25 results on '"Cui-Jun Zhang"'
Search Results
2. The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci.
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Zhang-Wei Liu, Chang-Rong Shao, Cui-Jun Zhang, Jin-Xing Zhou, Su-Wei Zhang, Lin Li, She Chen, Huan-Wei Huang, Tao Cai, and Xin-Jian He
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Genetics ,QH426-470 - Abstract
RNA-directed DNA methylation (RdDM) is required for transcriptional silencing of transposons and other DNA repeats in Arabidopsis thaliana. Although previous research has demonstrated that the SET domain-containing SU(VAR)3-9 homologs SUVH2 and SUVH9 are involved in the RdDM pathway, the underlying mechanism remains unknown. Our results indicated that SUVH2 and/or SUVH9 not only interact with the chromatin-remodeling complex termed DDR (DMS3, DRD1, and RDM1) but also with the newly characterized complex composed of two conserved Microrchidia (MORC) family proteins, MORC1 and MORC6. The effect of suvh2suvh9 on Pol IV-dependent siRNA accumulation and DNA methylation is comparable to that of the Pol V mutant nrpe1 and the DDR complex mutant dms3, suggesting that SUVH2 and SUVH9 are functionally associated with RdDM. Our CHIP assay demonstrated that SUVH2 and SUVH9 are required for the occupancy of Pol V at RdDM loci and facilitate the production of Pol V-dependent noncoding RNAs. Moreover, SUVH2 and SUVH9 are also involved in the occupancy of DMS3 at RdDM loci. The putative catalytic active site in the SET domain of SUVH2 is dispensable for the function of SUVH2 in RdDM and H3K9 dimethylation. We propose that SUVH2 and SUVH9 bind to methylated DNA and facilitate the recruitment of Pol V to RdDM loci by associating with the DDR complex and the MORC complex.
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- 2014
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3. IDN2 and its paralogs form a complex required for RNA-directed DNA methylation.
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Cui-Jun Zhang, Yong-Qiang Ning, Su-Wei Zhang, Qing Chen, Chang-Rong Shao, Yan-Wu Guo, Jin-Xing Zhou, Lin Li, She Chen, and Xin-Jian He
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Genetics ,QH426-470 - Abstract
IDN2/RDM12 has been previously identified as a component of the RNA-directed DNA methylation (RdDM) machinery in Arabidopsis thaliana, but how it functions in RdDM remains unknown. By affinity purification of IDN2, we co-purified two IDN2 paralogs IDP1 and IDP2 (IDN2 PARALOG 1 and 2). The coiled-coil domain between the XS and XH domains of IDN2 is essential for IDN2 homodimerization, whereas the IDN2 C-terminal XH domain but not the coiled-coil domain is required for IDN2 interaction with IDP1 and IDP2. By introducing the wild-type IDN2 sequence and its mutated derivatives into the idn2 mutant for complementation testing, we demonstrated that the previously uncharacterized IDN2 XH domain is required for the IDN2-IDP1/IDP2 complex formation as well as for IDN2 function. IDP1 is required for de novo DNA methylation, siRNA accumulation, and transcriptional gene silencing, whereas IDP2 has partially overlapping roles with IDP1. Unlike IDN2, IDP1 and IDP2 are incapable of binding double-stranded RNA, suggesting that the roles of IDP1 and IDP2 are different from those of IDN2 in the IDN2-IDP1/IDP2 complex and that IDP1 and IDP2 are essential for the functioning of the complex in RdDM.
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- 2012
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4. Numerical Investigation of Subcooled Flow Boiling Characteristics in Rod Bundle Channel of Petal-shape Fuel Element
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DU Lipeng;JIANG Zeping;CUI Jun;ZHANG Wenchao;HOU Yandong;CAI Weihua
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petal-shape fuel element ,subcooled boiling ,rpi wall boiling model ,numerical investigation ,Nuclear engineering. Atomic power ,TK9001-9401 ,Nuclear and particle physics. Atomic energy. Radioactivity ,QC770-798 - Abstract
The petal-shape fuel elements have the advantages of strong heat transfer performance and no need for a spacer grid, allowing the reactor’s power density and economics to be increased even further. The Eulerian two-fluid model in combination with the RPI wall boiling model was used to investigate the boiling properties of the subcooled flow in the rod bundle channel of a 2×2 petal-shape fuel element in the paper. First, the accuracy of the interphase force model and the RPI closure model was evaluated using experimental data from subcooled boiling in a circular tube to accurately replicate two-phase flow heat transfer in the channel of the petal-shape fuel element. For the subcooled boiling phenomenon in the channel of a petal-shape fuel element rod bundle at pressure of 15.5 MPa, the numerical study of the effects of different flow velocities (1.4, 2 and 2.5 m/s) and heat flow flux (450, 650, and 800 kW/m2) on the flow, heat transfer, and void fraction distribution in the channel was carried out. The results demonstrate that the coolant flow velocity in the channel is unevenly distributed, with the maximum flow velocity in the channel’s central region, and the fluid velocity on the windward side of the fuel element being greater than the leeward side. As the inlet flow velocity increases, the flow field on the leeward side (at Line2) becomes more nonuniform. The transverse flow in the channel is primarily found in the inner concave arc of the fuel element, and the intensity of the transverse flow varies with the distance of the adjacent fuel elements. Due to the uneven flow field, the subcooled boiling is more intense and the void fraction is larger in the inner concave arc region, while the void fraction exhibits a huge disparity between the inner concave arc and the outer convex arc of the fuel element. The void percent at the fuel element’s leeward side (15°, 110°, 195°, and 285°) is higher than the void fraction near the outer convex arc’s windward side (70°, 160°, 250°, and 340°). The temperature of the outer convex arc wall surface is significantly lower at the z/H=0.25 position compared to the inner concave arc wall surface, and the temperature of the outer convex arc wall surface is greater than the inner concave arc wall temperature after the z/H=0.25 cross section due to different flow field inhomogeneity and the existence of heat transfer at the inner and outer convex arcs. The phase heat flow density does not show a linear trend of quick drop under the impact of transverse flow, but show a minor rise, and the evaporative heat flow density progressively increases along the axial direction, while the quenching heat flow does not change significantly.
