1
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Stefan K, Barski A. Cis-regulatory atlas of primary human CD4+ T cells. BMC Genomics 2023; 24:253. [PMID: 37170195 PMCID: PMC10173520 DOI: 10.1186/s12864-023-09288-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/31/2023] [Indexed: 05/13/2023] Open
Abstract
Cis-regulatory elements (CRE) are critical for coordinating gene expression programs that dictate cell-specific differentiation and homeostasis. Recently developed self-transcribing active regulatory region sequencing (STARR-Seq) has allowed for genome-wide annotation of functional CREs. Despite this, STARR-Seq assays are only employed in cell lines, in part, due to difficulties in delivering reporter constructs. Herein, we implemented and validated a STARR-Seq-based screen in human CD4+ T cells using a non-integrating lentiviral transduction system. Lenti-STARR-Seq is the first example of a genome-wide assay of CRE function in human primary cells, identifying thousands of functional enhancers and negative regulatory elements (NREs) in human CD4+ T cells. We find an unexpected difference in nucleosome organization between enhancers and NRE: enhancers are located between nucleosomes, whereas NRE are occupied by nucleosomes in their endogenous locations. We also describe chromatin modification, eRNA production, and transcription factor binding at both enhancers and NREs. Our findings support the idea of silencer repurposing as enhancers in alternate cell types. Collectively, these data suggest that Lenti-STARR-Seq is a successful approach for CRE screening in primary human cell types, and provides an atlas of functional CREs in human CD4+ T cells.
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Affiliation(s)
- Kurtis Stefan
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7028, Cincinnati, OH, 45229-3026, USA
- Medical Scientist Training Program (MSTP), University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Artem Barski
- Division of Allergy & Immunology, Cincinnati Children's Hospital Medical Center, 3333 Burnet Avenue, MLC 7028, Cincinnati, OH, 45229-3026, USA.
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229-3026, USA.
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA.
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2
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Kang H, Liu Y, Fan T, Ma J, Wu D, Heitz T, Shen WH, Zhu Y. Arabidopsis CHROMATIN REMODELING 19 acts as a transcriptional repressor and contributes to plant pathogen resistance. THE PLANT CELL 2022; 34:1100-1116. [PMID: 34954802 PMCID: PMC8894922 DOI: 10.1093/plcell/koab318] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/21/2021] [Indexed: 06/14/2023]
Abstract
Chromatin remodelers act in an ATP-dependent manner to modulate chromatin structure and thus genome function. Here, we report that the Arabidopsis (Arabidopsis thaliana) remodeler CHROMATIN REMODELING19 (CHR19) is enriched in gene body regions, and its depletion causes massive changes in nucleosome position and occupancy in the genome. Consistent with these changes, an in vitro assay verified that CHR19 can utilize ATP to slide nucleosomes. A variety of inducible genes, including several important genes in the salicylic acid (SA) and jasmonic acid (JA) pathways, were transcriptionally upregulated in the chr19 mutant under normal growth conditions, indicative of a role of CHR19 in transcriptional repression. In addition, the chr19 mutation triggered higher susceptibility to the JA pathway-defended necrotrophic fungal pathogen Botrytis cinerea, but did not affect the growth of the SA pathway-defended hemibiotrophic bacterial pathogen Pseudomonas syringae pv. tomato DC3000. Expression of CHR19 was tissue-specific and inhibited specifically by SA treatment. Such inhibition significantly decreased the local chromatin enrichment of CHR19 at the associated SA pathway genes, which resulted in their full activation upon SA treatment. Overall, our findings clarify CHR19 to be a novel regulator acting at the chromatin level to impact the transcription of genes underlying plant resistance to different pathogens.
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Affiliation(s)
- Huijia Kang
- Department of Biochemistry, Institute of Plant Biology, School of Life
Sciences, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for
Genetics and Development, Fudan University, Shanghai 200438, China
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de
Strasbourg, Strasbourg Cedex 67084, France
| | - Yuhao Liu
- National Cancer Center/National Clinical Research Center for Cancer/Cancer
Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union
Medical College, Shenzhen 518116, China; Chinese
Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021,
China
| | - Tianyi Fan
- Department of Biochemistry, Institute of Plant Biology, School of Life
Sciences, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for
Genetics and Development, Fudan University, Shanghai 200438, China
| | - Jing Ma
- Department of Biochemistry, Institute of Plant Biology, School of Life
Sciences, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for
Genetics and Development, Fudan University, Shanghai 200438, China
| | - Di Wu
- Department of Biochemistry, Institute of Plant Biology, School of Life
Sciences, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for
Genetics and Development, Fudan University, Shanghai 200438, China
| | - Thierry Heitz
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de
Strasbourg, Strasbourg Cedex 67084, France
| | - Wen-Hui Shen
- Institut de Biologie Moléculaire des Plantes, CNRS, Université de
Strasbourg, Strasbourg Cedex 67084, France
| | - Yan Zhu
- Department of Biochemistry, Institute of Plant Biology, School of Life
Sciences, State Key Laboratory of Genetic Engineering, Collaborative Innovation Center for
Genetics and Development, Fudan University, Shanghai 200438, China
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3
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Al-Natour Z, Chalissery J, Hassan AH. Fun30 chromatin remodeler helps in dealing with torsional stress and camptothecin-induced DNA damage. Yeast 2020; 38:170-182. [PMID: 33141948 DOI: 10.1002/yea.3534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2020] [Revised: 10/04/2020] [Accepted: 10/26/2020] [Indexed: 12/19/2022] Open
Abstract
Fun30 is an ATP-dependent chromatin remodeler in budding yeast that is involved in cellular processes important for maintaining genomic stability such as gene silencing and DNA damage repair. Cells lacking Fun30 are moderately sensitive to the topoisomerase inhibitor camptothecin and exhibit a delay in cell cycle progression in the presence of camptothecin. Here, we show that Fun30 is required to cope with torsional stress in the absence of Top1. Moreover, we show through genetic studies that Fun30 acts in a parallel pathway to Mus81 endonuclease but is epistatic to Tdp1 phosphodiesterase and Rad1 endonuclease in the repair of camptothecin-induced DNA damage. More importantly, we show that DNA damage sensitivity of Fun30 deficient cells is enhanced in the absence of RNase H enzymes that remove RNA:DNA hybrids. We believe that chromatin remodeling by Fun30 may be important in dealing with torsional stress and camptothecin-induced DNA damage.
