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The X inactive-specific transcript (Xist) gene is the master regulator of X chromosome inactivation in mammals. Xist produces a long noncoding (lnc)RNA that accumulates over the entire length of the chromosome from which it is transcribed, recruiting factors to modify underlying chromatin and silence X-linked genes in cis. Recent years have seen significant progress in identifying important functional elements in Xist RNA, their associated RNA-binding proteins (RBPs), and the downstream pathways for chromatin modification and gene silencing. In this review, we summarize progress in understanding both how these pathways function in Xist-mediated silencing and the complex interplay between them.

To ensure stable transmission of genetic information to the next generation, germ cells frequently silence sex chromosomes, as well as autosomal loci that promote inappropriate differentiation programs. In Caenorhabditis elegans, silenced and active genomic domains are established in germ cells by the histone modification complexes MES-2/3/6 and MES-4, which promote silent and active chromatin states, respectively. These states are generally mutually exclusive and modulation of one state influences the pattern of the other. Here, we identify the zinc-finger protein OEF-1 as a novel modifier of this epigenetic balance in the C. elegans germline. Loss of oef-1 genetically enhances mes mutant phenotypes. Moreover, OEF-1 binding correlates with the active modification H3K36me3 and sustains H3K36me3 levels in the absence of MES-4 activity. OEF-1 also promotes efficient mRNA splicing activity, a process that is influenced by H3K36me3 levels. Finally, OEF-1 limits deposition of the silencing modification H3K27me3 on the X chromosome and at repressed autosomal loci. We propose that OEF-1 might act as an intermediary to mediate the downstream effects of H3K36me3 that promote transcript integrity, and indirectly affect gene silencing as a consequence.

RNA N6-methyladenosine (m6A) modification plays important roles in multiple aspects of RNA regulation. m6A is installed cotranscriptionally by the METTL3/14 complex, but its direct roles in RNA processing remain unclear. Here, we investigate the presence of m6A in nascent RNA of mouse embryonic stem cells. We find that around 10% of m6A peaks are located in alternative introns/exons, often close to 5′ splice sites. m6A peaks significantly overlap with RBM15 RNA binding sites and the histone modification H3K36me3. Acute depletion of METTL3 disrupts inclusion of alternative introns/exons in the nascent transcriptome, particularly at 5′ splice sites that are proximal to m6A peaks. For terminal or variable-length exons, m6A peaks are generally located on or immediately downstream from a 5′ splice site that is suppressed in the presence of m6A and upstream of a 5′ splice site that is promoted in the presence of m6A. Genes with the most immediate effects on splicing include several components of the m6A pathway, suggesting an autoregulatory function. Collectively, our findings demonstrate crosstalk between the m6A machinery and the regulation of RNA splicing.

Tripartite motif (TRIM) family proteins participate in a variety of important cellular processes, including apoptosis, cell-cycle arrest, DNA repair, and senescence. In this study, we demonstrated that a novel TRIM family member, TRIM67, was commonly silenced in colorectal cancer and its downregulation was associated with poor survival. Trim67 knockout in ApcMin/+ mice increased the incidence, multiplicity, and burden of colorectal tumors. Similarly, colon-specific knockout of Trim67 significantly accelerated azoxymethane-induced colorectal cancer in mice. RNA sequencing revealed that the antitumor effect of TRIM67 was mediated by activation of the p53 signaling pathway. TRIM67 interacted directly with the C-terminus of p53, inhibiting p53 degradation by its ubiquitin ligase MDM2. TRIM67 was also a transcriptional target of p53; upon cellular stress, p53 bound to the TRIM67 promoter and induced significant upregulation of TRIM67, thereby forming a TRIM67/p53 self-amplifying loop that boosts p53-induced cell growth inhibition and apoptosis. Consequently, loss of this p53-positive regulatory program profoundly compromised p53-mediated responses to chemotherapy-induced DNA damage. Dampened p53 response was also observed in tumors of Trim67 knockout mice and Trim67 knockout embryonic fibroblasts. TRIM67 reactivation restored p53 activation and sensitized colorectal cancer cells to chemotherapy in vitro and in vivo. TRIM67 thus functions as a pivotal tumor suppressor in colorectal cancer and is a potential target for improving chemotherapy responsiveness. Significance: The TRIM67/p53 axis represents a novel therapeutic target that could be harnessed to improve chemotherapy efficacy in colorectal cancer expressing wild-type p53 but with repressed p53 signaling.