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- 2023
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5. CRISPR/Cas9‐mediated restoration of Tamyb10 to create pre‐harvest sprouting‐resistant red wheat
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Yiwang Zhu, Yarong Lin, Yujin Fan, Yiwei Wang, Pengfeng Li, Jiang Xiong, Yuhan He, Shifeng Cheng, Xingguo Ye, Feng Wang, Justin Goodrich, Jian‐Kang Zhu, Ke Wang, and Cui‐Jun Zhang
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pre-harvest sprouting ,Tamyb10 ,functional recovery ,red wheat ,Plant Science ,Agronomy and Crop Science ,CRISPR/Cas9 ,Biotechnology - Abstract
Wheat pre-harvest sprouting (PHS) reduces yield and grain quality and occurs in almost every wheat-growing region around the world (Vetch et al., 2019). In general, red-grained wheat varieties are more tolerant to PHS than white-grained varieties (Himi et al., 2011). Moreover, the red pigment of the grain coat contains proanthocyanidins, whose antioxidant activity and free radical scavenging ability have health-promoting properties. Therefore, producing elite red wheat varieties is an important objective in breeding high-yield and high-quality wheat.
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- 2022
6. FHA2 is a plant‐specific ISWI subunit responsible for stamen development and plant fertility
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Xiao-Mei Hou, She Chen, Bo-Wen Gu, Xin-Jian He, Xue-Wei Cai, Lian-Mei Tan, and Cui-Jun Zhang
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0106 biological sciences ,0301 basic medicine ,Plant Infertility ,Protein subunit ,Mutant ,Arabidopsis ,Stamen ,Flowers ,Plant Science ,01 natural sciences ,Biochemistry ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Arabidopsis thaliana ,biology ,Arabidopsis Proteins ,Wild type ,Nuclear Proteins ,biology.organism_classification ,Phenotype ,Nucleosomes ,Cell biology ,Chromatin ,030104 developmental biology ,010606 plant biology & botany - Abstract
Imitation Switch (ISWI) chromatin remodelers are known to function in diverse multi-subunit complexes in yeast and animals. However, the constitution and function of ISWI complexes in Arabidopsis thaliana remain unclear. In this study, we identified forkhead-associated domain 2 (FHA2) as a plant-specific subunit of an ISWI chromatin-remodeling complex in Arabidopsis. By in vivo and in vitro analyses, we demonstrated that FHA2 directly binds to RLT1 and RLT2, two redundant subunits of the ISWI complex in Arabidopsis. The stamen filament is shorter in the fha2 and rlt1/2 mutants than in the wild type, whereas their pistil lengths are comparable. The shorter filament, which is due to reduced cell size, results in insufficient pollination and reduced fertility. The rlt1/2 mutant shows an early-flowering phenotype, whereas the phenotype is not shared by the fha2 mutant. Consistent with the functional specificity of FHA2, our RNA-seq analysis indicated that the fha2 mutant affects a subset of RLT1/2-regulated genes that does not include genes involved in the regulation of flowering time. This study demonstrates that FHA2 functions as a previously uncharacterized subunit of the Arabidopsis ISWI complex and is exclusively involved in regulating stamen development and plant fertility.
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- 2020
7. Large‐scale identification of expression quantitative trait loci in Arabidopsis reveals novel candidate regulators of immune responses and other processes
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Jian-Kang Zhu, Danni Liu, Cui-Jun Zhang, Zhaobo Lang, Xingang Wang, Dabao Zhang, Min Ren, Alberto P. Macho, and Min Zhang
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0106 biological sciences ,0301 basic medicine ,Chloroplasts ,Quantitative Trait Loci ,Arabidopsis ,Genome-wide association study ,Plant Science ,Computational biology ,Quantitative trait locus ,01 natural sciences ,Biochemistry ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,Gene ,Genetic association ,biology ,Arabidopsis Proteins ,Gene Annotation ,biology.organism_classification ,Phenotype ,Mitochondria ,030104 developmental biology ,Expression quantitative trait loci ,Genome-Wide Association Study ,010606 plant biology & botany - Abstract
The extensive phenotypic diversity within natural populations of Arabidopsis is associated with differences in gene expression. Transcript levels can be considered as inheritable quantitative traits, and used to map expression quantitative trait loci (eQTL) in genome-wide association studies (GWASs). In order to identify putative genetic determinants for variations in gene expression, we used publicly available genomic and transcript variation data from 665 Arabidopsis accessions and applied the single nucleotide polymorphism-set (Sequence) Kernel Association Test (SKAT) method for the identification of eQTL. Moreover, we used the penalized orthogonal-components regression (POCRE) method to increase the power of statistical tests. Then, gene annotations were used as test units to identify genes that are associated with natural variations in transcript accumulation, which correspond to candidate regulators, some of which may have a broad impact on gene expression. Besides increasing the chances to identify real associations, the analysis using POCRE and SKAT significantly reduced the computational cost required to analyze large datasets. As a proof of concept, we used this approach to identify eQTL that represent novel candidate regulators of immune responses. The versatility of this approach allows its application to any process that is subjected to natural variation among Arabidopsis accessions.
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- 2020
8. A plant‐specific SWR1 chromatin‐remodeling complex couples histone H2A.Z deposition with nucleosome sliding
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Chang-Rong Shao, She Chen, Xin-Jian He, Cui-Jun Zhang, Rong-Nan Lin, Xiao-Mei Hou, Lin Li, Xue-Wei Cai, Yin-Na Su, Yu-Xi Luo, and Lian-Mei Tan
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Immunoprecipitation ,Protein subunit ,Arabidopsis ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Chromatin remodeling ,Histones ,03 medical and health sciences ,0302 clinical medicine ,Gene expression ,Arabidopsis thaliana ,Protein Interaction Maps ,NuA4 histone acetyltransferase complex ,Molecular Biology ,Histone Acetyltransferases ,030304 developmental biology ,Adenosine Triphosphatases ,0303 health sciences ,General Immunology and Microbiology ,Arabidopsis Proteins ,General Neuroscience ,Articles ,Chromatin Assembly and Disassembly ,biology.organism_classification ,Chromatin ,Swr1 complex ,Nucleosomes ,Cell biology ,DNA-Binding Proteins ,030217 neurology & neurosurgery ,Transcription Factors - Abstract
Deposition of H2A.Z in chromatin is known to be mediated by a conserved SWR1 chromatin-remodeling complex in eukaryotes. However, little is known about whether and how the SWR1 complex cooperates with other chromatin regulators. Using immunoprecipitation followed by mass spectrometry, we found all known components of the Arabidopsis thaliana SWR1 complex and additionally identified the following three classes of previously uncharacterized plant-specific SWR1 components: MBD9, a methyl-CpG-binding domain-containing protein; CHR11 and CHR17 (CHR11/17), ISWI chromatin remodelers responsible for nucleosome sliding; and TRA1a and TRA1b, accessory subunits of the conserved NuA4 histone acetyltransferase complex. MBD9 directly interacts with CHR11/17 and the SWR1 catalytic subunit PIE1, and is responsible for the association of CHR11/17 with the SWR1 complex. MBD9, TRA1a, and TRA1b function as canonical components of the SWR1 complex to mediate H2A.Z deposition. CHR11/17 are not only responsible for nucleosome sliding but also involved in H2A.Z deposition. These results indicate that the association of the SWR1 complex with CHR11/17 may facilitate the coupling of H2A.Z deposition with nucleosome sliding, thereby co-regulating gene expression, development, and flowering time.