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Affiliation(s)
- Zeina Al-Natour
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Jisha Chalissery
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Ahmed H Hassan
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
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4
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Nucleosome Positioning Regulates the Establishment, Stability, and Inheritance of Heterochromatin in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2020; 117:27493-27501. [PMID: 33077593 DOI: 10.1073/pnas.2004111117] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Heterochromatic domains are complex structures composed of nucleosome arrays that are bound by silencing factors. This composition raises the possibility that certain configurations of nucleosome arrays facilitate heterochromatic silencing. We tested this possibility in Saccharomyces cerevisiae by systematically altering the distance between heterochromatic nucleosome-depleted regions (NDRs), which is predicted to affect local nucleosome positioning by limiting how nucleosomes can be packed between NDRs. Consistent with this prediction, serial deletions that altered the distance between heterochromatic NDRs revealed a striking oscillatory relationship between inter-NDR distance and defects in nucleosome positioning. Furthermore, conditions that caused poor nucleosome positioning also led to defects in both heterochromatin stability and the ability of cells to generate and inherit epigenetic transcriptional states. These findings strongly suggest that nucleosome positioning can contribute to formation and maintenance of functional heterochromatin and point to previously unappreciated roles of NDR positioning within heterochromatic domains.
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5
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Tong ZB, Ai HS, Li JB. The Mechanism of Chromatin Remodeler SMARCAD1/Fun30 in Response to DNA Damage. Front Cell Dev Biol 2020; 8:560098. [PMID: 33102471 PMCID: PMC7545370 DOI: 10.3389/fcell.2020.560098] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 09/07/2020] [Indexed: 01/22/2023] Open
Abstract
DNA packs into highly condensed chromatin to organize the genome in eukaryotes but occludes many regulatory DNA elements. Access to DNA within nucleosomes is therefore required for a variety of biological processes in cells including transcription, replication, and DNA repair. To cope with this problem, cells employ a set of specialized ATP-dependent chromatin-remodeling protein complexes to enable dynamic access to packaged DNA. In the present review, we summarize the recent advances in the functional and mechanistic studies on a particular chromatin remodeler SMARCAD1Fun30 which has been demonstrated to play a key role in distinct cellular processes and gained much attention in recent years. Focus is given to how SMARCAD1Fun30 regulates various cellular processes through its chromatin remodeling activity, and especially the regulatory role of SMARCAD1Fun30 in gene expression control, maintenance and establishment of heterochromatin, and DNA damage repair. Moreover, we review the studies on the molecular mechanism of SMARCAD1Fun30 that promotes the DNA end-resection on double-strand break ends, including the mechanisms of recruitment, activity regulation and chromatin remodeling.
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Affiliation(s)
- Ze-Bin Tong
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China.,Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Hua-Song Ai
- Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Department of Chemistry, Tsinghua University, Beijing, China
| | - Jia-Bin Li
- College of Pharmaceutical Sciences, Soochow University, Suzhou, China
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6
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Niu Q, Wang W, Wei Z, Byeon B, Das AB, Chen BS, Wu WH. Role of the ATP-dependent chromatin remodeling enzyme Fun30/Smarcad1 in the regulation of mRNA splicing. Biochem Biophys Res Commun 2020; 526:453-458. [PMID: 32234239 DOI: 10.1016/j.bbrc.2020.02.175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 02/26/2020] [Indexed: 10/24/2022]
Abstract
The yeast ATP-dependent chromatin remodeling enzyme Fun30 has been shown to regulate heterochromatin silencing, DNA repair, transcription, and chromatin organization. Although chromatin structure has been proposed to influence splice site recognition and regulation, whether ATP-dependent chromatin remodeling enzyme plays a role in regulating splicing is not known. In this study, we find that pre-mRNA splicing efficiency is impaired and the recruitment of spliceosome is compromised in Fun30-depleted cells. In addition, Fun30 is enriched in the gene body of individual intron-containing genes. Moreover, we show that pre-mRNA splicing efficiency is dependent on the chromatin remodeling activity of Fun30. The function of Fun30 in splicing is further supported by the observation that, Smarcad1, the mammalian homolog of Fun30, regulates alternative splicing. Taken together, these results provide evidence for a novel role of Fun30 in regulating splicing.
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Affiliation(s)
- Qiankun Niu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Wei Wang
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Zhe Wei
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Boseon Byeon
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Asim Bikas Das
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA
| | - Bo-Shiun Chen
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA; Department of Neurology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA; Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, 33302, Taiwan ROC
| | - Wei-Hua Wu
- Department of Neuroscience and Regenerative Medicine, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA; Department of Neurology, Medical College of Georgia, Augusta University, Augusta, GA, 30912, USA.