Xist RNA directs the process of X-chromosome inactivation in mammals by spreading in cis along the chromosome from which it is transcribed and recruiting chromatin modifiers to silence gene transcription. To elucidate mechanisms of Xist RNA cis-confinement, we established a sequential dual color labeling, super-resolution imaging approach to trace individual Xist RNA molecules over time, enabling us to define fundamental parameters of spreading. We demonstrate a feedback mechanism linking Xist RNA synthesis and degradation, and an unexpected physical coupling between preceding and newly synthesized Xist RNA molecules. Additionally, we show that the protein SPEN, a key factor for Xist-mediated gene-silencing, has a distinct function in Xist RNA localization, stability and in coupling behavior. Our results provide important insights towards understanding the unique dynamic properties of Xist RNA.One Sentence SummaryVisualizing Xist RNA dynamics in single cells during X chromosome inactivation

Summary Transcriptional fidelity depends on accurate promoter selection and initiation from the correct sites. In yeast, H3K36me3-mediated recruitment of the Rpd3S HDAC complex to gene bodies suppresses spurious transcription initiation. Here we describe an equivalent pathway in metazoans. PWWP2A/B is an H3K36me3 reader that forms a stable complex with HDAC1/2. We used CAGE-seq to profile all transcription initiation sites in wild-type mESCs and cells lacking PWWP2A/B. Loss of PWWP2A/B enhances spurious initiation from intragenic sites present in wild-type mESCs, and this effect is associated with increased levels of initiating Pol-II and histone acetylation. Spurious initiation events in Pwwp2a/b DKO mESCs do not overlap in genomic location or chromatin features with spurious sites that arise in Dnmt3b KO mESCs, previously reported to function in the suppression of intragenic transcriptional initiation, suggesting these pathways function cooperatively in maintaining the fidelity of transcription initiation in metazoans., Graphical Abstract, Highlights • Loss of PWWP2A/B leads to increased levels of spurious transcription initiation • Spurious TSS sites are predominantly in the gene bodies of highly expressed genes • Spurious sites are marked with increased histone acetylation and initiating Pol II • PWWP2-spurious TSSs are distinct from those caused by DNMT3B loss, Molecular Biology; Molecular Mechanism of Gene Regulation; Stem Cells Research

RNAN6-methyladenosine (m6A) modification plays important roles in multiple aspects of RNA regulation. m6A is installed co-transcriptionally by the METTL3/14 complex, but its direct roles in RNA processing remain unclear. Here we investigate the presence of m6A in nascent RNA of mouse embryonic stem cells (mESCs). We find that around 10% m6A peaks are in introns, often close to 5’-splice sites. RNA m6A peaks significantly overlap with RBM15 RNA binding sites and the histone modification H3K36me3. Interestingly, acute dTAG depletion of METTL3 reveals that inclusion of m6A-bearing alternative introns/exons in the nascent transcriptome is disrupted. For terminal or variable-length exons, m6A peaks are generally located upstream of a repressed 5’-splice site, and downstream of an enhanced 5’-splice site. Intriguingly, genes with the most immediate effects on splicing include several components of the m6A pathway, suggesting an autoregulatory function. Our findings demonstrate a direct crosstalk between m6A machinery and the regulation of RNA processing.

RNA N(6)-methyladenosine (m(6)A) modification plays important roles in multiple aspects of RNA regulation. m(6)A is installed cotranscriptionally by the METTL3/14 complex, but its direct roles in RNA processing remain unclear. Here, we investigate the presence of m(6)A in nascent RNA of mouse embryonic stem cells. We find that around 10% of m(6)A peaks are located in alternative introns/exons, often close to 5′ splice sites. m(6)A peaks significantly overlap with RBM15 RNA binding sites and the histone modification H3K36me3. Acute depletion of METTL3 disrupts inclusion of alternative introns/exons in the nascent transcriptome, particularly at 5′ splice sites that are proximal to m(6)A peaks. For terminal or variable-length exons, m(6)A peaks are generally located on or immediately downstream from a 5′ splice site that is suppressed in the presence of m(6)A and upstream of a 5′ splice site that is promoted in the presence of m(6)A. Genes with the most immediate effects on splicing include several components of the m(6)A pathway, suggesting an autoregulatory function. Collectively, our findings demonstrate crosstalk between the m(6)A machinery and the regulation of RNA splicing.

