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Molecular dynamics of de novo telomere heterochromatin formation in budding yeast

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Journal of Genetics and Genomics 2016年第7期43卷 451-465页

作者： Yi-Min Duan Bo-O.Zhou Jing Peng Xia-Jing Tong Qiong-Di Zhang Jin-Qiu Zhou The State Key Laboratory of Molecular Biology Shanghai Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences University of Chinese Academy of Sciences 320 Yue Yang Road Shanghai 200031 China School of Life Science and Technology Shanghai Tech University 100 Haike Road Shanghai 200031 China

In the budding yeast Saccharomyces cerevisiae, heterochromatin structure is found at three chromosome regions, which are homothallic mating-type loci, rDNA regions and telomeres. To address how telomere heterochromatin is assembled under physiological conditions, we employed a de novo telomere addition system, and analyzed the dynamic chromatin changes of the TRPI reporter gene during telomere elongation. We found that integrating a 255-bp, but not an 81-bp telomeric sequence near the TRP1 promoter could trigger Sir2 recruitment, active chromatin mark（s）＇ removal, chromatin compaction and TRP1 gene silencing, indicating that the length of the telomeric sequence inserted in the internal region of a chromosome is critical for determining the chromatin state at the proximal region. Interestingly, Rill but not Rif2 or yKu is indispensable for the formation of intra-chromosomal silent chromatin initiated by telomeric sequence. When an internal short telomeric sequence （e.g., 81 bp） gets exposed to become a de novo telomere, the herterochromatin features, such as Sir recruitment, active chromatin mark（s）＇ removal and chromatin compaction, are detected within a few hours before the de novo telomere reaches a stable length. Our results recapitulate the molecular dynamics and reveal a coherent picture of telomere het- erochromatin formation.

关键词： Telomere heterochromatin Nucleosome positioning Siry Ku

Alteration of Terminal heterochromatin and Chromosome Rearrangements in Derivatives of Wheat-Rye Hybrids

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Journal of Genetics and Genomics 2013年第8期40卷 413-420页

作者： Shulan Fu Zhenling Lv Xiang Guo Xiangqi Zhang Fangpu Han State Key Laboratory of Plant Cell and Chromosome Engineering Institute of Geneticsand Developmental BiologyChinese Academy of Sciences Key Laboratory of Plant Breeding and Genetics Sichuan Agriculture University

Wheat-rye addition and substitution lines and their self progenies revealed variations in telomeric heterochromatin and centromeres, Furthermore, a mitotically unstable dicentric chromosome and stable multicentric chromosomes were observed in the progeny of a Chinese Spring-lmperial rye 3R addition line. An unstable multicentric chromosome was found in the progeny of a 6R/6D substitution line. Drastic variation of terminal heterochromatin including movement and disappearance of terminal heterochromatin occurred in the progeny of wheat- rye addition line 3R, and the 5RS ditelosomic addition line. Highly stable minichromosomes were observed in the progeny ofa monosomic 4R addition line, a ditelosomic 5RS addition line and a 6R/6D substitution line. Minichromosomes, with and without the FISH signals for telomeric DNA （TTTAGGG）n, derived from a monosomic 4R addition line are stable and transmissible to the next generation. The results indicated that centromeres and terminal heterochromatin can be profoundly altered in wheat-rye hybrid derivatives.

关键词： Wheat-Rye addition lines Chromosome rearrangements Multiple centromeres Minichromosomes heterochromatin

The Long-Sought-After Plant heterochromatin Protein 1

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Molecular Plant 2019年第1期12卷 14-15页

作者： Rong Chen Molecular Plant

heterochromatin,being transcriptionally inactive,is the highly condensed form of chromatin that is associated with Histone H3 lysine 9 methylation (H3K9me)and DNA methylation in eukaryotic cells.In fission yeast and a... 详细信息

关键词： heterochromatin H3K9me animals

RNA Polymerase V Functions in Arabidopsis Interphase heterochromatin Organization Independently of the 24-nt siRNA-Directed DNA Methylation Pathway

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Molecular Plant 2009年第4期2卷 700-710页

作者： Olga Pontes Pedro Costa-Nunes Paul Vithayathil Craig S. Pikaard Biology Department Washington University 1 Brookings Drive St Louis MO 63130 USA