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7
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Bantele SCS, Pfander B. Nucleosome Remodeling by Fun30 SMARCAD1 in the DNA Damage Response. Front Mol Biosci 2019; 6:78. [PMID: 31555662 PMCID: PMC6737033 DOI: 10.3389/fmolb.2019.00078] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Accepted: 08/19/2019] [Indexed: 12/16/2022] Open
Abstract
Many cellular pathways are dedicated to maintain the integrity of the genome. In eukaryotes, the underlying DNA transactions occur in the context of chromatin. Cells utilize chromatin and its dynamic nature to regulate those genome integrity pathways. Accordingly, chromatin becomes restructured and modified around DNA damage sites. Here, we review the current knowledge of a chromatin remodeler Fun30SMARCAD1, which plays a key role in genome maintenance. Fun30SMARCAD1 promotes DNA end resection and the repair of DNA double-stranded breaks (DSBs). Notably, however, Fun30SMARCAD1 plays additional roles in maintaining heterochromatin and promoting transcription. Overall, Fun30SMARCAD1 is involved in distinct processes and the specific roles of Fun30SMARCAD1 at DSBs, replication forks and sites of transcription appear discordant at first view. Nonetheless, a picture emerges in which commonalities within these context-dependent roles of Fun30SMARCAD1 exist, which may help to gain a more global understanding of chromatin alterations induced by Fun30SMARCAD1.
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Affiliation(s)
- Susanne C S Bantele
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
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8
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Abstract
Network propagation is a powerful tool for genetic analysis which is widely used to identify genes and genetic modules that underlie a process of interest. Here we provide a graphical, web-based platform (http://anat.cs.tau.ac.il/WebPropagate/) in which researchers can easily apply variants of this method to data sets of interest using up-to-date networks of protein-protein interactions in several organisms.
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Affiliation(s)
- Hadas Biran
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Tovi Almozlino
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel
| | - Martin Kupiec
- Department of Molecular Microbiology and Biotechnology, Tel Aviv University, Tel Aviv 69978, Israel
| | - Roded Sharan
- Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
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9
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Ding D, Bergmaier P, Sachs P, Klangwart M, Rückert T, Bartels N, Demmers J, Dekker M, Poot RA, Mermoud JE. The CUE1 domain of the SNF2-like chromatin remodeler SMARCAD1 mediates its association with KRAB-associated protein 1 (KAP1) and KAP1 target genes. J Biol Chem 2017; 293:2711-2724. [PMID: 29284678 DOI: 10.1074/jbc.ra117.000959] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 12/13/2017] [Indexed: 12/13/2022] Open
Abstract
Chromatin in embryonic stem cells (ESCs) differs markedly from that in somatic cells, with ESCs exhibiting a more open chromatin configuration. Accordingly, ATP-dependent chromatin remodeling complexes are important regulators of ESC homeostasis. Depletion of the remodeler SMARCAD1, an ATPase of the SNF2 family, has been shown to affect stem cell state, but the mechanistic explanation for this effect is unknown. Here, we set out to gain further insights into the function of SMARCAD1 in mouse ESCs. We identified KRAB-associated protein 1 (KAP1) as the stoichiometric binding partner of SMARCAD1 in ESCs. We found that this interaction occurs on chromatin and that SMARCAD1 binds to different classes of KAP1 target genes, including zinc finger protein (ZFP) and imprinted genes. We also found that the RING B-box coiled-coil (RBCC) domain in KAP1 and the proximal coupling of ubiquitin conjugation to ER degradation (CUE) domain in SMARCAD1 mediate their direct interaction. Of note, retention of SMARCAD1 in the nucleus depended on KAP1 in both mouse ESCs and human somatic cells. Mutations in the CUE1 domain of SMARCAD1 perturbed the binding to KAP1 in vitro and in vivo Accordingly, an intact CUE1 domain was required for tethering this remodeler to the nucleus. Moreover, mutation of the CUE1 domain compromised SMARCAD1 binding to KAP1 target genes. Taken together, our results reveal a mechanism that localizes SMARCAD1 to genomic sites through the interaction of SMARCAD1's CUE1 motif with KAP1.
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Affiliation(s)
- Dong Ding
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Philipp Bergmaier
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Parysatis Sachs
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Marius Klangwart
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Tamina Rückert
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Nora Bartels
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany
| | - Jeroen Demmers
- Center for Proteomics, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Mike Dekker
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Raymond A Poot
- Department of Cell Biology, Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Jacqueline E Mermoud
- Institute of Molecular Biology and Tumour Research, Philipps University Marburg, Marburg 35043, Germany.
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10
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Abstract
In this issue of Molecular Cell, Taneja et al. (2017) uncover a dual role for the conserved chromatin remodeler Fft3 in the maintenance of silent heterochromatin and the suppression of replication barriers at euchromatic loci through controlled histone turnover.
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Affiliation(s)
- Anna Fortuny
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR 7216 CNRS/Université Paris Diderot, 35 rue Hélène Brion, 75205 Paris Cedex 13, France
| | - Sophie E Polo
- Laboratory of Epigenome Integrity, Epigenetics & Cell Fate Centre, UMR 7216 CNRS/Université Paris Diderot, 35 rue Hélène Brion, 75205 Paris Cedex 13, France.