Despite recent advances in our understanding of the function of long noncoding RNAs (lncRNAs), their roles and functions in DNA repair pathways remain poorly understood. By screening a panel of uncharacterized lncRNAs to identify those whose transcription is induced by double-strand breaks (DSBs), we identified a novel lncRNA referred to as LRIK that interacts with Ku, which enhances the ability of the Ku heterodimer to detect the presence of DSBs. Here, we show that depletion of LRIK generates significantly enhanced sensitivity to DSB-inducing agents and reduced DSB repair efficiency. In response to DSBs, LRIK enhances the recruitment of repair factors at DSB sites and facilitates γH2AX signaling. Our results demonstrate that LRIK is necessary for efficient repairing DSBs via nonhomologous end-joining pathway.

Background: X chromosome inactivation in mammals is regulated by the non-coding (nc) RNA, Xist, which represses the chromosome from which it is transcribed. High levels of the N6-methyladenosine (m6A) RNA modification occur within Xist exon I, close to the 5’ end of the transcript, and also further 3’, in Xist exon VII. The m6A modification is catalysed by the METTL3/14 complex that is directed to specific targets, including Xist, by the RNA binding protein RBM15/15B. m6A modification of Xist RNA has been reported to be important for Xist–mediated gene silencing. Methods: We use CRISPR/Cas9 mediated mutagenesis to delete sequences around the 5’ m6A region in interspecific XX mouse embryonic stem cells (mESCs). Following induction of Xist RNA expression, we assay chromosome silencing using allelic RNA-seq and Xist m6A distribution using m6A-seq. Additionally, we use Xist RNA FISH to analyse the effect of deleting the 5’ m6A region on the function of the endogenous Xist promoter. We purify epitope tagged RBM15 from mESCs, and then apply MS/MS analysis to define the RBM15 interactome. Results: We show that a deletion encompassing the entire Xist 5’ m6A region results in a modest reduction in Xist-mediated silencing, and that the 5’ m6A region overlaps essential DNA elements required for activation of the endogenous Xist promoter. Deletion of the Xist A-repeat, to which RBM15 binds, entirely abolishes deposition of m6A in the Xist 5’ m6A region without affecting the modification in exon VII. We show that in mESCs, RBM15 interacts with the m6A complex, the SETD1B histone modifying complex, and several proteins linked to RNA metabolism. Conclusions: Our findings support that RBM15 binding to the Xist A-repeat recruits the m6A complex to the 5’ Xist m6A region and that this region plays a role in Xist-mediated chromosome silencing.

This work discusses how to implement wetland restoration/creation from the viewpoint that wetland aquatic plants are divided into four life forms: emergent, submergent, floating and floating leaf plants. Caohai Lake and Baiyun Lake were selected to discuss the difference of the species richness changes during the creation/restoration process. Baiyun Lake and eight surrounding wetlands have been selected to discuss how the species rich-ness, the dispersal and the colonization potential among four plant life forms affect the species richness changes and community restoration in the target wetland. The community composition changes in the introduced single dominant submergent and emergent plant community in Baiyun Lake have also been tracked to discuss how invasive plants’ dispersal affects wetland restoration/creation. The result indicated that in the process of creation/restoration of Caohai Lake and Baiyun Lake, the emergent plants have been increasing, while the submergent, the floating and the floating leaf plants began to increase and then maintained a dynamic balance. The similarity of plant community composition between the target wetland Baiyun Lake and the surrounding wetlands increased gradually, which was mainly affected by distance and river-lake connectivity. In the natural wetlands, the most common plants are emergent plants, which account for approximately 80 percent of wetland plants; this implies a greater abundance of germplasm resources, dispersal and colonization potential of emergent plants than the other three plant life forms. In Baiyun Lake, invasive plants mainly affect the introduced emergent plants community. The study confirms that before implementing wetland restoration/creation, pre-restoration surveys are required to the target wetland and its surrounding wetland. The study also finds that in Guangdong province, China, the restoration of wetland vegetation should give more priority to the submergent plants. Generally emergent plants community’s invasive preventing and submergent plants germplasm resources introducing will be the focus of the human intervention in wetland restoration/creation.