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- 2020
9. Arabidopsis AGDP1 links H3K9me2 to DNA methylation in heterochromatin
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Kai Tang, P. Zhu, W.A. Tao, Heng Zhang, Yuhui Jiang, H. Wan, F. Wu, Ray A. Bressan, Xin-Jian He, Xingang Wang, Jian-Kang Zhu, Zhusheng Yang, Xiaofan Du, Cui-Jun Zhang, Jiamu Du, Li Pan, and Jianying Luo
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0106 biological sciences ,0301 basic medicine ,Heterochromatin ,Science ,Arabidopsis ,General Physics and Astronomy ,01 natural sciences ,DNA-binding protein ,General Biochemistry, Genetics and Molecular Biology ,Article ,Protein Structure, Secondary ,03 medical and health sciences ,Epigenetics ,Amino Acid Sequence ,Gene Silencing ,lcsh:Science ,Regulation of gene expression ,Multidisciplinary ,biology ,Chemistry ,Arabidopsis Proteins ,Lysine ,General Chemistry ,Methylation ,DNA Methylation ,Chromatin ,Cell biology ,030104 developmental biology ,Histone ,Genetic Loci ,DNA methylation ,biology.protein ,DNA Transposable Elements ,lcsh:Q ,Peptides ,010606 plant biology & botany ,Protein Binding - Abstract
Heterochromatin is a tightly packed form of chromatin that is associated with DNA methylation and histone 3 lysine 9 methylation (H3K9me). Here, we identify an H3K9me2-binding protein, Agenet domain (AGD)-containing p1 (AGDP1), in Arabidopsis thaliana. Here we find that AGDP1 can specifically recognize the H3K9me2 mark by its three pairs of tandem AGDs. We determine the crystal structure of the Agenet domain 1 and 2 cassette (AGD12) of Raphanus sativus AGDP1 in complex with an H3K9me2 peptide. In the complex, the histone peptide adopts a unique helical conformation. AGD12 specifically recognizes the H3K4me0 and H3K9me2 marks by hydrogen bonding and hydrophobic interactions. In addition, we find that AGDP1 is required for transcriptional silencing, non-CG DNA methylation, and H3K9 dimethylation at some loci. ChIP-seq data show that AGDP1 preferentially occupies long transposons and is associated with heterochromatin marks. Our findings suggest that, as a heterochromatin-binding protein, AGDP1 links H3K9me2 to DNA methylation in heterochromatin regions., DNA methylation and H3K9 dimethylation are two linked epigenetic marks of silenced chromatin in plants that depend on the activity of CMT3/2 and SUVH4/5/6. Here the authors identify AGDP1 as an H3K9me2-binding protein required for heterochromatic non-CG DNA methylation, H3K9 dimethylation, and transcriptional silencing.
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- 2018
10. Histone acetylation recruits the SWR1 complex to regulate active DNA demethylation in Arabidopsis
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Zhidan Wang, Huiming Zhang, Jian-Kang Zhu, Na Liu, Xuechen Xu, Rosa Lozano-Durán, Zhaobo Lang, Pan Liu, Heng Zhang, Xingang Wang, Yu Yang, Wenfeng Nie, Andrea Andreucci, Kai Tang, Cui-Jun Zhang, Mingguang Lei, Jing-Quan Yu, Frédéric Berger, Xiaoqiang Chai, Ramesh Yelagandula, Daisuke Miki, Mingxuan Zhang, and Huan Huang
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Bromodomain ,Chromatin remodeling ,DNA demethylation pathway ,Gene silencing ,Histone variant ,Multidisciplinary ,biology ,Chromatin ,Cell biology ,chemistry.chemical_compound ,Histone ,DNA demethylation ,chemistry ,Acetylation ,DNA methylation ,biology.protein ,DNA - Abstract
Active DNA demethylation is critical for controlling the DNA methylomes in plants and mammals. However, little is known about how DNA demethylases are recruited to target loci, and the involvement of chromatin marks in this process. Here, we identify 2 components of the SWR1 chromatin-remodeling complex, PIE1 and ARP6, as required for ROS1-mediated DNA demethylation, and discover 2 SWR1-associated bromodomain-containing proteins, AtMBD9 and nuclear protein X1 (NPX1). AtMBD9 and NPX1 recognize histone acetylation marks established by increased DNA methylation 1 (IDM1), a known regulator of DNA demethylation, redundantly facilitating H2A.Z deposition at IDM1 target loci. We show that at some genomic regions, H2A.Z and DNA methylation marks coexist, and H2A.Z physically interacts with ROS1 to regulate DNA demethylation and antisilencing. Our results unveil a mechanism through which DNA demethylases can be recruited to specific target loci exhibiting particular histone marks, providing a conceptual framework to understand how chromatin marks regulate DNA demethylation.