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11
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Liu L, Jiang T. Crystal structure of the ATPase-C domain of the chromatin remodeller Fun30 from Saccharomyces cerevisiae. Acta Crystallogr F Struct Biol Commun 2017; 73:9-15. [PMID: 28045388 PMCID: PMC5287370 DOI: 10.1107/s2053230x16019269] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 12/02/2016] [Indexed: 11/10/2022] Open
Abstract
Fun30 (Function unknown now 30) is a chromatin remodeller belonging to the Snf2 family. It has previously been reported to be a regulator of several cellular activities, including DNA repair, gene silencing and maintenance of chromatin structure. Here, the crystal structure of the Fun30 ATPase-C domain (the C-lobe of the ATPase domain) is reported at 1.95 Å resolution. Although the structure displays overall similarities to those of other Snf2 family members, a new structural module was found to be specific to the Fun30 subfamily. Fun30 ATPase-C was shown be monomeric in solution and showed no detectable affinity for dsDNA.
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Affiliation(s)
- Lan Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Yuquan Road, Beijing 100049, People’s Republic of China
| | - Tao Jiang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, People’s Republic of China
- University of Chinese Academy of Sciences, Yuquan Road, Beijing 100049, People’s Republic of China
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12
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Bi X, Ren Y, Kath M. Proliferating cell nuclear antigen (PCNA) contributes to the high-order structure and stability of heterochromatin in Saccharomyces cerevisiae. Chromosome Res 2016; 25:89-100. [PMID: 27987109 DOI: 10.1007/s10577-016-9540-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 11/29/2016] [Accepted: 12/02/2016] [Indexed: 10/20/2022]
Abstract
Heterochromatin plays important roles in the structure, maintenance, and function of the eukaryotic genome. It is associated with special histone modifications and specialized non-histone proteins and assumes a more compact structure than euchromatin. Genes embedded in heterochromatin are generally transcriptionally silent. It was found previously that several mutations of proliferating cell nuclear antigen (PCNA), a DNA replication processivity factor, reduce transcriptional silencing at heterochromatin loci in Saccharomyces cerevisiae. However, the notion that PCNA plays a role in transcriptional silencing was recently questioned because of a potential problem concerning the silencing assays used in prior studies. To determine if PCNA is a bona fide contributor to heterochromatin-mediated transcriptional silencing, we examined the effects of PCNA mutations on heterochromatin structure. We found evidence implicating PCNA in the maintenance of the high-order structure and stability of heterochromatin, which indicates a role of DNA replication in heterochromatin maintenance.
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Affiliation(s)
- Xin Bi
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA.
| | - Yue Ren
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
| | - Morgan Kath
- Department of Biology, University of Rochester, Rochester, NY, 14627, USA
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13
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Chen YF, Chou CC, Gartenberg MR. Determinants of Sir2-Mediated, Silent Chromatin Cohesion. Mol Cell Biol 2016; 36:2039-50. [PMID: 27185881 PMCID: PMC4946433 DOI: 10.1128/mcb.00057-16] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Revised: 02/26/2016] [Accepted: 05/09/2016] [Indexed: 11/20/2022] Open
Abstract
Cohesin associates with distinct sites on chromosomes to mediate sister chromatid cohesion. Single cohesin complexes are thought to bind by encircling both sister chromatids in a topological embrace. Transcriptionally repressed chromosomal domains in the yeast Saccharomyces cerevisiae represent specialized sites of cohesion where cohesin binds silent chromatin in a Sir2-dependent fashion. In this study, we investigated the molecular basis for Sir2-mediated cohesion. We identified a cluster of charged surface residues of Sir2, collectively termed the EKDK motif, that are required for cohesin function. In addition, we demonstrated that Esc8, a Sir2-interacting factor, is also required for silent chromatin cohesion. Esc8 was previously shown to associate with Isw1, the enzymatic core of ISW1 chromatin remodelers, to form a variant of the ISW1a chromatin remodeling complex. When ESC8 was deleted or the EKDK motif was mutated, cohesin binding at silenced chromatin domains persisted but cohesion of the domains was abolished. The data are not consistent with cohesin embracing both sister chromatids within silent chromatin domains. Transcriptional silencing remains largely intact in strains lacking ESC8 or bearing EKDK mutations, indicating that silencing and cohesion are separable functions of Sir2 and silent chromatin.
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Affiliation(s)
- Yu-Fan Chen
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Chia-Ching Chou
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
| | - Marc R Gartenberg
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers, The State University of New Jersey, Piscataway, New Jersey, USA
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14
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Al Kubaisy E, Arafat K, De Wever O, Hassan AH, Attoub S. SMARCAD1 knockdown uncovers its role in breast cancer cell migration, invasion, and metastasis. Expert Opin Ther Targets 2016; 20:1035-43. [PMID: 27232533 DOI: 10.1080/14728222.2016.1195059] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
OBJECTIVE Breast cancer is the most common cancer seen in women worldwide and breast cancer patients are at high risk of recurrence in the form of metastatic disease. Identification of genes associated with invasion and metastasis is crucial in order to develop novel anti-metastasis targeted therapy. It has been demonstrated that the DEAD-BOX helicase DP103 was implicated in breast cancer invasion and metastasis. SMARCAD1 is also a DEAD/H box-containing helicase, suggested to play a role in genetic instability. However, its involvement in cancer migration, invasion, and metastasis has never been explored. RESEARCH DESIGN AND METHODS Using two different designs of shRNA targeting SMARCAD1, we investigated the impact of SMARCAD1 knockdown on the migration, invasion, and metastasis potential of the breast cancer cells MDA-MB-231 and T47D. RESULTS We observed that SMARCAD1 knockdown in the invasive breast cancer cells MDA-MB-231, unlike in the non-invasive breast cancer cells T47D, was associated with an increased cell-cell adhesion and a significant decrease in cell migration, invasion, and metastasis due at least in part to a strong inhibition of STAT3 phosphorylation. CONCLUSIONS These results indicate that SMARCAD1 is involved in breast cancer metastasis and can be a promising target for metastatic breast cancer therapy.
