|
|
|
题名
|
作者
|
年代
|
出处
|
被引量
|
| 1 | Our recent progress in epigenetic research using the model ciliate, Tetrahymena thermophila显示文摘Epigenetic research focuses on heritable changes beyond the DNA sequence, which has led to a revolution in biologicalstudies and benefits in many other fields. The well-known model ciliate, Tetrahymena thermophila offers a unique system forepigenetic studies due to its nuclear dimorphism and special mode of sexual reproduction (conjugation), as well as abundantgenomic resources and genetic tools. In this paper, we summarize recent progress made by our research team and collaboratorsin understanding epigenetic mechanisms using Tetrahymena. This includes: (1) providing the first genome-wide basepair-resolution map of DNA N6-methyladenine (6mA) and revealed it as an integral part of the chromatin landscape;(2)dissecting the relative contribution of cis・ and trans- elements to nucleosome distribution by exploring the unique nucleardimorphism of Tetrahymena, (3) demonstrating the epigenetic controls of RNAi-dependent Polycomb repression pathwayson transposable elements, and (4) identifying a new histone monomethyltransferase, TXR1 (Tetrahymena Trithorax 1), thatfacilitates replication elongation through 让s substrate histone H3 lysine 27 monomethylation (H3K27mel). | Ting Cheng Yuanyuan Wang Jie Huang Xiao Chen Xiaolu Zhao Shan Gao Weibo Song | 2019 | Marine Life Science & Technology2019，1，1： | 4 |
| 2 | High mobility group protein 1: A collaborator in nucleosome dynamics and estrogen-responsive gene expression显示文摘High mobility group protein 1(HMGB1) is a multifunctional protein that interacts with DNA and chromatin to influence the regulation of transcription, DNA replication and repair and recombination. We show that HMGB1 alters the structure and stability of the canonical nucleosome(N) in a nonenzymatic,adenosine triphosphate-independent manner. As a result, the canonical nucleosome is converted to two stable, physically distinct nucleosome conformers. Although estrogen receptor(ER) does not bind to its consensus estrogen response element within a nucleosome, HMGB1 restructures the nucleosome to facilitate strong ER binding. The isolated HMGB1-restructured nucleosomes(N' and N'') remain stable and exhibit a number of characteristics that are distinctly different from the canonical nucleosome. These findings complement previous studies that showed(1) HMGB1 stimulates in vivo transcriptional activation at estrogen response elements and(2) knock down of HMGB1 expression by siR NA precipitously reduced transcriptional activation. The findings indicate that a major facet of the mechanism of HMGB1 action involves a restructuring of aspects of the nucleosome that appear to relax structural constraints within the nucleosome. The findings are extended to reveal the differences between ER and the other steroid hormone receptors. A working proposal outlines mechanisms that highlight the multiple facets that HMGB1 may utilize in restructuring the nucleosome. | William M Scovell | 2016 | World Journal of Biological Chemistry2016，7，2： | 4 |
| 3 | H3K27me3 Signal in the Cis Regulatory Elements Reveals the Differentiation Potential of Progenitors During Drosophila Neuroglial Development显示文摘Drosophila neural development undergoes extensive chromatin remodeling and precise epigenetic regulation.However,the roles of chromatin remodeling in establishment and maintenance of cell identity during cell fate transition remain enigmatic.Here,we compared the changes in gene expression,as well as the dynamics of nucleosome positioning and key histone modifications between the four major neural cell types during Drosophila neural development.We find that the neural progenitors can be separated from the terminally differentiated cells based on their gene expression profiles,whereas nucleosome distribution in the flanking regions of transcription start sites fails to identify the relationships between the progenitors and the differentiated cells.H3K27me3 signal in promoters and enhancers can not only distinguish the progenitors from the differentiated cells but also identify the differentiation path of the neural stem cells(NSCs)to the intermediate progenitor cells to the glial cells.In contrast,H3K9ac signal fails to identify the differentiation path,although it activates distinct sets of genes with neuron-specific and glia-related functions during the differentiation of the NSCs into neurons and glia,respectively.Together,our study provides novel insights into the crucial roles of chromatin remodeling in determining cell type during Drosophila neural development. | Xiaolong Chen Youqiong Ye Liang Gu Jin Sun Yanhua Du Wen-Ju Liu Wei Li Xiaobai Zhang Cizhong Jiang | 2019 | Genomics, Proteomics & Bioinformatics2019，17，3： | 1 |
