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Histone Lysine-to-Methionine Mutation as Anticancer Drug Target. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1283:85-96. [PMID: 33155140 DOI: 10.1007/978-981-15-8104-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Histone modification stands for a vital genetic information form, which shows tight correlation with the modulation of normal physiological activities by genes. Abnormal regulation of histone methylation due to histone modification enzyme changes and histone mutations plays an important role in the development of cancer. Histone mutations, especially H3K27M and H3K36M, have been identified in various cancers such as pediatric DIPG (diffuse intrinsic pontine glioma) and chondroblastoma respectively. "K to M" mutation results overall downregulation of methylation on these lysine residues. Also, "K to M" mutant histones can inhibit the enzymatic activity of the responsible HMT (histone methyltransferase); for instance, SETD2 indicates H3K36 methylation, and Ezh2 represents H3K27 methylation. In-depth analysis of the mechanism of tumor formation triggered by the K to M mutation results in possible targeted therapies. This chapter is going to briefly introduce the mechanism of histone lysine-to-methionine mutation and review the recently identified targeted therapeutic strategies.
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2
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Thonsri U, Wongkham S, Wongkham C, Hino S, Nakao M, Roytrakul S, Koga T, Seubwai W. High glucose-ROS conditions enhance the progression in cholangiocarcinoma via upregulation of MAN2A2 and CHD8. Cancer Sci 2020; 112:254-264. [PMID: 33141432 PMCID: PMC7780024 DOI: 10.1111/cas.14719] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 10/10/2020] [Accepted: 10/27/2020] [Indexed: 01/11/2023] Open
Abstract
Diabetes is a major risk factor in the development and progression of several cancers including cholangiocarcinoma (CCA). However, the molecular mechanism by which hyperglycemia potentiates progression of CCA is not clearly understood. Here, we showed that a high glucose condition significantly increased reactive oxygen species (ROS) production and promoted aggressive phenotypes of CCA cells, including proliferation and migration activities. Mannosidase alpha class 2a member 2 (MAN2A2), was upregulated at both mRNA and protein levels in a high glucose‐ and ROS‐dependent manner. In addition, cell proliferation and migration were significantly reduced by MAN2A2 knockdown. Based on our proteome and in silico analyses, we further found that chromodomain helicase DNA‐binding protein 8 (CHD8) was induced by ROS signaling and regulated MAN2A2 expression. Overexpression of CHD8 increased MAN2A2 expression, while CHD8 knockdown dramatically reduced proliferation and migration as well as MAN2A2 expression in CCA cells. Moreover, both MAN2A2 and CHD8 were highly expressed with positive correlation in CCA tumor tissues. Collectively, these data suggested that high glucose conditions promote CCA progression through ROS‐mediated upregulation of MAN2A2 and CHD8. Thus, glucose metabolism is a promising therapeutic target to control tumor progression in patients with CCA and diabetes.