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- 2019
11. The Arabidopsis acetylated histone-binding protein BRAT1 forms a complex with BRP1 and prevents transcriptional silencing
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Huan-Wei Huang, Cui-Jun Zhang, Lin Li, Lian-Mei Tan, Xin-Jian He, Tao Cai, Yong-Qiang Li, Chang-Rong Shao, She Chen, and Xiao-Mei Hou
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0301 basic medicine ,Science ,Arabidopsis ,General Physics and Astronomy ,Biology ,Models, Biological ,Article ,General Biochemistry, Genetics and Molecular Biology ,Histones ,03 medical and health sciences ,Protein Domains ,Transcription (biology) ,Gene Silencing ,RNA, Messenger ,Genetics ,Multidisciplinary ,Arabidopsis Proteins ,Acetylation ,General Chemistry ,DNA Methylation ,Argonaute ,Bromodomain ,DNA Demethylation ,030104 developmental biology ,Histone ,DNA demethylation ,Genetic Loci ,RNA, Plant ,DNA glycosylase ,Mutation ,DNA methylation ,biology.protein ,Protein Binding - Abstract
Transposable elements and other repetitive DNA sequences are usually subject to DNA methylation and transcriptional silencing. However, anti-silencing mechanisms that promote transcription in these regions are not well understood. Here, we describe an anti-silencing factor, Bromodomain and ATPase domain-containing protein 1 (BRAT1), which we identified by a genetic screen in Arabidopsis thaliana. BRAT1 interacts with an ATPase domain-containing protein, BRP1 (BRAT1 Partner 1), and both prevent transcriptional silencing at methylated genomic regions. Although BRAT1 mediates DNA demethylation at a small set of loci targeted by the 5-methylcytosine DNA glycosylase ROS1, the involvement of BRAT1 in anti-silencing is largely independent of DNA demethylation. We also demonstrate that the bromodomain of BRAT1 binds to acetylated histone, which may facilitate the prevention of transcriptional silencing. Thus, BRAT1 represents a potential link between histone acetylation and transcriptional anti-silencing at methylated genomic regions, which may be conserved in eukaryotes., Transposons and repetitive sequences are typically subject to transcription silencing. Here, Zhang et al. find that the bromodomain-containing protein BRAT1 forms a complex with BRP1, recognizes histone acetylation and acts to prevent transcriptional silencing in Arabidopsis.
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- 2016
12. The PEAT protein complexes are required for histone deacetylation and heterochromatin silencing
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Yong-Qiang Li, Xin-Jian He, She Chen, Cui-Jun Zhang, Jin-Xing Zhou, Lian-Mei Tan, Lin Li, Chang-Rong Shao, Yu-Jia Lu, and Xiao-Mei Hou
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0301 basic medicine ,Small interfering RNA ,Heterochromatin ,Arabidopsis ,Biology ,DNA-binding protein ,General Biochemistry, Genetics and Molecular Biology ,Histones ,Soil ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Gene silencing ,News & Views ,Gene Silencing ,Enhancer ,Molecular Biology ,General Immunology and Microbiology ,Arabidopsis Proteins ,General Neuroscience ,fungi ,Acetylation ,Articles ,Cell biology ,030104 developmental biology ,Histone ,Multiprotein Complexes ,DNA methylation ,biology.protein - Abstract
In eukaryotes, heterochromatin regions are typically subjected to transcriptional silencing. DNA methylation has an important role in such silencing and has been studied extensively. However, little is known about how methylated heterochromatin regions are subjected to silencing. We conducted a genetic screen and identified an epcr ( enhancer of polycomb‐related ) mutant that releases heterochromatin silencing in Arabidopsis thaliana . We demonstrated that EPCR1 functions redundantly with its paralog EPCR2 and interacts with PWWP domain‐containing proteins (PWWPs), AT‐rich interaction domain‐containing proteins (ARIDs), and telomere repeat binding proteins (TRBs), thus forming multiple functionally redundant protein complexes named PEAT (PWWPs‐EPCRs‐ARIDs‐TRBs). The PEAT complexes mediate histone deacetylation and heterochromatin condensation and thereby facilitate heterochromatin silencing. In heterochromatin regions, the production of small interfering RNAs (siRNAs) and DNA methylation is repressed by the PEAT complexes. The study reveals how histone deacetylation, heterochromatin condensation, siRNA production, and DNA methylation interplay with each other and thereby maintain heterochromatin silencing.
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- 2017
13. The PRP6-like splicing factor STA1 is involved in RNA-directed DNA methylation by facilitating the production of Pol V-dependent scaffold RNAs
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Ze-Yang Ma, Jian-Kang Zhu, Huan-Wei Huang, Xin-Jian He, Jin-Xing Zhou, Chao-Feng Huang, Kai Tang, Kun Dou, Cui-Jun Zhang, and Tao Cai
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Genetics ,Small RNA ,Arabidopsis Proteins ,Bisulfite sequencing ,Arabidopsis ,Nuclear Proteins ,RNA ,Coiled Bodies ,DNA-Directed RNA Polymerases ,Gene Regulation, Chromatin and Epigenetics ,DNA Methylation ,Biology ,Splicing factor ,Argonaute Proteins ,Mutation ,DNA methylation ,RNA splicing ,RNA, Small Untranslated ,Gene Silencing ,Epigenetics ,RNA, Small Interfering ,RNA-Directed DNA Methylation ,Genome, Plant - Abstract
DNA methylation is a conserved epigenetic marker in plants and animals. In Arabidopsis, DNA methylation can be established through an RNA-directed DNA methylation (RdDM) pathway. By screening for suppressors of ros1, we identified STA1, a PRP6-like splicing factor, as a new RdDM regulator. Whole-genome bisulfite sequencing suggested that STA1 and the RdDM pathway share a large number of common targets in the Arabidopsis genome. Small RNA deep sequencing demonstrated that STA1 is predominantly involved in the accumulation of the siRNAs that depend on both Pol IV and Pol V. Moreover, the sta1 mutation partially reduces the levels of Pol V-dependent RNA transcripts. Immunolocalization assay indicated that STA1 signals are exclusively present in the Cajal body and overlap with AGO4 in most nuclei. STA1 signals are also partially overlap with NRPE1. Localization of STA1 to AGO4 and NRPE1 signals is probably related to the function of STA1 in the RdDM pathway. Based on these results, we propose that STA1 acts downstream of siRNA biogenesis and facilitates the production of Pol V-dependent RNA transcripts in the RdDM pathway.