In Arabidopsis, pericentromeric repeats, retroelements, and silenced rRNA genes are assembled into heterochromatin within nuclear structures known as chromocenters. The mechanisms governing higher-order heterochromatin organization are poorly understood but 24-nt small interfering RNAs （siRNAs） are known to play key roles in heterochromatin formation. Nuclear RNA polymerase IV （Pol IV）, RNA-DEPENDENT RNA POLYMERASE 2 （RDR2）, and DICER-LIKE 3 （DCL3） are required for biogenesis of 24-nt siRNAs that associate with ARGONAUTE 4 （AGO4）. Nuclear RNA polymerase V （Pol V） collaborates with DRD1 （DEFICIENT IN RNA-DEPENDENT DNA METHYLATION 1） to generate transcripts at heterochromatic loci that are hypothesized to bind to siRNA-AGO4 complexes and subsequently recruit the de-novo DNA methylation and/or histone modifying machinery. Here, we report that decondensation of the major pericentromeric repeats and depletion of the heterochromatic mark histone H3 lysine 9 dimethylation at chromocenters occurs specifically in pol V and drdl mutants. Disruption of pericentromeric repeats condensation is coincident with transcriptional reactivation of specific classes of pericentromeric 180-bp repeats. We further demonstrate that Pol V functions independently of Pol IV, RDR2, and DCL3-mediated siRNA production to affect interphase heterochromatin organization, possibly by involving RNAs that recruit structural or chromatin-modifying proteins.

关键词： RNA polymerase V RNA-directed DNA methylation heterochromatin centromere gene expression.

Effects of SWI/SNF complex on DNA damage repair in heterochromatin of embryonic fibroblast cells

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Radiation Medicine and Protection 2023年第4期4卷 214-220页

作者： Hong Zhang Yinyin Shu Mintao Ji Obstetrics and Gynecology Department First Affiliated Hospital of Soochow UniversitySuzhou 215006China State Key Laboratory of Radiation Medicine and Protection School of Radiation Medicine and ProtectionCollaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education InstitutionsMedical College of Soochow UniversitySuzhou 215123China

Objective:To investigate the impact of SWI/SNF complex on heterochromatin DNA damage repair after exposure to X-ray irradiation,in order to explore the underlying mechanism.Methods:NIH3T3 and MRC5 cells were treated with 50 nmol/L siRNA targeting SWI/SNF complex subunits(BRM,ARID1A,BRG1 and SNF5),and YAP/TAZ.At 24 h after transfection,the cells were irradiated with 0.5 and 1 Gy of X-rays.At 20,60 and 240 min post-irradiation,γH2AX assay was performed to evaluate the radiation response in total or heterochromatin.Comet assay was used to determine the role of YAP/TAZ in DNA damage when the cells were irradiated with 4 Gy of X-rays.NIH3T3 were treated with 50 nmol/L siRNA targeting BRM/BRG1 and YAP/TAZ to determine their relationship on heterochromatin DNA damage repair.Results:In NIH3T3,SWI/SNF complex subunits(BRM,ARID1A and BRG1)knock-down increasedγH2AX in total and heterochromatin at 1 Gy 60 min post-irradiation(PheterochromatinγH2AX at 1 Gy 20 min post-irradiation(Pheterochromatin at 1 Gy 60 min post-irradiation(PheterochromatinγH2AX at 1 Gy 60 min post-irradiation(PheterochromatinγH2AX in NIH3T3 and MRC5(PheterochromatinγH2AX compared with single BRM/BRG1 knock-down at 0.5 Gy 60 min post-irradiation(Pheterochromatin through YAP/TAZ.This study provides a novel direction for DNA damage repair and sheds light on the role of SWI/SNF complex in response to DNA damage repair in heterochromatin.

关键词： SWI/SNF complex BRM/BRG1 heterochromatin DNA damage repair YAP/TAZ

53BP1 regulates heterochromatin through phase separation

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53BP1 regulates heterochromatin through phase separation

Focused piRNA pathway screens identified multiple pathways involved in heterochromatin formation

2021年全国生物相分离和相变学术研讨会

作者： Lei Zhang Xinran Geng Jinshan Tang Fangfang Wang Youwei Zhang National 111 Center for Cellular Regulation and Molecular Pharmaceutics Hubei University of Technology Department of Pharmacology Case Comprehensive Cancer CenterSchool of MedicineCase Western Reserve University

Human 53 BP1 is primarily known as a key player in regulating the DNA double strands break（DSB） repair choice;however,whether it is involved in other biological process is less well understood.Here we report a previously uncharacterized function of 53 BP1 at heterochromatin,where it undergoes liquid-liquid phase separation（LLPS） with the heterochromatin protein HPla in a mutually dependent manner.Depletion of 53 BP1 results in the loss of heterochromatin centers and the de-repression of heterochromatic tandem repetitive DNAs.We further identified domains and residues of 53 BP1 required for LLPS,which overlap with but are distinct from those involved in DSB repair.Remarkably,53 BP1 mutants that are defective in DSB repair but retain LLPS and heterochromatin maintenance function still protected cells from stress-induced DNA damage,growth inhibition and senescent phenotype.Our study illustrates a critical role for 53 BP1 in maintaining the heterochromatin integrity and genome stability independent of DSB repair.

关键词： 53BP1 nuclear punctate heterochromatin liquid-liquid phase separation HP1α DSB repair DNA damage genome stability

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Focused piRNA pathway screens identified multiple pathways i...

Genome-wide distribution and functions of the AAE complex in epigenetic regulation in Arabidopsis

中国生物化学与分子生物学会2019年全国学术会议暨学会...