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Affiliation(s)
- Unchalee Thonsri
- Faculty of Medicine, Department of Biochemistry, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Sopit Wongkham
- Faculty of Medicine, Department of Biochemistry, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Chaisiri Wongkham
- Faculty of Medicine, Department of Biochemistry, Khon Kaen University, Khon Kaen, Thailand.,Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand
| | - Shinjiro Hino
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Mitsuyoshi Nakao
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Sittiruk Roytrakul
- National Center for Genetic Engineering and Biotechnology (BIOTEC), Pathum Thani, Thailand
| | - Tomoaki Koga
- Department of Medical Cell Biology, Institute of Molecular Embryology and Genetics, Kumamoto University, Kumamoto, Japan
| | - Wunchana Seubwai
- Cholangiocarcinoma Research Institute, Khon Kaen University, Khon Kaen, Thailand.,Faculty of Medicine, Department of Forensic Medicine, Khon Kaen University, Khon Kaen, Thailand
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3
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The mechanisms of action of chromatin remodelers and implications in development and disease. Biochem Pharmacol 2020; 180:114200. [DOI: 10.1016/j.bcp.2020.114200] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2020] [Revised: 08/09/2020] [Accepted: 08/12/2020] [Indexed: 02/06/2023]
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4
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Zhou J, Li J, Serafim RB, Ketchum S, Ferreira CG, Liu JC, Coe KA, Price BD, Yusufzai T. Human CHD1 is required for early DNA-damage signaling and is uniquely regulated by its N terminus. Nucleic Acids Res 2019. [PMID: 29529298 PMCID: PMC5934646 DOI: 10.1093/nar/gky128] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
CHD1 is a conserved chromatin remodeling enzyme required for development and linked to prostate cancer in adults, yet its role in human cells is poorly understood. Here, we show that targeted disruption of the CHD1 gene in human cells leads to a defect in early double-strand break (DSB) repair via homologous recombination (HR), resulting in hypersensitivity to ionizing radiation as well as PARP and PTEN inhibition. CHD1 knockout cells show reduced H2AX phosphorylation (γH2AX) and foci formation as well as impairments in CtIP recruitment to the damaged sites. Chromatin immunoprecipitation following a single DSB shows that the reduced levels of γH2AX accumulation at DSBs in CHD1-KO cells are due to both a global reduction in H2AX incorporation and poor retention of H2AX at the DSBs. We also identified a unique N-terminal region of CHD1 that inhibits the DNA binding, ATPase, and chromatin assembly and remodeling activities of CHD1. CHD1 lacking the N terminus was more active in rescuing the defects in γH2AX formation and CtIP recruitment in CHD1-KO cells than full-length CHD1, suggesting the N terminus is a negative regulator in cells. Our data point to a role for CHD1 in the DSB repair process and identify a novel regulatory region of the protein.
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Affiliation(s)
- Jia Zhou
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
| | - Jiaqi Li
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Rodolfo B Serafim
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Steven Ketchum
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Catarina G Ferreira
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Jessica C Liu
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Graduate Program: Molecules, Cells, and Organisms, Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kathryn A Coe
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Brendan D Price
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA
| | - Timur Yusufzai
- Department of Radiation Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02215, USA.,Department of Biological Chemistry & Molecular Pharmacology, Harvard Medical School, Boston, MA 02215, USA
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5
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Il’ina IA, Konev AY. The role of aTp-dependent chromatin remodeling factors in chromatin assembly in vivo. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Chromatin assembly is a fundamental process essential for chromosome duplication subsequent to DNA replication. In addition, histone removal and incorporation take place constantly throughout the cell cycle in the course of DNA-utilizing processes, such as transcription, damage repair or recombination. In vitro studies have revealed that nucleosome assembly relies on the combined action of core histone chaperones and ATP-utilizing molecular motor proteins such as ACF or CHD1. Despite extensive biochemical characterization of ATP-dependent chromatin assembly and remodeling factors, it has remained unclear to what extent nucleosome assembly is an ATP-dependent process in vivo. Our original and published data about the functions of ATP-dependent chromatin assembly and remodeling factors clearly demonstrated that these proteins are important for nucleosome assembly and histone exchange in vivo. During male pronucleus reorganization after fertilization CHD1 has a critical role in the genomescale, replication-independent nucleosome assembly involving the histone variant H3.3. Thus, the molecular motor proteins, such as CHD1, function not only in the remodeling of existing nucleosomes but also in de novo nucleosome assembly from DNA and histones in vivo. ATP-dependent chromatin assembly and remodeling factors have been implicated in the process of histone exchange during transcription and DNA repair, in the maintenance of centromeric chromatin and in the loading and remodeling of nucleosomes behind a replication fork. Thus, chromatin remodeling factors are involved in the processes of both replication-dependent and replication-independent chromatin assembly. The role of these proteins is especially prominent in the processes of large-scale chromatin reorganization; for example, during male pronucleus formation or in DNA repair. Together, ATP-dependent chromatin assembly factors, histone chaperones and chromatin modifying enzymes form a “chromatin integrity network” to ensure proper maintenance and propagation of chromatin landscape.
