingham et al., Science 309:1570-1573, 2005; ENCODE-consortium, Science 306:636-640, 2004; Carninci et al., Science 309:1559-1563, 2005; Bertone et al., Science 306:2242-2246, 2004). Studies on ncRNAs have been radically progressed mainly regarding microRNAs, piRNAs, siRNAs, and related small ncRNAs of which length are relatively short nucleotides (Fire et al., Nature 391:806-811, 1998; Filipowicz et al., Nat Rev Genet 9:102-114, 2008; Lau et al., Science 313:363-367, 2006; Brennecke et al., Science 322:1387-1392, 2008; Siomi and Siomi, Nature 457:396-404, 2009). These small RNAs play roles in regulation of translation and gene silencing while long ncRNAs with length more than 200 nucleotides have been emerging and turn out to be involved in regulation of transcription (Kapranov et al., Science 316:1484-1488, 2007; Ponting et al., Cell 136:629-641, 2009; Kurokawa et al., RNA Biol 6:233-236, 2009). Recently, we have identified novel, long ncRNAs bearing capability of repression of transcription (Wang et al., Nature 454:126-130, 2008).RNA-binding protein, translocated in liposarcoma (TLS), binds CREB-binding protein CBP/adenovirus p300 and inhibits their histone acetyltransferase (HAT) activities (Wang et al., Nature 454:126-130, 2008). The HAT inhibitory activity of TLS requires specific binding of RNA. The systematic evolution of ligands by exponential enrichment experiments with randomized sequences revealed that TLS specifically recognizes RNA oligonucleotides containing GGUG as a consensus sequence although the GGUG sequence is not an absolute requirement for the TLS binding (Lerga et al., J Biol Chem 276:6807-6816, 2001). TLS is specifically recruited to the CBP/p300-associated binding sites of the cyclin D1 gene (CCND1) and the cyclin E1 gene (CCNE1) promoters (Wang et al., Nature 454:126-130, 2008; Impey et al., Cell 119:1041-1054, 2004). Our extensive exploration for naturally occurring RNA molecule that binds TLS has indicated that long ncRNAs (promoter-associated ncRNAs: pncRNAs) transcribed from the CCND1 promoter bind TLS and inhibit the HAT activities on the sites to repress the transcription of the CCND1 gene (Wang et al., Nature 454:126-130, 2008). We have optimized RT-PCR, chromatin immunoprecipitation, RNA immunoprecipitation, and RNA gel-shift assay in order to detect these pncRNAs. The methods that we have developed successfully identified these low-abundant, long ncRNAs and provide the data showing that the CCND1 pncRNAs bind TLS and induce its HAT inhibitory activity to repress the transcription of CCND1 gene upon genotoxic stress.
- Published
- 2011
90. Promoter-Associated Noncoding RNA from the CCND1 Promoter
- Author
-
Riki Kurokawa, Xiaoyuan Song, Shigeki Arai, and Xiangting Wang
- Subjects
RNA silencing ,Transcription (biology) ,Chemistry ,Intron ,RNA ,Promoter ,Non-coding RNA ,Noncoding DNA ,Molecular biology ,Gene - Abstract
More than 90% of the human genome have been found to be transcribed and most of the transcripts are noncoding (nc) RNAs (Willingham et al., Science 309:1570-1573, 2005; ENCODE-consortium, Science 306:636-640, 2004; Carninci et al., Science 309:1559-1563, 2005; Bertone et al., Science 306:2242-2246, 2004). Studies on ncRNAs have been radically progressed mainly regarding microRNAs, piRNAs, siRNAs, and related small ncRNAs of which length are relatively short nucleotides (Fire et al., Nature 391:806-811, 1998; Filipowicz et al., Nat Rev Genet 9:102-114, 2008; Lau et al., Science 313:363-367, 2006; Brennecke et al., Science 322:1387-1392, 2008; Siomi and Siomi, Nature 457:396-404, 