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Affiliation(s)
- Elham Al Kubaisy
- a Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences , United Arab Emirates University , Al-Ain , UAE
| | - Kholoud Arafat
- a Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences , United Arab Emirates University , Al-Ain , UAE
| | - Olivier De Wever
- b Laboratory of Experimental Cancer Research , University Hospital , Gent , Belgium
| | - Ahmed H Hassan
- c Department of Biochemistry, College of Medicine & Health Sciences , United Arab Emirates University , Al-Ain , UAE
| | - Samir Attoub
- a Department of Pharmacology & Therapeutics, College of Medicine & Health Sciences , United Arab Emirates University , Al-Ain , UAE.,d Institut National de la Santé et de la Recherche Médicale (INSERM) , Paris , France
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15
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Chen X, Niu H, Yu Y, Wang J, Zhu S, Zhou J, Papusha A, Cui D, Pan X, Kwon Y, Sung P, Ira G. Enrichment of Cdk1-cyclins at DNA double-strand breaks stimulates Fun30 phosphorylation and DNA end resection. Nucleic Acids Res 2016; 44:2742-53. [PMID: 26801641 PMCID: PMC4824098 DOI: 10.1093/nar/gkv1544] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/28/2015] [Indexed: 01/15/2023] Open
Abstract
DNA double-strand breaks (DSBs) are one of the most cytotoxic types of DNA lesion challenging genome integrity. The activity of cyclin-dependent kinase Cdk1 is essential for DSB repair by homologous recombination and for DNA damage signaling. Here we identify the Fun30 chromatin remodeler as a new target of Cdk1. Fun30 is phosphorylated by Cdk1 on Serine 28 to stimulate its functions in DNA damage response including resection of DSB ends. Importantly, Cdk1-dependent phosphorylation of Fun30-S28 increases upon DNA damage and requires the recruitment of Fun30 to DSBs, suggesting that phosphorylation increases in situ at the DNA damage. Consistently, we find that Cdk1 and multiple cyclins become highly enriched at DSBs and that the recruitment of Cdk1 and cyclins Clb2 and Clb5 ensures optimal Fun30 phosphorylation and checkpoint activation. We propose that the enrichment of Cdk1-cyclin complexes at DSBs serves as a mechanism for enhanced targeting and modulating of the activity of DNA damage response proteins.
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Affiliation(s)
- Xuefeng Chen
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 40072, China
| | - Hengyao Niu
- Department of Biochemistry and Biophysics, Yale University School of Medicine, New Haven, CT, USA
| | - Yang Yu
- Department of Molecular ad Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Jingjing Wang
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 40072, China
| | - Shuangyi Zhu
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 40072, China
| | - Jianjie Zhou
- College of Life Sciences and Institute for Advanced Studies, Wuhan University, Wuhan, Hubei 40072, China
| | - Alma Papusha
- Department of Molecular ad Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Dandan Cui
- Department of Molecular ad Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Xuewen Pan
- Department of Molecular ad Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
| | - Youngho Kwon
- Department of Biochemistry and Biophysics, Yale University School of Medicine, New Haven, CT, USA
| | - Patrick Sung
- Department of Biochemistry and Biophysics, Yale University School of Medicine, New Haven, CT, USA
| | - Grzegorz Ira
- Department of Molecular ad Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA
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16
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Bi X, Yu Q, Siler J, Li C, Khan A. Functions of Fun30 chromatin remodeler in regulating cellular resistance to genotoxic stress. PLoS One 2015; 10:e0121341. [PMID: 25806814 PMCID: PMC4373758 DOI: 10.1371/journal.pone.0121341] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 01/30/2015] [Indexed: 01/14/2023] Open
Abstract
The Saccharomyces cerevisiae Fun30 chromatin remodeler has recently been shown to facilitate long-range resection of DNA double strand break (DSB) ends, which proceeds homologous recombination (HR). This is believed to underlie the role of Fun30 in promoting cellular resistance to DSB inducing agent camptothecin. We show here that Fun30 also contributes to cellular resistance to genotoxins methyl methanesulfonate (MMS) and hydroxyurea (HU) that can stall the progression of DNA replication. We present evidence implicating DNA end resection in Fun30-dependent MMS-resistance. On the other hand, we show that Fun30 deletion suppresses the MMS- and HU-sensitivity of cells lacking the Rad5/Mms2/Ubc13-dependent error-free DNA damage tolerance mechanism. This suppression is not the result of a reduction in DNA end resection, and is dependent on the key HR component Rad51. We further show that Fun30 negatively regulates the recovery of rad5Δ mutant from MMS induced G2/M arrest. Therefore, Fun30 has two functions in DNA damage repair: one is the promotion of cellular resistance to genotoxic stress by aiding in DNA end resection, and the other is the negative regulation of a Rad51-dependent, DNA end resection-independent mechanism for countering replicative stress. The latter becomes manifest when Rad5 dependent DNA damage tolerance is impaired. In addition, we find that the putative ubiquitin-binding CUE domain of Fun30 serves to restrict the ability of Fun30 to hinder MMS- and HU-tolerance in the absence of Rad5.