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Affiliation(s)
- Iu. A. Il’ina
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”
| | - A. Yu. Konev
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”
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6
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Histone Chaperone Asf1 Is Required for the Establishment of Repressive Chromatin in Schizosaccharomyces pombe fbp1 Gene Repression. Mol Cell Biol 2018; 38:MCB.00194-18. [PMID: 29967244 DOI: 10.1128/mcb.00194-18] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 06/23/2018] [Indexed: 11/20/2022] Open
Abstract
The arrangement of nucleosomes in chromatin plays a role in transcriptional regulation by restricting the accessibility of transcription factors and RNA polymerase II to cis-acting elements and promoters. For gene activation, the chromatin structure is altered to an open configuration. The mechanism for this process has been extensively analyzed. However, the mechanism by which repressive chromatin is reconstituted to terminate transcription has not been fully elucidated. Here, we investigated the mechanisms by which chromatin is reconstituted in the fission yeast Schizosaccharomyces pombefbp1 gene, which is robustly induced upon glucose starvation but tightly repressed under glucose-rich conditions. We found that the chromatin structure in the region upstream from fbp1 is closed by a two-step process. When cells are returned to glucose-rich medium following glucose starvation, changes in the nucleosome pattern alter the chromatin configuration at the transcription factor binding site to an inaccessible state, after which the nucleosome density upstream from fbp1 gradually increases via histone loading. Interestingly, this histone loading was observed in the absence of the Tup family corepressors Tup11 and Tup12. Analysis of strains carrying either gene disruptions or mutations affecting nine fission yeast histone chaperone genes demonstrated that the histone chaperone Asf1 induces nucleosome loading during glucose repression. These data establish a previously unappreciated chromatin reconstitution mechanism in fbp1 repression.
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7
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Sundaramoorthy R, Hughes AL, El-Mkami H, Norman DG, Ferreira H, Owen-Hughes T. Structure of the chromatin remodelling enzyme Chd1 bound to a ubiquitinylated nucleosome. eLife 2018; 7:35720. [PMID: 30079888 PMCID: PMC6118821 DOI: 10.7554/elife.35720] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 07/24/2018] [Indexed: 12/23/2022] Open
Abstract
ATP-dependent chromatin remodelling proteins represent a diverse family of proteins that share ATPase domains that are adapted to regulate protein-DNA interactions. Here, we present structures of the Saccharomyces cerevisiae Chd1 protein engaged with nucleosomes in the presence of the transition state mimic ADP-beryllium fluoride. The path of DNA strands through the ATPase domains indicates the presence of contacts conserved with single strand translocases and additional contacts with both strands that are unique to Snf2 related proteins. The structure provides connectivity between rearrangement of ATPase lobes to a closed, nucleotide bound state and the sensing of linker DNA. Two turns of linker DNA are prised off the surface of the histone octamer as a result of Chd1 binding, and both the histone H3 tail and ubiquitin conjugated to lysine 120 are re-orientated towards the unravelled DNA. This indicates how changes to nucleosome structure can alter the way in which histone epitopes are presented.