2009). These small RNAs play roles in regulation of translation and gene silencing while long ncRNAs with length more than 200 nucleotides have been emerging and turn out to be involved in regulation of transcription (Kapranov et al., Science 316:1484-1488, 2007; Ponting et al., Cell 136:629-641, 2009; Kurokawa et al., RNA Biol 6:233-236, 2009). Recently, we have identified novel, long ncRNAs bearing capability of repression of transcription (Wang et al., Nature 454:126-130, 2008).RNA-binding protein, translocated in liposarcoma (TLS), binds CREB-binding protein CBP/adenovirus p300 and inhibits their histone acetyltransferase (HAT) activities (Wang et al., Nature 454:126-130, 2008). The HAT inhibitory activity of TLS requires specific binding of RNA. The systematic evolution of ligands by exponential enrichment experiments with randomized sequences revealed that TLS specifically recognizes RNA oligonucleotides containing GGUG as a consensus sequence although the GGUG sequence is not an absolute requirement for the TLS binding (Lerga et al., J Biol Chem 276:6807-6816, 2001). TLS is specifically recruited to the CBP/p300-associated binding sites of the cyclin D1 gene (CCND1) and the cyclin E1 gene (CCNE1) promoters (Wang et al., Nature 454:126-130, 2008; Impey et al., Cell 119:1041-1054, 2004). Our extensive exploration for naturally occurring RNA molecule that binds TLS has indicated that long ncRNAs (promoter-associated ncRNAs: pncRNAs) transcribed from the CCND1 promoter bind TLS and inhibit the HAT activities on the sites to repress the transcription of the CCND1 gene (Wang et al., Nature 454:126-130, 2008). We have optimized RT-PCR, chromatin immunoprecipitation, RNA immunoprecipitation, and RNA gel-shift assay in order to detect these pncRNAs. The methods that we have developed successfully identified these low-abundant, long ncRNAs and provide the data showing that the CCND1 pncRNAs bind TLS and induce its HAT inhibitory activity to repress the transcription of CCND1 gene upon genotoxic stress.
- Published
- 2011
91. The Long Arm of Long Noncoding RNAs: Roles as Sensors Regulating Gene Transcriptional Programs
- Author
-
Xiangting Wang, Xiaoyuan Song, Michael G. Rosenfeld, and Christopher K. Glass
- Subjects
Regulation of gene expression ,Genetics ,RNA, Untranslated ,Transcription, Genetic ,Concept ,RNA ,RNA-Binding Proteins ,RNA-binding protein ,Computational biology ,Biology ,DNA Methylation ,Non-coding RNA ,Genome ,Models, Biological ,General Biochemistry, Genetics and Molecular Biology ,Gene Expression Regulation ,DNA methylation ,Epigenetics ,Gene - Abstract
A major surprise arising from genome-wide analyses has been the observation that the majority of the genome is transcribed, generating noncoding RNAs (ncRNAs). It is still an open question whether some or all of these ncRNAs constitute functional networks regulating gene transcriptional programs. However, in light of recent discoveries and given the diversity and flexibility of long ncRNAs and their abilities to nucleate molecular complexes and to form spatially compact arrays of complexes, it becomes likely that many or most ncRNAs act as sensors and integrators of a wide variety of regulated transcriptional responses and probably epigenetic events. Because many RNA-binding proteins, on binding RNAs, show distinct allosteric conformational alterations, we suggest that a ncRNA/RNA-binding protein-based strategy, perhaps in concert with several other mechanistic strategies, serves to integrate transcriptional, as well as RNA processing, regulatory programs.