作者： Na Miao Ming Yang Peng Zhou Xin Lu Yang Yu Institute of Biophysics Key Laboratory of RNA Biology Chinese Academy of Sciences University of Chinese Academy of Sciences

Piwi-interacting RNA(piRNA) pathway is a small RNA based "innate immune"" system to defend transposons in animal germlines. About 200～300 genes have been identified as piRNA pathway candidate genes in Drosophila. Panoramix(Panx) links Piwi:piRNA complexes and general heterochromatin machinery. However, the mechanism of Panx-mediated heterochromatin formation is unclear. Here, we report a small scale RNAi screen to identify factors required for Panx induced heterochromatin formation. We identified ～40 genes that act downstream of Panx. dNxf2 is one of top candidates in the screen. It was found that dNxf2 functions to silence piRNA guided transposon as a complex with Panx and dNxt1. CG14438 is another top candidates whose function in heterochromatin formation is unknown, although it has been copurified with HP1 a. Loss of CG14438 leads to animal sterility and transposon overexpression, similar to other core piRNA pathway components. Further detailed dissection about the mechanism of CG14438 mediated heterochromatin formation will be presented.

关键词： piRNA RNAi screen heterochromatin

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Journal of Integrative Plant Biology 2021年第4期63卷 707-722页

作者： Yi-Zhe Zhang Juncheng Lin Zhizhong Ren Chun-Xiang Chen Daisuke Miki Si-Si Xie Jian Zhang Ya-Nan Chang Jing Jiang Jun Yan Qingshun Q.Li Jian-Kang Zhu Cheng-Guo Duan Shanghai Center for Plant Stress Biology and CAS Center of Excellence for Molecular Plant Sciences Chinese Academy of SciencesShanghai 201602China University of Chinese Academy of Sciences Beijing 100049China Key Laboratory of the Ministry of Education for Coastal and Wetland Ecosystems College of the Environment and EcologyXiamen UniversityXiamen 361102China State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China School of Life Sciences East China Normal UniversityShanghai 200241China Graduate College of Biomedical Sciences Western University of Health SciencesPomona 91766USA Department of Horticulture and Landscape Architecture Purdue UniversityWest Lafayette 47907USA

heterochromatin is widespread in eukaryotic genomes and has diverse impacts depending on its genomic context.Previous studies have shown that a protein complex,the ASI1-AIPP1-EDM2(AAE)complex,participates in polyadenylation regulation of several intronic heterochromatin-containing genes.However,the genome-wide functions of AAE are still unknown.Here,we show that the ASI1 and EDM2 mostly target the common genomic regions on a genome-wide level and preferentially interacts with genetic heterochromatin.Polyadenylation(poly(A)sequencing reveals that AAE complex has a substantial influence on poly(A)site usage of heterochromatin-containing genes,includingnotonlyintronicheterochromatincontaining genes but also the genes showing overlap with heterochromatin.Intriguingly,AAE is also involved in the alternative splicing regulation of a number of heterochromatin-overlapping genes,such as the disease resistance gene RPP4.We provided evidence that genic heterochromatin is indispensable for the recruitment of AAE in polyadenylation and splicing regulation.In addition to conferring RNA processing regulation at genic heterochromatin-containing genes,AAE also targets some transposable elements(TEs)outside of genes(including TEs sandwiched by genes and island TEs)for epigenetic silencing.Our results reveal new functions of AAE in RNA processing and epigenetic silencing,and thus representimportantadvancesinepigenetic regulation.

关键词： alternative polyadenylation alternative splicing epigenetic regulation heterochromatin transcription

Histone modifications dictate specific biological readouts

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Journal of Genetics and Genomics 2009年第2期36卷 75-88页

作者： Anjana Munshi Gowhar Shafi Nishat Aliya Akka Jyothy Institute of Genetics and Hospital for Genetic Diseases Indo-American Cancer Institute and Research Centre Banjara Hills

The basic unit of chromatin is the nucleosomal core particle, containing 147 bp of DNA that wraps twice around an octamer of core histones. The core histones bear a highly dynamic N-terminal amino acid tail around 20-35 residues in length and rich in basic amino acids. These tails extending from the surface of nucleosome play an important role in folding of nucleosomal arrays into higher order chromatin structure, which plays an important role in eukaryotic gene regulation. The amino terminal tails protruding from the nuclesomes get modified by the addition of small groups such as methyl, acetyl and phosphoryl groups. In this review, we focus on these complex modi- fication patterns and their biological functions. Moreover, these modifications seem to be part of a complex scheme where distinct histone modifications act in a sequential manner or in combination to form a ＂histone code＂ read by other proteins to control the structure and/or function of the chromatin fiber. Errors in this histone code may be involved in many human diseases especially cancer, the nature of which could be therapeutically exploited. Increasing evidence suggests that many proteins bear multiple, distinct modifications, and the ability of one modification to antagonize or synergize the deposition of another can have significant biological consequences.

关键词： histone modifications gene expression and silencing heterochromatin therapeutic exploitation histone code