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Affiliation(s)
- Xin Bi
- Department of Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
| | - Qun Yu
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Jasmine Siler
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Chong Li
- Department of Biology, University of Rochester, Rochester, New York, United States of America
| | - Ali Khan
- Department of Biology, University of Rochester, Rochester, New York, United States of America
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17
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Steglich B, Strålfors A, Khorosjutina O, Persson J, Smialowska A, Javerzat JP, Ekwall K. The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast. PLoS Genet 2015; 11:e1005101. [PMID: 25798942 PMCID: PMC4370569 DOI: 10.1371/journal.pgen.1005101] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 02/25/2015] [Indexed: 12/21/2022] Open
Abstract
In eukaryotic cells, local chromatin structure and chromatin organization in the nucleus both influence transcriptional regulation. At the local level, the Fun30 chromatin remodeler Fft3 is essential for maintaining proper chromatin structure at centromeres and subtelomeres in fission yeast. Using genome-wide mapping and live cell imaging, we show that this role is linked to controlling nuclear organization of its targets. In fft3∆ cells, subtelomeres lose their association with the LEM domain protein Man1 at the nuclear periphery and move to the interior of the nucleus. Furthermore, genes in these domains are upregulated and active chromatin marks increase. Fft3 is also enriched at retrotransposon-derived long terminal repeat (LTR) elements and at tRNA genes. In cells lacking Fft3, these sites lose their peripheral positioning and show reduced nucleosome occupancy. We propose that Fft3 has a global role in mediating association between specific chromatin domains and the nuclear envelope. In the genome of eukaryotic cells, domains of active and repressive chromatin alternate along the chromosome arms. Insulator elements are necessary to shield these different environments from each other. In the fission yeast Schizosaccharomyces pombe, the chromatin remodeler Fft3 is required to maintain the repressed subtelomeric chromatin. Here we show that Fft3 maintains nucleosome structure of insulator elements at the subtelomeric borders. We also observe that subtelomeres and insulator elements move away from the nuclear envelope in cells lacking Fft3. The nuclear periphery is known to harbor repressive chromatin in many eukaryotes and has been implied in insulator function. Our results suggest that chromatin remodeling through Fft3 is required to maintain proper chromatin structure and nuclear organization of insulator elements.
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Affiliation(s)
- Babett Steglich
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Annelie Strålfors
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Olga Khorosjutina
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Jenna Persson
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Agata Smialowska
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
| | - Jean-Paul Javerzat
- Univ. Bordeaux, Institut de Biochimie et Génétique Cellulaires, UMR 5095, Bordeaux, France
- CNRS, Institut de Biochimie et Génétique Cellulaires, UMR 5095, Bordeaux, France
| | - Karl Ekwall
- Department of Biosciences and Nutrition; Center for Innovative Medicine, Karolinska Institutet, Novum Building, Huddinge, Sweden
- * E-mail:
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18
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Bi X. Heterochromatin structure: lessons from the budding yeast. IUBMB Life 2014; 66:657-66. [PMID: 25355678 DOI: 10.1002/iub.1322] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2014] [Revised: 10/12/2014] [Accepted: 10/14/2014] [Indexed: 12/28/2022]
Abstract
The eukaryotic genome can be roughly divided into euchromatin and heterochromatin domains that are structurally and functionally distinct. Heterochromatin is characterized by its high compactness and its inhibitory effect on DNA transactions such as gene expression. Formation of heterochromatin involves special histone modifications and the recruitment and spread of silencing complexes and causes changes in the primary and higher order structures of chromatin. The past two decades have seen dramatic advances in dissecting the molecular aspects of heterochromatin because of the identification of the histone code for heterochromatin as well as its writers and erasers (histone-modifying enzymes) and readers (silencing factors recognizing histone modifications). How heterochromatic histone modifications and silencing factors contribute to the special primary and higher order structures of heterochromatin has begun to be understood. The budding yeast Saccharomyces cerevisiae has long been used as a model organism for heterochromatin studies. Results from these studies have contributed significantly to the elucidation of the general principles governing the formation, maintenance, and function of heterochromatin. This review is focused on investigations into the structural aspects of heterochromatin in S. cerevisiae. Current understanding of other aspects of heterochromatin including how it promotes gene silencing and its epigenetic inheritance is briefly summarized.
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Affiliation(s)
- Xin Bi
- Department of Biology, University of Rochester, Rochester, NY, USA
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19
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Byeon B, Wang W, Barski A, Ranallo RT, Bao K, Schones DE, Zhao K, Wu C, Wu WH. The ATP-dependent chromatin remodeling enzyme Fun30 represses transcription by sliding promoter-proximal nucleosomes. J Biol Chem 2013; 288:23182-93. [PMID: 23779104 DOI: 10.1074/jbc.m113.471979] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The evolutionarily conserved ATP-dependent chromatin remodeling enzyme Fun30 has recently been shown to play important roles in heterochromatin silencing and DNA repair. However, how Fun30 remodels nucleosomes is not clear. Here we report a nucleosome sliding activity of Fun30 and its role in transcriptional repression. We observed that Fun30 repressed the expression of genes involved in amino acid and carbohydrate metabolism, the stress response, and meiosis. In addition, Fun30 was localized at the 5' and 3' ends of genes and within the open reading frames of its targets. Consistent with its role in gene repression, we observed that Fun30 target genes lacked histone modifications often associated with gene activation and showed an increased level of ubiquitinated histone H2B. Furthermore, a genome-wide nucleosome mapping analysis revealed that the length of the nucleosome-free region at the 5' end of a subset of genes was changed in Fun30-depleted cells. In addition, the positions of the -1, +2, and +3 nucleosomes at the 5' end of target genes were shifted significantly, whereas the position of the +1 nucleosome remained largely unchanged in the fun30Δ mutant. Finally, we demonstrated that affinity-purified, single-component Fun30 exhibited a nucleosome sliding activity in an ATP-dependent manner. These results define a role for Fun30 in the regulation of transcription and indicate that Fun30 remodels chromatin at the 5' end of genes by sliding promoter-proximal nucleosomes.