- Published
- 2011
92. Molecular mechanisms of a disease susceptibility variant of SIRT1: Genotoxic stress‐induced, CTCF‐dependent activation of SIRT1 gene expression
- Author
-
Xiaoyuan Song, Michael G. Rosenfeld, Ravindranath Duggirala, Yousin Suh, Miook Cho, John Blangero, Jeehae Han, and Helen Hazuda
- Subjects
Genetics ,Disease susceptibility ,CTCF ,Cancer research ,Genotoxic Stress ,Biology ,Molecular Biology ,Biochemistry ,SIRT1 Gene ,Biotechnology - Published
- 2010
93. Unphosphorylated H1 Is Enriched in a Specific Region of the Promoter when CDC2 Is Down-Regulated during Starvation▿
- Author
-
Xiaoyuan Song and Martin A. Gorovsky
- Subjects
Chromatin Immunoprecipitation ,Genes, Protozoan ,Green Fluorescent Proteins ,Down-Regulation ,Tetrahymena thermophila ,Dephosphorylation ,Histones ,Histone H1 ,Transcription (biology) ,CDC2 Protein Kinase ,Animals ,Phosphorylation ,Promoter Regions, Genetic ,Molecular Biology ,Feedback, Physiological ,Cyclin-dependent kinase 1 ,biology ,Kinase ,urogenital system ,Cell Biology ,Articles ,Molecular biology ,Genes, cdc ,Histone ,Starvation ,embryonic structures ,biology.protein ,biological phenomena, cell phenomena, and immunity ,Chromatin immunoprecipitation - Abstract
Tetrahymena thermophila macronuclear histone H1 is phosphorylated by a cdc2 kinase, and H1 phosphorylation regulates CDC2 expression by a positive feedback mechanism. In starved wild-type cells, decreased expression of the CDC2 gene is correlated with a global reduction in the phosphorylation of H1 and reduced phosphorylation of H1 in the region upstream of the CDC2 gene. To determine whether the reduced H1 phosphorylation upstream of the CDC2 gene is merely a reflection of global dephosphorylation or is due to specific targeting of dephosphorylation of H1 to the CDC2 promoter during starvation, the CDC2 promoter was mapped, and the distributions of phosphorylated and unphosphorylated H1 across the CDC2 gene were determined using chromatin immunoprecipitation. Unphosphorylated H1 is specifically enriched in a region of the CDC2 promoter when the gene's expression is reduced during starvation but not when CDC2 is highly active in growing cells. The region of unphosphorylated H1 coincides with a region that is essential for CDC2 expression. These studies are the first in vivo demonstration that the phosphorylation of H1 is being regulated at a fine level and that unphosphorylated H1 can be specifically targeted to a promoter, where it likely regulates transcription in a gene-specific manner.
- Published
- 2006
94. Shining the Light on Senescence Associated LncRNAs.
- Author
-
Ghanam, A. R., Qianlan Xu, Shengwei Ke, Azhar, Muhammad, Qingyu Cheng, and Xiaoyuan Song
- Subjects
OLD age ,LINCRNA ,CELL cycle - Abstract
Cellular senescence can be described as a complex stress response that leads to irreversible cell cycle arrest. This process was originally described as an event that primary cells go through after many passages of cells during cell culture. More recently, cellular senescence is viewed as a programmed process by which the cell displays a senescence phenotype when exposed to a variety of stresses. Cellular senescence has been implicated in tumor suppression and aging such that senescence may contribute to both tumor progression and normal tissue repair. Here, we review different forms of cellular senescence, as well as current biomarkers used to identify senescent cells in vitro and in vivo. Additionally, we highlight the role of senescence-associated long noncoding RNAs (lncRNAs). [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
95. The H1 phosphorylation state regulates expression of CDC2 and other genes in response to starvation in Tetrahymena thermophila
- Author
-
Xiaoyuan Song, Yali Dou, Yifan Liu, and Martin A. Gorovsky
- Subjects
Genes, Protozoan ,Down-Regulation ,Gene Expression ,Biology ,Tetrahymena thermophila ,Histones ,Gene expression ,CDC2 Protein Kinase ,Okadaic Acid ,Transcriptional regulation ,Animals ,Phosphorylation ,Molecular Biology ,Regulation of gene expression ,Feedback, Physiological ,Cyclin-dependent kinase 1 ,Kinase ,Tetrahymena ,Cell Biology ,biology.organism_classification ,Molecular biology ,enzymes and coenzymes (carbohydrates) ,Gene Expression Regulation ,Starvation ,Food Deprivation ,Peptide Hydrolases - Abstract
In Tetrahymena thermophila, highly phosphorylated histone H1 of growing cells becomes partially dephosphorylated when cells are starved in preparation for conjugation. To determine the effects of H1 phosphorylation on gene expression, PCR-based subtractive hybridization was used to clone cDNAs that were differentially expressed during starvation in two otherwise-isogenic strains differing only in their H1s. H1 in A5 mutant cells lacked phosphorylation, and H1 in E5 cells mimicked constitutive H1 phosphorylation. Sequences enriched in A5 cells included genes encoding proteases. Sequences enriched in E5 cells included genes encoding cdc2 kinase and a Ser/Thr kinase. These results indicate that H1 phosphorylation plays an important role in regulating the pattern of gene expression during the starvation response and that its role in transcription regulation can be either positive or negative. Treatment of starved cells with a phosphatase inhibitor caused CDC2 gene overexpression. Expression of the E5 version of H1 in starved cells containing endogenous, wild-type H1 caused the wild-type H1 to remain highly phosphorylated. These results argue that Cdc2p is the kinase that phosphorylates Tetrahymena H1, establish a positive feedback mechanism between H1 phosphorylation and CDC2 expression, and indicate that CDC2 gene expression is regulated by an H1 phosphatase.