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- 2013
14. An atypical component of RNA-directed DNA methylation machinery has both DNA methylation-dependent and -independent roles in locus-specific transcriptional gene silencing
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Jun Liu, Bai Ge, Jian-Kang Zhu, Cui-Jun Zhang, Qing Chen, Wei Chen, Xin Deng, Jin-Xing Zhou, Xin-Jian He, and Su-Wei Zhang
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Genetics ,Small interfering RNA ,Transcription, Genetic ,Arabidopsis Proteins ,Arabidopsis ,Cell Biology ,DNA Methylation ,Biology ,Epigenetics of physical exercise ,Genetic Loci ,RNA interference ,Transcription (biology) ,DNA methylation ,Gene silencing ,Original Article ,RNA Interference ,Gene Silencing ,Epigenetics ,RNA, Small Interfering ,Molecular Biology ,RNA-Directed DNA Methylation - Abstract
RNA-directed DNA methylation (RdDM) is an important de novo DNA methylation pathway in plants. RdDM mediates the transcriptional silencing of many endogenous genomic loci, most of which are transposon related. A forward genetics screen identified DTF1 (DNA-binding transcription factor 1) as a new component for RdDM in Arabidopsis. Loss-of-function mutations in DTF1 release the transcriptional silencing of RdDM target loci and reduce the accumulation of 24-nt small interfering RNAs (siRNAs) from some of the targets. Interestingly, in the dtf1 mutant plants, the release of transcriptional gene silencing at solo-LTR is accompanied by decreased siRNA accumulation but not by reduced DNA methylation. These results suggest that DTF1 is an atypical component of RdDM and has both DNA methylation-dependent and -independent roles in transcriptional gene silencing. We suggest that besides DNA methylation, siRNAs may cause some other uncharacterized epigenetic modifications that lead to transcriptional gene silencing.
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- 2011
15. Identification of NaCl stress-responsive apoplastic proteins in rice shoot stems by 2D-DIGE
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Weina Ge, Alma L. Burlingame, Yafang Zhang, Yun Song, Cui-Jun Zhang, and Yi Guo
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Biophysics ,Sodium Chloride ,Biology ,Carbohydrate metabolism ,Biochemistry ,Article ,Differential analysis ,Two-Dimensional Difference Gel Electrophoresis ,Fight-or-flight response ,Cell Wall ,Gene Expression Regulation, Plant ,Stress, Physiological ,Tandem Mass Spectrometry ,Botany ,Rice plant ,Plant Proteins ,Plant Stems ,Spots ,Gene Expression Profiling ,fungi ,food and beverages ,Oryza ,Apoplast ,Salinity ,Shoot ,Extracellular Space ,Chromatography, Liquid ,Signal Transduction - Abstract
Plants have evolved sophisticated systems to cope with adverse environmental conditions such as cold, drought, and salinity. Although a number of stress response networks have been proposed, the role of plant apoplast in plant stress response has been ignored. To investigate the role of apoplastic proteins in the salt stress response, 10-day old rice plants were treated with 200 mM NaCl for 1, 6 or 12 h, and the soluble apoplast proteins of rice shoot stems were extracted for differential analysis, compared with untreated controls, by 2-D DIGE saturation labeling techniques. One hundred twenty-two significantly changed spots were identified by LC-MS/MS, and 117 spots representing 69 proteins have been identified. Of these proteins, 37 are apoplastic proteins according to the bioinformatic analysis. These proteins are mainly involved in the processes of carbohydrate metabolism, oxido-reduction, and protein processing and degradation. According to their functional categories and cluster analysis, a stress response model of apoplastic proteins has been proposed. These data indicate that the apoplast is important in plant stress signal reception and response.
- Published
- 2011
16. The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci
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Huan-Wei Huang, Tao Cai, Cui-Jun Zhang, Jin-Xing Zhou, She Chen, Zhang-Wei Liu, Chang-Rong Shao, Lin Li, Su-Wei Zhang, and Xin-Jian He
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Cancer Research ,RNA, Untranslated ,lcsh:QH426-470 ,Chromosomal Proteins, Non-Histone ,Arabidopsis ,Biology ,DNA-binding protein ,chemistry.chemical_compound ,RNA interference ,Genetics ,RNA, Small Interfering ,Molecular Biology ,RNA-Directed DNA Methylation ,Genetics (clinical) ,Ecology, Evolution, Behavior and Systematics ,Adenosine Triphosphatases ,RNA polymerase V ,Arabidopsis Proteins ,RNA ,DNA-Directed RNA Polymerases ,Histone-Lysine N-Methyltransferase ,DNA Methylation ,Chromatin Assembly and Disassembly ,Chromatin ,Protein Structure, Tertiary ,DNA-Binding Proteins ,lcsh:Genetics ,Histone ,chemistry ,DNA methylation ,biology.protein ,Epigenetics ,DNA modification ,Histone modification ,DNA ,Research Article - Abstract
RNA-directed DNA methylation (RdDM) is required for transcriptional silencing of transposons and other DNA repeats in Arabidopsis thaliana. Although previous research has demonstrated that the SET domain-containing SU(VAR)3–9 homologs SUVH2 and SUVH9 are involved in the RdDM pathway, the underlying mechanism remains unknown. Our results indicated that SUVH2 and/or SUVH9 not only interact with the chromatin-remodeling complex termed DDR (DMS3, DRD1, and RDM1) but also with the newly characterized complex composed of two conserved Microrchidia (MORC) family proteins, MORC1 and MORC6. The effect of suvh2suvh9 on Pol IV-dependent siRNA accumulation and DNA methylation is comparable to that of the Pol V mutant nrpe1 and the DDR complex mutant dms3, suggesting that SUVH2 and SUVH9 are functionally associated with RdDM. Our CHIP assay demonstrated that SUVH2 and SUVH9 are required for the occupancy of Pol V at RdDM loci and facilitate the production of Pol V-dependent noncoding RNAs. Moreover, SUVH2 and SUVH9 are also involved in the occupancy of DMS3 at RdDM loci. The putative catalytic active site in the SET domain of SUVH2 is dispensable for the function of SUVH2 in RdDM and H3K9 dimethylation. We propose that SUVH2 and SUVH9 bind to methylated DNA and facilitate the recruitment of Pol V to RdDM loci by associating with the DDR complex and the MORC complex., Author Summary Small RNA-induced transcriptional silencing at transposable elements and other DNA repeats is an evolutionarily conserved mechanism in plants, fungi, and animals. In Arabidopsis thaliana, an RNA-directed DNA methylation pathway is involved in transcriptional silencing. Noncoding RNAs produced by the plant-specific DNA-dependent RNA polymerase V are required for RNA-directed DNA methylation. A chromatin-remodeling complex was previously demonstrated to be required for the occupancy of DNA-dependent RNA polymerase V at RNA-directed DNA methylation loci. Our results suggest that two putative histone methyltransferases are inactive in their enzymatic activity and act as adaptor proteins to facilitate the recruitment of DNA-dependent RNA polymerase V to chromatin by associating with the chromatin-remodeling complex. In combination with previous studies, we propose that the inactive histone methyltransferases bind to methylated DNA, thereby linking DNA methylation to Pol V transcription at RNA-directed DNA methylation loci.