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Affiliation(s)
- Boseon Byeon
- Institute of Molecular Medicine and Genetics, Department of Neurology, Medical College of Georgia, Georgia Regents University, Augusta, Georgia 30912, USA
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20
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Vasicova P, Stradalova V, Halada P, Hasek J, Malcova I. Nuclear import of chromatin remodeler Isw1 is mediated by atypical bipartite cNLS and classical import pathway. Traffic 2012; 14:176-93. [PMID: 23121014 DOI: 10.1111/tra.12025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2012] [Revised: 10/29/2012] [Accepted: 11/01/2012] [Indexed: 11/28/2022]
Abstract
The protein Isw1 of Saccharomyces cerevisiae is an imitation-switch chromatin-remodeling factor. We studied the mechanisms of its nuclear import and found that the nuclear localization signal (NLS) mediating the transport of Isw1 into the nucleus is located at the end of the C-terminus of the protein (aa1079-1105). We show that it is an atypical bipartite signal with an unconventional linker of 19 aa (KRIR X(19) KKAK) and the only nuclear targeting signal within the Isw1 molecule. The efficiency of Isw1 nuclear import was found to be modulated by changes to the amino acid composition in the vicinity of the KRIR motif, but not by the linker length. Live-cell imaging of various karyopherin mutants and in vitro binding assays of Isw1NLS to importin-α revealed that the nuclear translocation of Isw1 is mediated by the classical import pathway. Analogous motifs to Isw1NLS are highly conserved in Isw1 homologues of other yeast species, and putative bipartite cNLS were identified in silico at the end of the C-termini of imitation switch (ISWI) proteins from higher eukaryotes. We suggest that the C-termini of the ISWI family proteins play an important role in their nuclear import.
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Affiliation(s)
- Pavla Vasicova
- Laboratory of Cell Reproduction, Institute of Microbiology v.v.i., Academy of Sciences of the Czech Republic, Videnska 1083, Cz-14220, Prague 4, Czech Republic
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21
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SWI/SNF-like chromatin remodeling factor Fun30 supports point centromere function in S. cerevisiae. PLoS Genet 2012; 8:e1002974. [PMID: 23028372 PMCID: PMC3459985 DOI: 10.1371/journal.pgen.1002974] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 08/08/2012] [Indexed: 12/22/2022] Open
Abstract
Budding yeast centromeres are sequence-defined point centromeres and are, unlike in many other organisms, not embedded in heterochromatin. Here we show that Fun30, a poorly understood SWI/SNF-like chromatin remodeling factor conserved in humans, promotes point centromere function through the formation of correct chromatin architecture at centromeres. Our determination of the genome-wide binding and nucleosome positioning properties of Fun30 shows that this enzyme is consistently enriched over centromeres and that a majority of CENs show Fun30-dependent changes in flanking nucleosome position and/or CEN core micrococcal nuclease accessibility. Fun30 deletion leads to defects in histone variant Htz1 occupancy genome-wide, including at and around most centromeres. FUN30 genetically interacts with CSE4, coding for the centromere-specific variant of histone H3, and counteracts the detrimental effect of transcription through centromeres on chromosome segregation and suppresses transcriptional noise over centromere CEN3. Previous work has shown a requirement for fission yeast and mammalian homologs of Fun30 in heterochromatin assembly. As centromeres in budding yeast are not embedded in heterochromatin, our findings indicate a direct role of Fun30 in centromere chromatin by promoting correct chromatin architecture.
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22
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The Saccharomyces cerevisiae chromatin remodeler Fun30 regulates DNA end resection and checkpoint deactivation. Mol Cell Biol 2012; 32:4727-40. [PMID: 23007155 DOI: 10.1128/mcb.00566-12] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Fun30 is a Swi2/Snf2 homolog in budding yeast that has been shown to remodel chromatin both in vitro and in vivo. We report that Fun30 plays a key role in homologous recombination, by facilitating 5'-to-3' resection of double-strand break (DSB) ends, apparently by facilitating exonuclease digestion of nucleosome-bound DNA adjacent to the DSB. Fun30 is recruited to an HO endonuclease-induced DSB and acts in both the Exo1-dependent and Sgs1-dependent resection pathways. Deletion of FUN30 slows the rate of 5'-to-3' resection from 4 kb/h to about 1.2 kb/h. We also found that the resection rate is reduced by DNA damage-induced phosphorylation of histone H2A-S129 (γ-H2AX) and that Fun30 interacts preferentially with nucleosomes in which H2A-S129 is not phosphorylated. Fun30 is not required for later steps in homologous recombination. Like its homolog Rdh54/Tid1, Fun30 is required to allow the adaptation of DNA damage checkpoint-arrested cells with an unrepaired DSB to resume cell cycle progression.