- Published
- 2005
96. The H1 Phosphorylation State Regulates Expression of CDC2 and Other Genes in Response to Starvation in Tetrahymena thermophila.
- Author
-
Yali Dou, Xiaoyuan Song, Yifan Liu, and Gorovsky, Martin A.
- Subjects
- *
TETRAHYMENA , *GENE expression , *PHOSPHORYLATION , *STARVATION , *HISTONES , *BACTERIAL conjugation - Abstract
In Tetrahymena thermophila, highly phosphorylated histone Hi of growing cells becomes partially dephosphorylated when cells are starved in preparation for conjugation. To determine the effects of H1 phosphorylation on gene expression, PCR-based subtractive hybridization was used to clone cDNAs that were differentially expressed during starvation in two otherwise-isogenic strains differing only in their H1s. H1 in A5 mutant cells lacked phosphorylation, and H1 in E5 cells mimicked constitutive H1 phosphorylation. Sequences enriched in A5 cells included genes encoding proteases. Sequences enriched in ES cells included genes encoding cdc2 kinase and a Ser/Thr kinase. These results indicate that H1 phosphorylation plays an important role in regulating the pattern of gene expression during the starvation response and that its role in transcription regulation can be either positive or negative. Treatment of starved cells with a phosphatase inhibitor caused CDC2 gene overexpression. Expression of the E5 version of Hi in starved cells containing endogenous, wild-type Hi caused the wild-type H1 to remain highly phosphorylated. These results argue that Cdc2p is the kinase that phosphorylates Tetrahymena H1, establish a positive feedback mechanism between H1 phosphor- ylation and CDC2 expression, and indicate that CDC2 gene expression is regulated by an H1 phosphatase. [ABSTRACT FROM AUTHOR]
- Published
- 2005
- Full Text
- View/download PDF
97. A robust inducible-repressible promoter greatly facilitates gene knockouts, conditional expression, and overexpression of homologous and heterologous genes in Tetrahymena thermophila.
- Author
-
Yuhua Shang, Xiaoyuan Song, Bowen, Josephine, Corstanje, Robert, Yan Gao, Gaertig, Jacek, and Gorovsky, Martin A.
- Subjects
- *
TETRAHYMENA , *GENES , *METALLOTHIONEIN - Abstract
Examines the facilitation of gene knockout, conditional expression, and overexpression of homologous and heterologous genes in Tetrahymena thermophila. Details on northern blot analysis; Effects of cloning the metallothionein genes; Creation of transformation vectors.
- Published
- 2002
- Full Text
- View/download PDF
98. Phosphorylation of the SQ H2A.X Motif Is Required for Proper Meiosis and Mitosis in Tetrahymena thermophila.
- Author
-
Xiaoyuan Song, Gjoneska, Elizabeta, Qinghu Ren, Taverna, Sean D., Allis, C. David, and Gorovsky, Martin A.