- Published
- 2014
17. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV
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Xin-Jian He, Kai Tang, Bai Ge, Su Wei Zhang, Heng Zhang, Xiaobing Shi, Tao Cai, Kaori Tanaka, Jun Ma, Cui Jun Zhang, Zhang Wei Liu, Ze Yang Ma, Liang Zeng, Pengcheng Wang, Jian-Kang Zhu, and Renyi Liu
- Subjects
Small RNA ,Transcription, Genetic ,Arabidopsis ,Chromatin remodeling ,Histones ,Two-Hybrid System Techniques ,Epigenetics ,Gene Silencing ,Cloning, Molecular ,RNA, Small Interfering ,RNA-Directed DNA Methylation ,RNA polymerase IV ,DNA Polymerase beta ,Genetics ,Homeodomain Proteins ,Multidisciplinary ,biology ,Arabidopsis Proteins ,RNA-Directed DNA Polymerase ,DNA Methylation ,Biological Sciences ,DNA-Binding Proteins ,Histone ,RNA, Plant ,DNA methylation ,Mutation ,biology.protein - Abstract
DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. DTF1 interacts directly with the chromatin remodeling protein CLASSY 1 (CLSY1), and both DTF1 and CLSY1 are associated in vivo with Pol IV but not Pol V, which functions downstream in the RdDM effector complex. DTF1 and DTF2 (a DTF1-like protein) contain a SAWADEE domain, which was found to bind specifically to histone H3 containing H3K9 methylation. Taken together, our results show that DTF1 is a core component of the RdDM pathway, and suggest that DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci.
- Published
- 2013
18. The splicing machinery promotes RNA-directed DNA methylation and transcriptional silencing in Arabidopsis
- Author
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Kun Dou, Jin-Xing Zhou, Ze-Yang Ma, Jian-Kang Zhu, Huan-Wei Huang, Cui-Jun Zhang, Renyi Liu, Jun Liu, Tao Cai, Xin-Jian He, and Su-Wei Zhang
- Subjects
Transcription, Genetic ,RNA Splicing ,Exonic splicing enhancer ,Arabidopsis ,General Biochemistry, Genetics and Molecular Biology ,Article ,Splicing factor ,Molecular Biology ,RNA-Directed DNA Methylation ,Post-transcriptional regulation ,Genetics ,Regulation of gene expression ,General Immunology and Microbiology ,biology ,Arabidopsis Proteins ,General Neuroscience ,food and beverages ,DNA ,DNA-Directed RNA Polymerases ,DNA Methylation ,Gene Expression Regulation ,RNA splicing ,DNA methylation ,biology.protein ,Demethylase ,RNA ,RNA Polymerase II - Abstract
DNA methylation in transposons and other DNA repeats is conserved in plants as well as in animals. In Arabidopsis thaliana, an RNA-directed DNA methylation (RdDM) pathway directs de novo DNA methylation. We performed a forward genetic screen for suppressors of the DNA demethylase mutant ros1 and identified a novel Zinc-finger and OCRE domain-containing Protein 1 (ZOP1) that promotes Pol IV-dependent siRNA accumulation, DNA methylation, and transcriptional silencing. Whole-genome methods disclosed the genome-wide effects of zop1 on Pol IV-dependent siRNA accumulation and DNA methylation, suggesting that ZOP1 has both RdDM-dependent and -independent roles in transcriptional silencing. We demonstrated that ZOP1 is a pre-mRNA splicing factor that associates with several typical components of the splicing machinery as well as with Pol II. Immunofluorescence assay revealed that ZOP1 overlaps with Cajal body and is partially colocalized with NRPE1 and DRM2. Moreover, we found that the other development-defective splicing mutants tested including mac3a3b, mos4, mos12 and mos14 show defects in RdDM and transcriptional silencing. We propose that the splicing machinery rather than specific splicing factors is involved in promoting RdDM and transcriptional silencing.
- Published
- 2013
19. OsTRXh1 regulates the redox state of the apoplast and influences stress responses in rice
- Author
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Cui-Jun Zhang and Yi Guo
- Subjects
chemistry.chemical_classification ,Reactive oxygen species ,fungi ,food and beverages ,Oryza ,Plant Science ,Biology ,Sodium Chloride ,Plants, Genetically Modified ,Genetically modified rice ,Redox ,Apoplast ,Cell biology ,Article Addendum ,Cell wall ,Thioredoxins ,Biochemistry ,chemistry ,Extracellular ,Thioredoxin ,Signal transduction ,Reactive Oxygen Species ,Oxidation-Reduction ,Abscisic Acid ,Signal Transduction - Abstract
The plant cell apoplast is the compartment beyond the cell plasmalemma, including the cell wall and intercellular space. Many environmental elements can trigger reactive oxygen species (ROS) burst at the plasma membrane which then alters the redox state of the apoplast. Recently, h-type thioredoxin (Trx), OsTRXh1, was identified to be involved in apoplastic redox state regulation in rice. OsTRXh1 is conserved redox-active Trx and can be secreted into the extracellular regions. Through transgenic rice plant, we found that OsTRXh1 regulated ROS accumulation in apoplast and influenced plant development and stress responses. This provides new insights into apoplastic redox state regulation pathway and expands our understanding of h-type Trxs function.