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23
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Chen X, Cui D, Papusha A, Zhang X, Chu CD, Tang J, Chen K, Pan X, Ira G. The Fun30 nucleosome remodeller promotes resection of DNA double-strand break ends. Nature 2012; 489:576-80. [PMID: 22960743 PMCID: PMC3640768 DOI: 10.1038/nature11355] [Citation(s) in RCA: 189] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 06/27/2012] [Indexed: 02/07/2023]
Abstract
Chromosomal double-strand breaks (DSBs) are resected by 5′-nucleases to form 3′ single-strand DNA (ssDNA) substrates for binding by homologous recombination and DNA damage checkpoint proteins. Two redundant pathways of extensive resection were described both in cells 1-3 and in vitro4-6, one relying on Exo1 exonuclease and the other on Sgs1 helicase and Dna2 nuclease. However, it remains unknown how resection proceeds within the context of chromatin where histones and histone-bound proteins represent barriers for resection enzymes. Here, we have identified the yeast nucleosome remodeling enzyme Fun30 as novel factor promoting DSB end resection. Fun30 is the major nucleosome remodeler promoting extensive Exo1- and Sgs1-dependent resection of DSBs while the RSC and INO80 chromatin remodeling complexes play redundant roles with Fun30 in resection adjacent to DSB ends. ATPase and helicase domains of Fun30, which are needed for nucleosome remodeling 7, are also required for resection. Fun30 is robustly recruited to DNA breaks and spreads around the DSB coincident with resection. Fun30 becomes less important for resection in the absence of the histone-bound Rad9 checkpoint adaptor protein known to block 5′ strand processing 8 and in the absence of either histone H3 K79 methylation or γ-H2A, which mediate recruitment of the Rad9 9, 10. Together these data suggest that Fun30 helps to overcome the inhibitory effect of Rad9 on DNA resection.
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Affiliation(s)
- Xuefeng Chen
- Department of Molecular & Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77030, USA
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24
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Functions of chromatin remodeling factors in heterochromatin formation and maintenance. SCIENCE CHINA-LIFE SCIENCES 2012; 55:89-96. [DOI: 10.1007/s11427-012-4267-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Accepted: 12/04/2011] [Indexed: 10/14/2022]
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25
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Li Q, Zhang Z. Linking DNA replication to heterochromatin silencing and epigenetic inheritance. Acta Biochim Biophys Sin (Shanghai) 2012; 44:3-13. [PMID: 22194009 DOI: 10.1093/abbs/gmr107] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Chromatin is organized into distinct functional domains. During mitotic cell division, both genetic information encoded in DNA sequence and epigenetic information embedded in chromatin structure must be faithfully duplicated. The inheritance of epigenetic states is critical in maintaining the genome integrity and gene expression state. In this review, we will discuss recent progress on how proteins known to be involved in DNA replication and DNA replication-coupled nucleosome assembly impact on the inheritance and maintenance of heterochromatin, a tightly compact chromatin structure that silences gene transcription. As heterochromatin is important in regulating gene expression and maintaining genome stability, understanding how heterochromatin states are inherited during S phase of the cell cycle is of fundamental importance.
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Mermoud JE, Rowbotham SP, Varga-Weisz PD. Keeping chromatin quiet: how nucleosome remodeling restores heterochromatin after replication. Cell Cycle 2011; 10:4017-25. [PMID: 22101266 DOI: 10.4161/cc.10.23.18558] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Disruption of chromatin organization during replication poses a major challenge to the maintenance and integrity of genome organization. It creates the need to accurately reconstruct the chromatin landscape following DNA duplication but there is little mechanistic understanding of how chromatin based modifications are restored on newly synthesized DNA. ATP-dependent chromatin remodeling activities serve multiple roles during replication and recent work underscores their requirement in the maintenance of proper chromatin organization. A new component of chromatin replication, the SWI/SNF-like chromatin remodeler SMARCAD1, acts at replication sites to facilitate deacetylation of newly assembled histones. Deacetylation is a pre-requisite for the restoration of epigenetic signatures in heterochromatin regions following replication. In this way, SMARCAD1, in concert with histone modifying activities and transcriptional repressors, reinforces epigenetic instructions to ensure that silenced loci are correctly perpetuated in each replication cycle. The emerging concept is that remodeling of nucleosomes is an early event imperative to promote the re-establishment of histone modifications following DNA replication.
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27
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A region of the nucleosome required for multiple types of transcriptional silencing in Saccharomyces cerevisiae. Genetics 2011; 188:535-48. [PMID: 21546544 DOI: 10.1534/genetics.111.129197] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Extended heterochromatin domains, which are repressive to transcription and help define centromeres and telomeres, are formed through specific interactions between silencing proteins and nucleosomes. This study reveals that in Saccharomyces cerevisiae, the same nucleosomal surface is critical for the formation of multiple types of heterochromatin, but not for local repression mediated by a related transcriptional repressor. Thus, this region of the nucleosome may be generally important to long-range silencing. In S. cerevisiae, the Sir proteins perform long-range silencing, whereas the Sum1 complex acts locally to repress specific genes. A mutant form of Sum1p, Sum1-1p, achieves silencing in the absence of Sir proteins. A genetic screen identified mutations in histones H3 and H4 that disrupt Sum1-1 silencing and fall in regions of the nucleosome previously known to disrupt Sir silencing and rDNA silencing. In contrast, no mutations were identified that disrupt wild-type Sum1 repression. Mutations that disrupt silencing fall in two regions of the nucleosome, the tip of the H3 tail and a surface of the nucleosomal core (LRS domain) and the adjacent base of the H4 tail. The LRS/H4 tail region interacts with the Sir3p bromo-adjacent homology (BAH) domain to facilitate Sir silencing. By analogy, this study is consistent with the LRS/H4 tail region interacting with Orc1p, a paralog of Sir3p, to facilitate Sum1-1 silencing. Thus, the LRS/H4 tail region of the nucleosome may be relatively accessible and facilitate interactions between silencing proteins and nucleosomes to stabilize long-range silencing.
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