| 4 | Both combinatorial K4me0-K36me3 marks on sister histone H3s of a nucleosome are required for Dnmt3a-Dnmt3L mediated de novo DNA methylation显示文摘A nucleosome contains two copies of each histone H2A,H2B,H3 and H4.Histone H3 K4me0 and K36me3are two key chromatin marks for de novo DNA methylation catalyzed by DNA methyltransferases in mammals.However,it remains unclear whether K4me0 and K36me3 marks on both sister histone H3s regulate de novo DNA methylation independently or cooperatively.Here,taking advantage of the bivalent histone H3 system in yeast,we examined the contributions of K4 and K36 on sister histone H3s to genomic DNA methylation catalyzed by ectopically co-expressed murine Dnmt3a and Dnmt3L.The results show that lack of both K4me0 and K36me3 on one sister H3 tail,or lack of K4me0 and K36me3 on respective sister H3s results in a dramatic reduction of 5mC,revealing a synergy of two sister H3s in DNA methylation regulation.Accordingly,the Dnmt3a or Dnmt3L mutation that disrupts the interaction of Dnmt3aADD domain-H3K4me0,Dnmt3LADD domain-H3K4me0,orDnmt3aPWWP domain-H3K36me3 causes a significant reduction of DNA methylation.These results support the model that each heterodimeric Dnmt3a-Dnmt3L reads both K4me0 and K36me3 marks on one tail of sister H3s,and the dimer of heterodimeric Dnmt3a-Dnmt3L recognizes two tails of sister histone H3s to efficiently execute de novo DNA methylation. | Ting Gong Xin Gu Yu-Ting Liu Zhen Zhou Ling-Li Zhang Yang Wen Wei-Li Zhong Guo-Liang Xu Jin-Qiu Zhou | 2020 | Journal of Genetics and Genomics2020，47，2： | 1 |
| 5 | Dynamic nucleosome organization after fertilization reveals regulatory factors for mouse zygotic genome activation显示文摘Chromatin remodeling is essential for epigenome reprogramming after frilization.However,the underlying mechanisms of chromatin remodeling remain to be explored.Here,we investigated the dynamic changes in nucleosome occupancy and positioning in pronucleus-stage zygotes using ultra low-input MNase seq.We observed distinct features of inheritance and reconstruction of nucleosome positioning in both paternal and maternal genomes.Genome wide de novo nucleosome occupancy in the paternal genome was observed as early as 1 h after the injection of sperm into ooplasm.The nucleosome positioning pattern was continually rebuilt to form nucleosome-depleted regions(NDRs)at promoters and transcription factor(TF)binding sites with differential dynamics in paternal and maternal genomes.NDRs formed more quickly on the promoters of genes involved in zygotic genome activation(ZGA),and this formation is closely linked to histone acetylation,but not transcription elongation or DNA replication.Importantly,we found that NDR establishment on the binding motifs of specific TFs might be associated with their potential pioneer functions in ZGA.Further investigations suggested that the predicted factors MLX and RFX1 played important roles in regulating minor and major ZGA,respectively.Our data not only elucidate the nucleosome positioning dynamics in both male and female pronuclei fllowing frtiliatin,but also provide an eficient method for identifying key transcription regulators during development. | Chenfei Wang Chuan Chen Xiaoyu Liu Chong Li Qiu Wu Xiaolan Chen Lingyue Yang Xiaochen Kou Yanhong Zhao Hong Wang Yawei Gao Yong Zhang Shaorong Gao | 2022 | Cell Research2022，32，9： | 1 |
| 6 | Nuclear reassembly in vitro is independent of nucleosome/chromatin assembly显示文摘It was shown that nuclear reassembly was induced by small pieces of DNA fragments in cell free extracts of Xenopus. In an attempt to learn the relationship between the nuclear reassembly and nucleosome/chromatin assembly, limited amounts of CM Cellulose are used to eliminate the capacity of the egg extract S 150 to assemble chromatin, while the forming of nucleosomes is checked with DNA supercoiling by plasmid DNA pBR322 incubated in the extract, and further analysed by micrococcal nuclease digestion. This depleted extract is then used to induce nuclear reassembly around demembraned sperms with membrane vesicles. It is found that CM Cellulose depletes histones H2A and H2B efficiently and blocks the assembly of nucleosomes, the demembraned sperms are yet reconstituted into nuclei in the treated S 150, although the chromatin in reassembled nuclei does not produce protected DNA fragments when digested with micrococcal nuclease. It suggests that in the cell free system of Xenopus, DNA can be formed into nuclei without assembly of nucleosomes or chromatin. | 蒋争凡 张博 翟中和 | 1998 | Science China(Life Sciences)1998，41，5： | 1 |