Background The wide variety of specialized permissive and repressive mechanisms by which germ cells regulate developmental gene expression are not well understood genome-wide. Isolation of germ cells with high integrity and purity from living animals is necessary to address these open questions, but no straightforward methods are currently available. Results Here we present an experimental paradigm that permits the isolation of nuclei from C. elegans germ cells at quantities sufficient for genomic analyses. We demonstrate that these nuclei represent a very pure population and are suitable for both transcriptome analysis (RNA-seq) and chromatin immunoprecipitation (ChIP-seq) of histone modifications. From these data, we find unexpected germline- and soma-specific patterns of gene regulation. Conclusions This new capacity removes a major barrier in the field to dissect gene expression mechanisms in the germ line of C. elegans. Consequent discoveries using this technology will be relevant to conserved regulatory mechanisms across species. Electronic supplementary material The online version of this article (10.1186/s12864-019-5893-9) contains supplementary material, which is available to authorized users.

The biology of non-coding RNA (ncRNA) and the regulation of mammalian gene expression is a rapidly expanding field. In this review, we consider how recent advances in technology, enabling the precise mapping of modifications to RNA transcripts, has provided new opportunities to dissect post-transcriptional gene regulation. With this has come the realisation that in the absence of translation, the modification of ncRNAs may play a fundamental role in their regulation, protein interactome and subsequent downstream effector functions. We focus upon modification of RNA by N6-methyladenosine (m6A); its readers, writers and erasers, before considering the differing role of m6A modified lncRNAs MALAT1 and Xist.This article is part of a Special Issue entitled: mRNA modifications in gene expression control edited by Dr. Soller Matthias and Dr. Fray Rupert.

Table S1 Quantification of fraction of germline nuclei (DOCX 14 kb)

Figure S8 Heatmap of H3K4me3 levels for genes with tissue-enriched expression. Heatmap displaying the levels of H3K4me3 for genes with SOM-enriched expression or IGN-enriched expression, as assayed by IGN H3K4me3 ChIP-seq and SOM H3K4me3 ChIP-seq. (PDF 3310 kb)

Figure S1 Isolated germline nuclei from a second germline transgenic strain. (A) Young adult pie-1p::GFP::H2B transgenic worm showing germline expression. GFP::H2B is expressed in the nuclei of germ cells at all developmental stages, including oocytes and embryos. (B) Isolated nuclei from pie-1p::GFP::H2B young adult worms were immunostained with GFP (green) and stained with DAPI (blue). Nuclei stained with both GFP and DAPI (89.1%, n = 2111) were considered germline nuclei. Two independent experiments were performed. (C) Isolated nuclei from wild type VC2010 N2 young adult worms were immunostained with GFP (green) and stained with DAPI (Blue). Scale bars, 20 μm in (A), 5 μm in (B) and (C). (PDF 6536 kb)

Figure S5 GO analysis of genes present exclusively in the dissected gonad dataset. Eighteen of the most significant Gene Ontology Biological Process terms for the 6606 transcripts present exclusively in the dissected gonad [23] when compared to the IGN dataset in Fig. 3e. (PDF 862 kb)

Figure S6 Analysis of Intron reads for IGN RNA-seq and SOM RNA-seq. (A) The percentage of intron reads (reads that overlap with introns or fully located in introns) for indicated RNA-seq samples. (B) Smoothed scatter plot showing the TP10M value of intron reads for each gene in IGN and SOM samples. TP10M values were calculated by the sum of intronic reads for each gene, then normalized to 10 million mapped reads. (PDF 1629 kb)

Figure S4 Representative RNA-seq profiles and transcript abundance of IGN and SOM. (A-B) Genome browser views of representative RNA-seq profiles of wild type IGN (red) and SOM (blue) on genomic regions from chromosome IV (A) and I (B), showing tissue-specific transcript abundance. The green box highlights an example of primary or partially processed transcripts of suco-1 in IGN. Black arrows indicate signal detected in an intron in IGN (B). (C) A boxplot displaying the overall abundance and distribution of gene expression levels (FPKM) for 3965 SOM-enriched transcripts (blue) and 5075 IGN-enriched transcripts (red) in either IGN RNA-seq or SOM RNA-seq. Each box indicates the median and interquartile range of FPKM level. (PDF 1247 kb)

Figure S2 A small fraction of sperm are present in total isolated germline nuclei. Isolated total nuclei from young adult pie-1p::GFP::H2B transgenic worms. Nuclei were immunostained with GFP (green) and stained with DAPI (Blue). Arrows indicate two non-GFP stained nuclei with characteristics of sperm. Scale bar, 5â Îźm. (PDF 4083 kb)