- Subjects
- *
PHOSPHORYLATION , *DNA repair , *CILIATA , *SACCHAROMYCES cerevisiae , *TETRAHYMENA , *MEIOSIS - Abstract
Phosphorylation of the C terminus SQ motif that defines H2A.X variants is required for efficient DNA double-strand break (DSB) repair in diverse organisms but has not been studied in ciliated protozoa. Tetrahymena H2A.X is one of two similarly expressed major H2As, thereby differing both from mammals, where H2A.X is a quantitatively minor component, and from Saccharomyces cerevisiae where it is the only type of major H2A. Tetrahymena H2A.X is phosphorylated in the SQ motif in both the mitotic micronucleus and the amitotic macronucleus in response to DSBs induced by chemical agents and in the micronucleus during prophase of meiosis, which occurs in the absence of a synaptonemal complex. H2A.X is phosphorylated when programmed DNA rearrangements occur in developing macronuclei, as for immunoglobulin gene rearrangements in mammals, but not during the DNA fragmentation that accompanies breakdown of the parental macronucleus during conjugation, correcting the previous interpretation that this process is apoptosis-like. Using strains containing a mutated (S134A) SQ motif, we demonstrate that phosphorylation of this motif is important for Tetrahymena cells to recover from exogenous DNA damage and is required for normal micronuclear meiosis and mitosis and, to a lesser extent, for normal amitotic macronuclear division; its absence, while not lethal, leads to the accumulation of DSBs in both micro- and macronuclei. These results demonstrate multiple roles of H2A.X phosphorylation in maintaining genomic integrity in different phases of the Tetrahymena life cycle. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
99. Unphosphorylated H1 Is Enriched in a Specific Region of the Promoter when CDC2 Is Down-Regulated during Starvation.
- Author
-
Xiaoyuan Song and Gorovsky, Martin A.
- Subjects
- *
TETRAHYMENA , *HISTONES , *PHOSPHORYLATION , *GENE expression , *CHROMOSOMES - Abstract
Tetrahymena thermophila macronuclear histone H1 is phosphorylated by a cdc2 kinase, and H1 phosphorylation regulates CDC2 expression by a positive feedback mechanism. In starved wild-type cells, decreased expression of the CDC2 gene is correlated with a global reduction in the phosphorylation of H1 and reduced phosphorylation of H1 in the region upstream of the CDC2 gene. To determine whether the reduced H1 phosphorylation upstream of the CDC2 gene is merely a reflection of global dephosphorylation or is due to specific targeting of dephosphorylation of H1 to the CDC2 promoter during starvation, the CDC2 promoter was mapped, and the distributions of phosphorylated and unphosphorylated H1 across the CDC2 gene were determined using chromatin immunoprecipitation. Unphosphorylated H1 is specifically enriched in a region of the CDC2 promoter when the gene's expression is reduced during starvation but not when CDC2 is highly active in growing cells. The region of unphosphorylated H1 coincides with a region that is essential for CDC2 expression. These studies are the first in vivo demonstration that the phosphorylation of H1 is being regulated at a fine level and that unphosphorylated H1 can be specifically targeted to a promoter, where it likely regulates transcription in a gene-specific manner. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
100. Research Advances in Vestibular Rehabilitation Mechanism and Treatment
- Author
-
QI Xiaoyuan, SONG Ning, GU Ping, YANG Xu
- Subjects
neurological rehabilitation ,vestibular diseases ,repair ,adaptation, physiological ,acclimatization ,mechanism of action ,review ,Medicine - Abstract
Recent years have seen rapid advances in clinical diagnosis and treatment of vestibular diseases, especially vestibular evaluation and rehabilitation technologies, greatly promoting the developments in individualization and precision of rehabilitation for peripheral and central vestibular diseases. The vestibular rehabilitation helps to correct inappropriate strategy of equilibrium and/or to accelerate a good but slow compensation phenomenon, effectively improve vestibular, visual, and proprioceptive inputs to balance coordination control ability, improve the compensatory function of central nervous system, so as to reduce or eliminate the symptoms of dizziness, vertigo, and balance instability, eventually restoring the normal vestibular status. Given this background, we reviewed the advances in mechanisms of rehabilitation, pre-rehabilitation evaluation, rehabilitation program formulation and treatment regarding vestibular diseases, offering insights into clinical implementation and research concerning vestibular rehabilitation in China.
- Published
- 2022
- Full Text
- View/download PDF
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