| 7 | Structural basis of nucleosome deacetylation and DNA linker tightening by Rpd3S histone deacetylase complex显示文摘In Saccharomyces cerevisiae,cryptic transcription at the coding region is prevented by the activity of Sin3 histone deacetylase(HDAC)complex Rpd3S,which is carried by the transcribing RNA polymerase Ⅱ(RNAPⅡ)to deacetylate and stabilize chromatin.Despite its fundamental importance,the mechanisms by which Rpd3S deacetylates nucleosomes and regulates chromatin dynamics remain elusive.Here,we determined several cryo-EM structures of Rpd3S in complex with nucleosome core particles(NCPs),including the H3/H4 deacetylation states,the alternative deacetylation state,the linker tightening state,and a state in which Rpd3S co-exists with the Hho1 linker histone on NCP.These structures suggest that Rpd3S utilizes a conserved Sin3 basic surface to navigate through the nucleosomal DNA,guided by its interactions with H3K36 methylation and the extra-nucleosomal DNA linkers,to target acetylated H3K9 and sample other histone tails.Furthermore,our structures illustrate that Rpd3S reconfigures the DNA linkers and acts in concert with Hho1 to engage the NCP,potentially unraveling how Rpd3S and Hho1 work in tandem for gene silencing. | Shuqi Dong Huadong Li Meilin Wang Nadia Rasheed Binqian Zou Xijie Gao Jiali Guan Weijie Li Jiale Zhang Chi Wang Ningkun Zhou Xue Shi Mei Li Min Zhou Junfeng Huang He Li Ying Zhang Koon Ho Wong Xiaofei Zhang William Chong Hang Chao Jun He | 2023 | Cell Research2023，33，10： | 1 |
| 8 | Deciphering the regulatory code of histone modifications in plants显示文摘Eukaryotic genomes are compacted into histone-wrapped chromatin,which provides an opportunity to fine-tune the gene expression by dynamically impeding or reinforcing the accessibility of the genome to the transcription factors(TFs)and cofactors.The modification of histones is one of the various mechanisms to regulate DNA exposure by altering the physical properties of nucleosomes(Klemm et al.,2019).In plants,histone modifications play a critical role in establishing the cell identity and responding to environmental cues,including responses to temperature,alterations of flowering time(Liu et al.,2010;He et al.,2021). | Zhaohong Li Dongwei Li Ye Li Xiaoping Guo Ruolin Yang | 2022 | Journal of Genetics and Genomics2022，49，11： | 0 |
| 9 | Chromatin and Nucleosome Organizations and DNA Replication of Nucleus Reassembled in vitro Using Purified Exogenous DNA and Xenopus Egg Extracts显示文摘It has been demonstrated in the last ten years that the nuclear reassembly may occur in the cell-free systems from frog egg extracts added with exogenous naked DNA. However, there remains an open question : is the cell-free reassembled nucleus structurally similar to the nucleus in the intact cell ? That is, does the cell-free reassembled nucleus contain nucleosomes and chromatin? For this issue, we have designed experiments for identifying the internal structures of the cell-free reassembled nucleus. These experiments show that the nucleus reassembled in vitro also contains chromatin which is composed of typical 10 nm nucleosome fibers of 'beads-on-a-string', 30 nm filaments and the next higher-order structures. The digestion experiment with the enzyme micrococcal nuclease has demonstrated that the DNA in the nucleosome of the reconstituted chromatin is about 200 base pairs (bp) in length, of which 165 bp may be in the nucleosome particle, and 35 bp may be in the linker between two particles. | 张传茂 张博 翟中和 | 1994 | Science China Chemistry1994，37，6： | 0 |
| 10 | Keeping innate immune response in check: when cGAS meets the nucleosome显示文摘Cao et al.report on cryo-EM structures of human cyclic GMPAMP synthase(cGAS)sensor bound to the nucleosome core particle,thereby defining the molecular mechanism of how cGAS avoids activation by chromatinized self-DNA.Notably,disruption of cGAS dimer formation and prevention of dsDNA recognition by the sensor at the nucleosome level impede cGAS activation. | Wei Xie Dinshaw J.Patel | 2020 | Cell Research2020，30，12： | 0 |
| 11 | DPB3 and DPB4 proteins regulate Medicago flowering and leaf anthocyanin biosynthesis显示文摘As important subunits of the leading-strand DNA polymerase epsilon,chromatin remodeling,and histone acetylation complexes,the H2A/H2B-like histone-fold domain-containing proteins DNA PO-LYMERASE II SUBUNIT B3(DPB3)and DPB4 play key roles in nucleosome assembly and heterochromatin maintenance during DNA replication in yeast,Drosophila,and mammals(He et al.,2017;Bellelli et al.,2018;Yu et al.,2018;Casari et al.,2021). | Yingying Meng Chongnan Wang Qiqi Li Wenkai Ji Jiangqi Wen Kirankumar S.Mysore Yanxi Pei Lifang Niu Hao Lin | 2023 | Journal of Genetics and Genomics2023，50，6： | 0 |