Figure S3 DEseq2 analysis of gene expression levels in SOM and IGN. (A) MA plot showing the differential gene expression pattern for SOM and IGN samples. The differentially expressed genes between SOM and IGN were represented with red dots (p adjâ

Figure S7 Confirmation of germline-enriched H3K27ac modification in isolated germ nuclei by ChIP-qPCR. Two previously characterized germline-expressed (him-3 and oef-1) and soma-expressed genes (elt-2 and myo-3) were examined for abundance of H3K27ac in IGN by ChIP-qPCR. Three sets of primers were tested for each germline-specific gene. C37H5.15 served as positive control. Elt-2 served as negative control and was used to calculate fold enrichment. ChIP results are expressed as percent of input using Ct values (A) and fold enrichment of H3K27ac modification normalized to elt-2 (B). (PDF 1136 kb)

// Lihui Liu 1, 2, 3, * , Haiyan Yue 1, 2, 3, * , Qinghua Liu 1, 2, * , Jiao Yuan 1, 2, * , Jing Li 4 , Guifeng Wei 1, 2 , Xiaomin Chen 1, 2 , Youyong Lu 5 , Mingzhou Guo 6 , Jianjun Luo 1, 2 , Runsheng Chen 1, 2, 7 1 Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China 2 Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China 3 Graduate School of Chinese Academy of Sciences, Beijing 100049, China 4 Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Peking Union Medical College Hospital, Center of Excellence in Tissue Engineering, School of Basic Medicine, Peking Union Medical College, Beijing 100005, China 5 Laboratory of Molecular Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education), Peking University Cancer Hospital and Institute, Beijing 100142, China 6 Department of Gastroenterology and Hepatology, Chinese PLA General Hospital, Beijing 100853, China 7 Research Network of Computational Biology, RNCB, Beijing 100101, China * These authors contributed equally to this work Correspondence to: Runsheng Chen, e-mail: rschen@ibp.ac.cn Jianjun Luo, e-mail: luojianj@moon.ibp.ac.cn Keywords: long noncoding RNAs, MT1JP, TIAR, p53, tumor suppressor Received: September 09, 2015 Accepted: February 05, 2016 Published: February 19, 2016 ABSTRACT Accumulating evidence suggests that long noncoding RNAs (lncRNAs) play important roles in transcriptional regulation, whereas the extent to which the lncRNAs also function at the posttranscriptional level is less known. In the present study, we report a lncRNA named MT1JP which acts as a tumor suppressor through a posttranscriptional mechanism. We found that MT1JP is differentially expressed in tumor tissues by analyzing data from a customized microarray applied to 76 pairs of matched normal and cancer tissue samples. By associating with the RNA-binding protein TIAR, MT1JP enhanced the translation of the master transcription factor p53, thereby regulating a series of pathways involving p53, such as the cell cycle, apoptosis and proliferation. When MT1JP was down-regulated, the protein level of p53 declined, which in turn accelerated cell deterioration and tumor formation. Moreover, differential expression of MT1JP in cancerous and normal tissues suggests that it may be a promising prognostic marker and a therapeutic target. Taken together, we identified MT1JP as a critical factor in restraining cell transformation by modulating p53 translation through interactions with TIAR, and this finding is likely to shed new light on future investigations about posttranscriptional or translational effects of lncRNAs during cell transformation.

Xist RNA, the master regulator of X chromosome inactivation, acts in cis to induce chromosome-wide silencing. Whilst recent studies have defined candidate silencing factors, their relative contribution to repressing different genes, and their relationship with one another is poorly understood. Here we describe a systematic analysis of Xist-mediated allelic silencing in mouse embryonic stem cell-based models. Using a machine learning approach we identify distance to the Xist locus and prior gene expression levels as key determinants of silencing efficiency. We go on to show that Spen, recruited through the Xist A-repeat, plays a central role, being critical for silencing of all except a subset of weakly expressed genes. Polycomb, recruited through the Xist B/C-repeat, also plays a key role, favouring silencing of genes with pre-existing H3K27me3 chromatin. LBR and the Rbm15/m6A-methyltransferase complex make only minor contributions to gene silencing. Together our results provide a comprehensive model for Xist-mediated chromosome silencing., Xist RNA is the master regulator of X chromosome inactivation. Here the authors describe a systematic analysis of Xist-mediated allelic silencing in mouse ESC models and define the contribution of different pathways that regulate gene silencing.