- Published
- 2012
20. IDN2 and its paralogs form a complex required for RNA-directed DNA methylation
- Author
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Chang-Rong Shao, Xin-Jian He, Su-Wei Zhang, Cui-Jun Zhang, Jin-Xing Zhou, Lin Li, Yong-Qiang Ning, She Chen, Qing Chen, and Yanwu Guo
- Subjects
Cancer Research ,Small interfering RNA ,lcsh:QH426-470 ,Mutant ,Arabidopsis ,RNA-binding protein ,Biology ,RNA interference ,Genetics ,Molecular Biology ,RNA-Directed DNA Methylation ,Genetics (clinical) ,Ecology, Evolution, Behavior and Systematics ,Sequence Homology, Amino Acid ,Arabidopsis Proteins ,RNA-Binding Proteins ,RNA ,DNA Methylation ,biology.organism_classification ,Chromatin ,Protein Structure, Tertiary ,Complementation ,lcsh:Genetics ,Multiprotein Complexes ,DNA methylation ,Epigenetics ,DNA modification ,Histone modification ,Research Article - Abstract
IDN2/RDM12 has been previously identified as a component of the RNA–directed DNA methylation (RdDM) machinery in Arabidopsis thaliana, but how it functions in RdDM remains unknown. By affinity purification of IDN2, we co-purified two IDN2 paralogs IDP1 and IDP2 (IDN2 PARALOG 1 and 2). The coiled-coil domain between the XS and XH domains of IDN2 is essential for IDN2 homodimerization, whereas the IDN2 C-terminal XH domain but not the coiled-coil domain is required for IDN2 interaction with IDP1 and IDP2. By introducing the wild-type IDN2 sequence and its mutated derivatives into the idn2 mutant for complementation testing, we demonstrated that the previously uncharacterized IDN2 XH domain is required for the IDN2-IDP1/IDP2 complex formation as well as for IDN2 function. IDP1 is required for de novo DNA methylation, siRNA accumulation, and transcriptional gene silencing, whereas IDP2 has partially overlapping roles with IDP1. Unlike IDN2, IDP1 and IDP2 are incapable of binding double-stranded RNA, suggesting that the roles of IDP1 and IDP2 are different from those of IDN2 in the IDN2-IDP1/IDP2 complex and that IDP1 and IDP2 are essential for the functioning of the complex in RdDM., Author Summary In eukaryotes, transposable elements and other DNA repeats are important parts of genomes. Suppression of these sequences is required for genome stability and integrity. DNA methylation is an important chromatin modification that prevents the expression and movement of these repeat sequences. Small interfering RNAs initiate DNA methylation and transcriptional gene silencing of the sequences. In the plant model organism Arabidopsis thaliana, DNA methylation is mediated by an RNA–directed DNA methylation (RdDM) pathway. Here we report that the double-stranded RNA-binding protein IDN2 and it paralogs IDP1 and IDP2 (IDN2 PARALOG 1 and 2) cooperate and form a novel complex that is required for RNA–directed DNA methylation. Unlike IDN2, IDP1 and IDP2 have no double-stranded RNA binding ability. We propose that the IDN2-IDP1/2 is a complex that functions at a downstream step of the RdDM pathway. The findings significantly increase our understanding of the plant RdDM pathway as well as of the RNA–mediated chromatin changes in yeast and animals.
- Published
- 2012
21. An apoplastic h-type thioredoxin is involved in the stress response through regulation of the apoplastic reactive oxygen species in rice
- Author
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Cui-Jun Zhang, Weina Ge, Yafang Zhang, Bing-Chun Zhao, Yun Song, Yi Guo, and Da-Ye Sun
- Subjects
Physiology ,Recombinant Fusion Proteins ,Molecular Sequence Data ,Thioredoxin h ,Plant Science ,Genetically modified crops ,Environmental Stress and Adaptation to Stress ,Biology ,chemistry.chemical_compound ,Plant Growth Regulators ,Gene Expression Regulation, Plant ,Stress, Physiological ,Botany ,Genetics ,Extracellular ,Animals ,Amino Acid Sequence ,Hydrogen peroxide ,Abscisic acid ,Phylogeny ,Plant Proteins ,chemistry.chemical_classification ,Reactive oxygen species ,Oryza sativa ,food and beverages ,Oryza ,Hydrogen Peroxide ,Plants, Genetically Modified ,Apoplast ,Cell biology ,Plant Leaves ,Phenotype ,chemistry ,Seedlings ,Rabbits ,Thioredoxin ,Extracellular Space ,Reactive Oxygen Species ,Oxidation-Reduction ,Sequence Alignment ,Abscisic Acid - Abstract
Thioredoxins (Trxs) are a multigenic family of proteins in plants that play a critical role in redox balance regulation through thiol-disulfide exchange reactions. There are 10 members of the h-type Trxs in rice (Oryza sativa), and none of them has been clearly characterized. Here, we demonstrate that OsTRXh1, a subgroup I h-type Trx in rice, possesses reduction activity in vitro and complements the hydrogen peroxide sensitivity of Trx-deficient yeast mutants. OsTRXh1 is ubiquitously expressed in rice, and its expression is induced by salt and abscisic acid treatments. Intriguingly, OsTRXh1 is secreted into the extracellular space, and salt stress in the apoplast of rice induces its expression at the protein level. The knockdown of OsTRXh1 results in dwarf plants with fewer tillers, whereas the overexpression of OsTRXh1 leads to a salt-sensitive phenotype in rice. In addition, both the knockdown and overexpression of OsTRXh1 decrease abscisic acid sensitivity during seed germination and seedling growth. We also analyzed the levels of hydrogen peroxide produced in transgenic plants, and the results show that more hydrogen peroxide is produced in the extracellular space of OsTRXh1 knockdown plants than in wild-type plants, whereas the OsTRXh1 overexpression plants produce less hydrogen peroxide under salt stress. These results show that OsTRXh1 regulates the redox state of the apoplast and influences plant development and stress responses.
- Published
- 2011
22. Proteomic analyses of apoplastic proteins from germinating Arabidopsis thaliana pollen
- Author
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Weina Ge, Cui-Jun Zhang, Yun Song, Yi Guo, Alma L. Burlingame, and Yafang Zhang
- Subjects
Proteomics ,Proteome ,Cell Survival ,Difference gel electrophoresis ,Biophysics ,Arabidopsis ,Germination ,medicine.disease_cause ,Biochemistry ,Models, Biological ,Article ,Analytical Chemistry ,Two-Dimensional Difference Gel Electrophoresis ,Pollen ,Botany ,medicine ,otorhinolaryngologic diseases ,Arabidopsis thaliana ,Pollination ,Molecular Biology ,Plant Proteins ,biology ,Arabidopsis Proteins ,fungi ,food and beverages ,biology.organism_classification ,Plants, Genetically Modified ,Fusion protein ,Cell biology ,Pollen tube - Abstract
Pollen grains play important roles in the reproductive processes of flowering plants. The roles of apoplastic proteins in pollen germination and in pollen tube growth are comparatively less well understood. To investigate the functions of apoplastic proteins in pollen germination, the global apoplastic proteins of mature and germinated Arabidopsis thaliana pollen grains were prepared for differential analyses by using 2-dimensional fluorescence difference gel electrophoresis (2-D DIGE) saturation labeling techniques. One hundred and three proteins differentially expressed (p value ≤ 0.01) in pollen germinated for 6h compare with un-germination mature pollen, and 98 spots, which represented 71 proteins, were identified by LC-MS/MS. By bioinformatics analysis, 50 proteins were identified as secreted proteins. These proteins were mainly involved in cell wall modification and remodeling, protein metabolism and signal transduction. Three of the differentially expressed proteins were randomly selected to determine their subcellular localizations by transiently expressing YFP fusion proteins. The results of subcellular localization were identical with the bioinformatics prediction. Based on these data, we proposed a model for apoplastic proteins functioning in pollen germination and pollen tube growth. These results will lead to a better understanding of the mechanisms of pollen germination and pollen tube growth.