| 12 | DNA damage in nucleosomes显示文摘Eukaryotic genomic DNA is packed into chromatin, whose fundamental structural unit is the nucleosome. As DNA-histone protein complexes, nucleosomes show different properties toward exogenous and endogenous DNA-damaging agents. This review summarizes nucleosome DNA damage due to different sources, including alkylating agents, radicals, UV radiation and reactive DNA damage intermediates. In most cases, the histone core protects the associated DNA against damage via its structure and/or scavenging of damaging agents. In contrast, histones react with damaged DNA and, in some instances, catalyze DNA damage in the nucleosome. The biological consequence of nucleosome DNA damage and future prospects in this field are briefly discussed. | Mengtian Ren Jing Bai Zhen Xi Chuanzheng Zhou | 2019 | Science China Chemistry2019，62，5： | 0 |
| 13 | Interactions between HMG proteins (HMG1/2 and HMG14/17) and human ε-globin gene promoter (ε-promoter)显示文摘High mobility group (HMG) proteins are abundant non-histone proteins in the nuclei of eukaryocytes. It has been shown that HMG proteins may play important roles in the structure and function of chromatin. In the present study, the binding of HMG proteins (HMG1/2 and HMG14/17) to the human e-globin gene promoter (e-promo-ter, -177-+1 bp) has been examined by using both the in vitro nucleosome reconstitution and the electrophoresis mobility shift assay (EMSA). We found that HMG1/2 proteins could bind to the naked e-promoter DNA, however, HMG14/17 could not. Using the in vitro nucleosome reconstitution, we revealed that HMG14/17 could bind to the mononucleosome reconstituted in vitro with E-promoter, while HMG1/2 could not. Those results indicate that the binding of HMG proteins to e-promoter is dynamic as the nucleosome assembling and disassembling. We speculated that this selective binding of HMG proteins to e-promoter might play a critical role in the regulation of e-globin gene expression. | Chunhui Hou Jian Huang Shubing Zhang Ruolan Qian | 2002 | Chinese Science Bulletin2002，47，18： | 0 |
| 14 | License to flower:LEAFY has pioneer activity显示文摘The transition to reproductive development is a key step in the lifecycle of a plant and requires fine-tuning of gene expression through the concerted action of several transcription factors(TFs).While most TFs bind naked DNA(without nucleosomes)in a sequence-specific manner,in mammals a special group with key roles in cell fate reprogramming,named pioneer TFs,can bind nucleosome-occupied DNA.In Arabidopsis,LEAFY(LFY)promotes floral fate through activation of floral homeotic genes(Parcy et al.,1998),some of which are targeted by the Polycomb Repressive Complex 2 and localize to closed chromatin environments.Hence,LFY has been proposed to act as a pioneer TF,but whether/how it can bind occluded DNA remained unknown. | Inês Trindade | 2021 | Molecular Plant2021，14，5： | 0 |
| 15 | Structural basis for nucleosome binding and catalysis by the yeast Rpd3S/HDAC holoenzyme显示文摘Dear Editor,Histone deacetylases(HDACs)are evolutionally conserved enzymes that remove acetyl modifications from histones and play a central role in epigenetic gene silencing.1 Class I HDACs are promising targets for epigenetic therapies for a range of diseases such as cancers,inflammations,infections,and neurological diseases.2 Yeast Rpd3 is the founding member of class I HDACs,which forms two distinct complexes:the∼1.2 MDa Rpd3L deacetylating histones at promoter regions,and the∼0.6 MDa Rpd3S targeting transcribed regions to suppress intragenic transcription initiation.3,4 Rpd3S consists of three core proteins:Rpd3,Sin3,and Ume15 along with two dedicated chromatin binding subunits:Eaf3 and Rco1.6 The structures of the yeast Rpd3S complex and its human homolog Sin3B complex have been recently reported.7,8 Here,we report the cryo-electron microscopy(cryo-EM)structure of the Rpd3S holoenzyme binding a nucleosome at 3.7Åresolution(Supplementary information,Table S1). | Yueyue Zhang Mengxue Xu Po Wang Jiahui Zhou Guangxian Wang Shuailong Han Gang Cai Xuejuan Wang | 2023 | Cell Research2023，33，12： | 0 |