// Guifeng Wei 1,2,* , Huaxia Luo 1,2,* , Yu Sun 1,2,* , Jiagen Li 3 , Liqing Tian 1 , Wei Liu 1,2 , Lihui Liu 1,2 , Jianjun Luo 1 , Jie He 3 and Runsheng Chen 1,4 1 Bioinformatics Laboratory and CAS Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China 2 University of Chinese Academy of Sciences, Beijing, China 3 Department of Thoracic Surgery, Cancer Institute and Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China 4 Research Network of Computational Biology, RNCB, Beijing, China * These authors have contributed equally to this work Correspondence to: Runsheng Chen, email: // Jie He, email: // Keywords : ESCC, long noncoding RNAs, tumor suppressor, metastasis, Epist Received : March 16, 2015 Accepted : May 02, 2015 Published : May 19, 2015 Abstract Esophageal Squamous Cell Carcinoma (ESCC) is among the most common malignant cancers worldwide. In the past, extensive efforts have been made to characterize the involvement of protein-coding genes in ESCC tumorigenesis but few for long noncoding RNAs (lncRNAs). To investigate the transcriptome profile and functional relevance of lncRNAs, we performed an integrative analysis of a customized combined lncRNA-mRNA microarray and RNA-seq data on ESCCs and matched normal tissues. We identified numerous lncRNAs that were differentially expressed between the normal and tumor tissues, termed “ESCC-associated lncRNAs (ESCALs)”, of which, the majority displayed restricted expression pattern. Also, a subset of ESCALs appeared to be associated with ESCC patient survival. Gene set enrichment analysis (GSEA) further suggested that over half of the ESCALs were positively- or negatively- associated with metastasis. Among these, we identified a novel nuclear-retained lncRNA, named Epist , which is generally highly expressed in esophagus, and which is down-regulated during ESCC progression. Epist over-expression and knockdown studies further suggest that Epist inhibits the metastasis, acting as a tumor suppressor in ESCC. Collectively, our analysis of the ESCC transcriptome identified the potential tumor suppressing lncRNA Epist , and provided a foundation for future efforts to identify functional lncRNAs for cancerous therapeutic targeting.

Long noncoding RNAs (lncRNAs) are pervasively transcribed in the human genome. Recent studies suggest that the involvement of lncRNAs in human diseases could be far more prevalent than previously appreciated. Here we have identified a lncRNA termed Lnc_bc060912 whose expression is increased in human lung and other tumors. Lnc_bc060912 is 1.2 kb in length and is composed of two exons. The expression of Lnc_bc060912 was repressed by p53. Lnc_bc060912 suppressed cell apoptosis. Using a recently developed method for RNA-pulldown with formaldehyde cross-linking, we found that Lnc_bc060912 interacted with the two DNA damage repair proteins PARP1 and NPM1. Together, these results suggest that Lnc_bc060912, via PARP1 and NPM1, affects cell apoptosis and may play important roles in tumorigenesis and cancer progression.

Synaptic vesicles (SV) store various neurotransmitters that are released at the synapse. The molecular mechanisms of biogenesis, exocytosis, and endocytosis for SV, however, remain largely elusive. In this study, using Complex Object Parametric Analysis and Sorter (COPAS) to monitor the fluorescence of synapto-pHluorin (SpH), we performed a whole-genome RNAi screen in C. elegans to identify novel genetic modulators in SV cycling. One hundred seventy six genes that up-regulating SpH fluorescence and 96 genes that down-regulating SpH fluorescence were identified after multi-round screen. Among these genes, B0035.1 (bugz-1) encodes ortholog of mammalian C2H2 zinc-finger protein BuGZ/ZNF207, which is a spindle assembly checkpoint protein essential for mitosis in human cells. Combining electrophysiology, imaging and behavioral assays, we reveal that depletion of BuGZ-1 results in defects in locomotion. We further demonstrate that BuGZ-1 promotes SV recycling by regulating the expression levels of endocytosis-related genes such as rab11.1. Therefore, we have identified a bunch of potential genetic modulators in SV cycling, and revealed an unexpected role of BuGZ-1 in regulating synaptic transmission.