- Published
- 2011
23. Identification of an apoplastic protein involved in the initial phase of salt stress response in rice root by two-dimensional electrophoresis
- Author
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Yi Guo, Lei Zhang, Yun Song, Jun-Feng Zhao, Cui-Jun Zhang, and Li-Hong Tian
- Subjects
Physiology ,Molecular Sequence Data ,Plant Science ,Genetically modified crops ,Sodium Chloride ,Oryza ,Plant Roots ,Mass Spectrometry ,Malondialdehyde ,Botany ,Genetics ,Electrophoresis, Gel, Two-Dimensional ,RNA, Messenger ,Cloning, Molecular ,Codon ,Promoter Regions, Genetic ,Plant Proteins ,Oryza sativa ,biology ,fungi ,Plant physiology ,food and beverages ,Protoplast ,biology.organism_classification ,Plant cell ,Genetically modified rice ,Apoplast ,Article Addendum ,Biochemistry ,RNA, Plant - Abstract
The apoplast of plant cells, which carries out multiple functions in plant metabolism and signaling, is not only a barrier but also the linker between the environment and the protoplast. To investigate the role of apoplastic proteins in the salt stress response, 10-d-old rice (Oryza sativa) plants were treated with 200 mm NaCl for 1, 3, or 6 h, and the soluble apoplast proteins were extracted for differential analysis compared with untreated controls using two-dimensional electrophoresis. Ten protein spots that increased or decreased significantly in abundance were identified by mass spectrometry. These proteins included some well-known biotic and abiotic stress-related proteins. Among them, an apoplastic protein, with extracellular domain-like cysteine-rich motifs (DUF26), O. sativa root meander curling (OsRMC), has shown drastically increased abundance in response to salt stress during the initial phase. OsRMC RNA interference transgenic rice has been generated to assess the function of OsRMC in the salt stress response. The results show that knocking down the expression level of OsRMC in transgenic rice led to insensitive seed germination, enhanced growth inhibition, and improved salt stress tolerance to NaCl than in untransgenic plants. These results indicate that plant apoplastic proteins may have important roles in the plant salt stress response.
- Published
- 2008
24. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV.
- Author
-
Heng Zhang, Ze-Yang Ma, Liang Zeng, Tanaka, Kaori, Cui-Jun Zhang, Jun Ma, Ge Bai, Pengcheng Wang, Su-Wei Zhang, Zhang-Wei Liu, Tao Cai, Kai Tang, Renyi Liu, Xiaobing Shi, Xin-Jian He, and Jian-Kang Zhu
- Subjects
RNA methylation ,DNA methylation ,EPIGENETICS ,EUKARYOTIC genomes ,RNA polymerases ,SMALL interfering RNA - Abstract
DNA methylation is an important epigenetic mark in many eukaryotic organisms. De novo DNA methylation in plants can be achieved by the RNA-directed DNA methylation (RdDM) pathway, where the plant-specific DNA-dependent RNA polymerase IV (Pol IV) transcribes target sequences to initiate 24-nt siRNA production and action. The putative DNA binding protein DTF1/SHH1 of Arabidopsis has been shown to associate with Pol IV and is required for 24-nt siRNA accumulation and transcriptional silencing at several RdDM target loci. However, the extent and mechanism of DTF1 function in RdDM is unclear. We show here that DTF1 is necessary for the accumulation of the majority of Pol IV-dependent 24-nt siRNAs. It is also required for a large proportion of Pol IV-dependent de novo DNA methylation. Interestingly, there is a group of RdDM target loci where 24-nt siRNA accumulation but not DNA methylation is dependent on DTF1. DTF1 interacts directly with the chromatin remodeling protein CLASSY 1 (CLSY1), and both DTF1 and CLSY1 are associated in vivo with Pol IV but not Pol V, which functions downstream in the RdDM effector complex. DTF1 and DTF2 (a DTF1-like protein) contain a SAWADEE domain, which was found to bind specifically to histone H3 containing H3K9 methylation. Taken together, our results show that DTF1 is a core component of the RdDM pathway, and suggest that DTF1 interacts with CLSY1 to assist in the recruitment of Pol IV to RdDM target loci where H3K9 methylation may be an important feature. Our results also suggest the involvement of DTF1 in an important negative feedback mechanism for DNA methylation at some RdDM target loci. [ABSTRACT FROM AUTHOR]
- Published
- 2013
- Full Text
- View/download PDF
25. Identification of an Apoplastic Protein Involved in the Initial Phase of Salt Stress Response in Rice Root by Two-Dimensional Electrophoresis.
- Author
-
Lei Zhang, Li-Hong Tian, Jun-Feng Zhao, Yun Song, Cui-Jun Zhang, and Yi Guo
- Subjects
PLANT proteins ,RICE ,PROTOPLASTS ,ELECTROPHORESIS ,PLANT roots ,RNA ,GERMINATION - Abstract
The apoplast of plant cells, which carries out multiple functions in plant metabolism and signaling, is not only a barrier but also the linker between the environment and the protoplast. To investigate the role of apoplastic proteins in the salt stress response, 10-d-old rice (Oryza sativa) plants were treated with 200 mMi NaCl for 1, 3, or 6 h, and the soluble apoplast proteins were extracted for differential analysis compared with untreated controls using two-dimensional electrophoresis. Ten protein spots that increased or decreased significantly in abundance were identified by mass spectrometry. These proteins included some well-known biotic and abiotic stress-related proteins. Among them, an apoplastic protein, with extracellular domain-like cysteine-rich motifs (DUF26), 0. sativa root meander curling (OsRMC), has shown drastically increased abundance in response to salt stress during the initial phase. OsRMC RNA interference transgenic rice has been generated to assess the function of OsRMC in the salt stress response. The results show that knocking down the expression level of OsRMC in transgenic rice led to insensitive seed germination, enhanced growth inhibition, and improved salt stress tolerance to NaCl than in untransgenic plants. These results indicate that plant apoplastic proteins may have important roles in the plant salt stress response. [ABSTRACT FROM AUTHOR]
- Published
- 2009
- Full Text
- View/download PDF
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