| 16 | Histones, histone chaperones and nucleosome assembly显示文摘Chromatin structure governs a number of cellular processes including DNA replication,transcription,and DNA repair.During DNA replication,chromatin structure including the basic repeating unit of chromatin,the nucleosome,is temporarily disrupted,and then reformed immediately after the passage of the replication fork.This coordinated process of nucleosome assembly during DNA replication is termed replication—coupled nucleosome assembly.Disruption of this process can lead to genome instability,a hallmark of cancer cells.Therefore,addressing how replication-coupled nucleosome assembly is regulated has been of great interest.Here,we review the current status of this growing field of interest,highlighting recent advances in understanding the regulation of this important process by the dynamic interplay of histone chaperones and histone modifications. | Rebecca J.Burgess Zhiguo Zhang | 2010 | Protein & Cell2010，1，7： | 0 |
| 17 | The engagement of histone lysine methyltransferases with nucleosomes: structural basis, regulatory mechanisms, and therapeutic implications显示文摘Histone lysine methyltransferases(HKMTs)deposit methyl groups onto lysine residues on histones and play important roles in regulating chromatin structure and gene expression.The structures and functions of HKMTs have been extensively investigated in recent decades,significantly advancing our understanding of the dynamic regulation of histone methylation.Here,we review the recent progress in structural studies of representative HKMTs in complex with nucleosomes(H3K4,H3K27,H3K36,H3K79,and H4K20 methyltransferases),with emphasis on the molecular mechanisms of nucleosome recognition and trans-histone crosstalk by these HKMTs.These structural studies inform HKMTs'roles in tumorigenesis and provide the foundations for developing new therapeutic approachestargetingHKMTs incancers. | Yanjing Li Kexue Gei Tingting Li Run Cai Yong Chen | 2023 | Protein & Cell2023，14，3： | 0 |
| 18 | Interactions between HMG proteins and the core sequence of DNaseI hypersensitive site 2 in the locus control region (LCR) of the human β-Mike globin gene cluster显示文摘HMG proteins are abundant chromosomal non-histone proteins. It has been suggested that the HMG proteins may play an important role in the structure and function of chromatin. In the present study, the binding of HMG proteins (HMG1/2 and HMG14/17) to the core DNA sequence of DNasel hypersensitive site 2 (HS2core DNA sequence, -10681-10970 bp) in the locus control region (LCR) of the human β-like globin gene cluster has been examined by using both the in vitro nucleosome reconstitution and the gel mobility shift assays. Here we show that HMG1/2 can bind to the naked HS2core DNA sequence, however, HMG 14/17 cannot. Using the in vitro nucleosome reconstitution we demonstrate that HMG14/17 can bind to the HS2core DNA sequence which is assembled into nucleosomes with the core histone octamer transferred from chicken erythrocytes. In contrast, HMG 1/2 cannot bind to the nucleosomes reconstituted in vitro with the HS2core DNA sequence. These results indicate that the binding patterns between HMG proteins and | 赵晖 张树冰 蒋俶 钱若兰 | 2000 | Science China(Life Sciences)2000，43，6： | 0 |
| 19 | Split decision:why it matters?显示文摘The establishment and faithful maintenance of epigenetic information in the context of chromatin are crucial for a great number of biologic phenomena,including position effect variegation,Polycomb silencing,X-chromosome inactivation and genomic imprinting.However,mechanisms by which that the correct histone modification patterns propagate into daughter cells during mitotic divisions remain to be elucidated.The partitioning pattern of parental histone H3-H4 tetramers is a critical question toward our understanding of the epigenetic inheritance.In this review,we discuss why the histone H3-H4 tetramer split decision matters. | Hui WU Bing ZHU | 2011 | Frontiers in Biology2011，6，2： | 0 |
| 20 | Roles of histones and nucleosomes in gene transcription显示文摘This article reviews the latest research developments in the field of eukaryotic gene regulation by the structural alterations of chromatin and nucleosomes. The following issues are briefly addressed: (i) nucleosome and histone modifications by both the ATP-dependent remodeling complexes and the histone acetyltransferases and their roles in gene activation; (ii) competitive binding of histones and transcription factors on gene promoters, and transcription repression by nucleosomes; and (iii) influences of linker histone HI on gene regulation. Meanwhile, the significance and impact of these new research progresses, as well as issues worthwhile for further study are commented. | Baiqu Huang Qinhua Zeng Xiaohui Bi Yuhong Wang Yuxin Li | 2001 | Chinese Science Bulletin2001，46，3： | 0 |
您所在的机构暂未开通此部分的功能，请联系管理员