Increasing evidence indicates that long noncoding RNAs (lncRNAs) have important roles in various physiological processes and dysfunction of lncRNAs could be a prevalent cause in human diseases. Here we functionally characterized the nuclear-enriched lncRNA SNHG1, which is highly expressed in multiple types of cancer. We also provide evidence that SNHG1 promotes cancer cell growth by regulating gene expression both in cis and in trans. SNHG1 was involved in the AKT signaling pathway as it promotes the neighboring transcription of the protein-coding gene SLC3A2 in cis by binding the Mediator complex to facilitate the establishment of enhancer-promoter interaction. In trans, SNHG1 directly interacted with central domain of FUBP1 and antagonize the binding of FBP-interacting repressor to FUBP1, thereby coordinating the expression of the oncogene MYC. Collectively, our findings demonstrate that lncRNA SNHG1 can function both in cis and in trans with distinct mechanisms to regulate transcription, promoting tumorigenesis and cancer progression.

Summary The Polycomb-repressive complexes PRC1 and PRC2 play a key role in chromosome silencing induced by the non-coding RNA Xist. Polycomb recruitment is initiated by the PCGF3/5-PRC1 complex, which catalyzes chromosome-wide H2A lysine 119 ubiquitylation, signaling recruitment of other PRC1 complexes, and PRC2. However, the molecular mechanism for PCGF3/5-PRC1 recruitment by Xist RNA is not understood. Here we define the Xist RNA Polycomb Interaction Domain (XR-PID), a 600 nt sequence encompassing the Xist B-repeat element. Deletion of XR-PID abolishes Xist-dependent Polycomb recruitment, in turn abrogating Xist-mediated gene silencing and reversing Xist-induced chromatin inaccessibility. We identify the RNA-binding protein hnRNPK as the principal XR-PID binding factor required to recruit PCGF3/5-PRC1. Accordingly, synthetically tethering hnRNPK to Xist RNA lacking XR-PID is sufficient for Xist-dependent Polycomb recruitment. Our findings define a key pathway for Polycomb recruitment by Xist RNA, providing important insights into mechanisms of chromatin modification by non-coding RNA., Graphical Abstract, Highlights • A 600 nt element in Xist RNA, XR-PID, is required for Polycomb recruitment • Deletion of XR-PID abrogates Xist-mediated chromosome silencing • hnRNPK binds XR-PID to recruit the Polycomb-initiating complex PCGF3/5-PRC1 • Tethering hnRNPK to Xist RNA bypasses the requirement for XR-PID, This study advances our understanding of the molecular mechanism of X chromosome inactivation in mammals, defining XR-PID, the critical element in Xist RNA that recruits Polycomb complexes to the inactive X chromosome, and further demonstrating that the RNA binding protein hnRNPK bridges XR-PID with the initiating Polycomb complex, PCGF3/5-PRC1.

In the last decade, it has been demonstrated that brain functional asymmetry occurs not only in vertebrates but also in invertebrates. However, the mechanisms underlying functional asymmetry remain unclear. In the present study, we trained honeybees of the same parentage and age, on the proboscis extension reflex (PER) paradigm with only one antenna in use. The comparisons of gene expression between the left and right hemispheres were carried out using high throughput sequencing. Our research revealed that gene expression in the honeybee brain is also asymmetric, with more genes having higher expression in the right hemisphere than the left hemisphere. Our studies show that during olfactory learning, the left hemisphere is more responsible for long term memory and the right hemisphere is more responsible for the learning and short term memory.

Noncoding RNAs are increasingly being recognized as important players in eukaryote biology. However, despite major efforts in mapping the Caenorhabditis elegans transcriptome over the last couple of years, nonpolyadenylated and intermediate-size noncoding RNAs (is-ncRNAs) are still incompletely explored. We have combined an enzymatic approach with full-length RNA-Seq of is-ncRNAs in C. elegans. A total of 473 novel is-ncRNAs has been identified, of which a substantial fraction was associated with transcription factor binding sites and developmentally regulated expression patterns. Analysis of sequence and secondary structure permitted classification of more than 200 is-ncRNAs into several known RNA classes, while another 33 is-ncRNAs were identified as belonging to two previously uncharacterized groups of is-ncRNAs. Three of the unclassified is-ncRNAs contain the 5′ Alu domain common to SRP RNAs and specifically bound with the SRP9/14 heterodimer in vitro. One of these (inc394) showed 65% sequence identity with the human, neuron-specific BC200 RNA. Structure-based clustering analysis and in vitro binding experiments supported the notion that the nematode stem-bulge RNAs (sbRNAs) are homologs (or functional analogs) of the Y RNAs. Moreover, analysis of the differential libraries showed that some mature snoRNAs undergo secondary 5′ cap modification after processing of the primary transcript, thus suggesting the existence of a wider range of functional RNAs arising from processed and modified fragments of primary transcripts.

Monitoring of spatial and temporal distribution of chlorophyll (Chl-a) concentrations in the aquatic milieu is always challenging and often interesting. However, the recent advancements in satellite digital data play a significant role in providing outstanding results for the marine environmental investigations. The present paper is aimed to review 'remote sensing research in Chinese seas' within the period of 24 years from 1978 to 2002. Owing to generalized distributional pattern, the Chl-a concentrations are recognized high towards northern Chinese seas than the southern. Moreover, the coastal waters, estuaries, and upwelling zones always exhibit relatively high Chl-a concentrations compared with offshore waters. On the basis of marine Chl-a estimates obtained from satellite and other field measured environmental parameters, we have further discussed on the applications of satellite remote sensing in the fields of harmful algal blooms (HABs), primary production and physical oceanographic currents of the regional seas. Concerned with studies of HABs, satellite remote sensing proved more advantageous than any other conventional methods for large-scale applications. Probably, it may be the only source of authentic information responsible for the evaluation of new research methodologies to detect HABs. At present, studies using remote sensing methods are mostly confined to observe algal bloom occurrences, hence, it is essential to coordinate the mechanism of marine ecological and oceanographic dynamic processes of HABs using satellite remote sensing data with in situ measurements of marine environmental parameters. The satellite remote sensing on marine environment and HABs is believed to have a great improvement with popular application of technology. (C) 2007 COSPAR. Published by Elsevier Ltd. All rights reserved.

The identification and characterization of long non-coding RNAs (lncRNAs) in diverse biological processes has recently developed rapidly. The large amounts of non-coding RNAs scale consistent with developmental complexity in eukaryotes, indicating that most of these transcripts may have functions in the regulation of biological processes and disorder in the organisms. In particular, Understanding of the overall biological significance of lncRNAs in cancers still remains limited. Here, we found a nuclear-retained lncRNA, termed Lnc_ASNR (apoptosis suppressing-noncoding RNA), which serves as a repressor of apoptosis. Lnc_ASNR was discovered in a set of microarray data derived from four kinds of tumor and adjacent normal tissue samples and displayed significant up-regulation in the tumor tissues. Using an RNA-pull down assay, we found that Lnc_ASNR interacted with the protein ARE/poly (U)-binding/degradation factor 1(AUF1), which is reported to promote rapid degradation of the Bcl-2 mRNA, an inhibitor of apoptosis. Lnc_ASNR binds to AUFI in nucleus, decreasing the cytoplasmic proportion of AUF1 which targets the B-cell lymphoma-2 (Bcl-2) mRNA. Taken together, the overall effect of Lnc_ASNR expression is thus a decrease in cell apoptosis indicating that Lnc_ASNR may play a vital role in tumorigenesis and carcinogenesis.

The occurrences of harmful algal blooms (HABs), in terms of frequency and area in the Chinese coastal waters, have been increasing since 1980s and caused considerable economic losses. In the present study, we have analyzed spatial and seasonal characteristics of HAB events in the southern Yellow Sea and East China Sea along Chinese coast from 1933 to 2004. With a total 435 HAB records, the most frequent HAB occurrence area (FHA) is off the Yangtze River mouth and another two FHA areas are located south of the Yangtze River estuary along about isobaths of 30–60 m coastal water in the East China Sea. The time of HAB occurrence shifted during our study period: from autumn (August–October) before 1980s to July–August in 1980s, during May–July in 1990s, and May–June for the period of 2000–2004. Causative species were found to be different: Noctiluca scintillans and Skeletonema costatum were dominant causative species prior to 2000; and Prorocentrum donghaiense Lu was dominant from 2000 to 2004 and also caused large blooms in May. Trichodesmium sp. caused many HABs in autumn (August–October) prior to 1980s with only one HAB between 1980 and 2004. The changes of the dominant HAB species may have affected the timings of HAB occurrence, as well as the increasing HAB-affected areas in recent years.