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Affiliation(s)
| | - Amanda L Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hassane El-Mkami
- School of Physics and Astronomy, University of St Andrews, St Andrews, United Kingdom
| | - David G Norman
- Nucleic Acids Structure Research Group, University of Dundee, Dundee, United Kingdom
| | - Helder Ferreira
- School of Biology, University of St Andrews, St Andrews, United Kingdom
| | - Tom Owen-Hughes
- Centre for Gene Regulation and Expression, School of Life Sciences, University of Dundee, Dundee, United Kingdom
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8
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Chen X, Zhao E, Fu YV. Using single-molecule approach to visualize the nucleosome assembly in yeast nucleoplasmic extracts. Sci Bull (Beijing) 2017; 62:399-404. [PMID: 36659283 DOI: 10.1016/j.scib.2017.02.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In eukaryotic cells, the smallest subunit of chromatin is the nucleosome, which consists of a segment of DNA wound on histone protein cores. Despite many years of effort, the process of nucleosome assembly and disassembly is still not very clear. Here, we present a convenient method to investigate the process of nucleosome assembly at the single molecule level. We invented a novel system derived from the yeast nucleoplasmic extracts (YNPE), and demonstrated that the YNPE supports the nucleosome assembly under physiological condition. By combining the total internal reflection fluorescence microscopy with microfluidic flow-cell technique, the dynamic process of nucleosome assembly in YNPE was visualized at single-molecule level. Our system provides a novel in vitro single-molecule tool to investigate the dynamics of nucleosome assembly under physiological conditions.
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Affiliation(s)
- Xiuqiang Chen
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ershuang Zhao
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu V Fu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China; Savaid Medical School, University of Chinese Academy of Sciences, Beijing 100049, China.
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9
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Lee Y, Song JJ. Reconstitution and Crystallization of Sir 3/4 in a Complex with Nucleosome. B KOREAN CHEM SOC 2015. [DOI: 10.1002/bkcs.10578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Yejin Lee
- Department of Biological Sciences, Cancer Metastasis Control Center; KAIST Institute for BioCentury, KAIST; Daejeon 305-338 Korea
| | - Ji-Joon Song
- Department of Biological Sciences, Cancer Metastasis Control Center; KAIST Institute for BioCentury, KAIST; Daejeon 305-338 Korea
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10
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Liu JC, Ferreira CG, Yusufzai T. Human CHD2 is a chromatin assembly ATPase regulated by its chromo- and DNA-binding domains. J Biol Chem 2014; 290:25-34. [PMID: 25384982 DOI: 10.1074/jbc.m114.609156] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Chromodomain helicase DNA-binding protein 2 (CHD2) is an ATPase and a member of the SNF2-like family of helicase-related enzymes. Although deletions of CHD2 have been linked to developmental defects in mice and epileptic disorders in humans, little is known about its biochemical and cellular activities. In this study, we investigate the ATP-dependent activity of CHD2 and show that CHD2 catalyzes the assembly of chromatin into periodic arrays. We also show that the N-terminal region of CHD2, which contains tandem chromodomains, serves an auto-inhibitory role in both the DNA-binding and ATPase activities of CHD2. While loss of the N-terminal region leads to enhanced chromatin-stimulated ATPase activity, the N-terminal region is required for ATP-dependent chromatin remodeling by CHD2. In contrast, the C-terminal region, which contains a putative DNA-binding domain, selectively senses double-stranded DNA of at least 40 base pairs in length and enhances the ATPase and chromatin remodeling activities of CHD2. Our study shows that the accessory domains of CHD2 play central roles in both regulating the ATPase domain and conferring selectivity to chromatin substrates.
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Affiliation(s)
- Jessica C Liu
- From the Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215 and Graduate Program: Molecules, Cells, and Organisms, Department of Molecular and Cellular Biology, Harvard University, Cambridge, Massachusetts 02138
| | - Catarina G Ferreira
- From the Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215 and
| | - Timur Yusufzai
- From the Department of Radiation Oncology, Dana-Farber Cancer Institute and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02215 and
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11
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Abstract
A large family of chromatin remodelers that noncovalently modify chromatin is crucial in cell development and differentiation. They are often the targets of cancer, neurological disorders, and other human diseases. These complexes alter nucleosome positioning, higher-order chromatin structure, and nuclear organization. They also assemble chromatin, exchange out histone variants, and disassemble chromatin at defined locations. We review aspects of the structural organization of these complexes, the functional properties of their protein domains, and variation between complexes. We also address the mechanistic details of these complexes in mobilizing nucleosomes and altering chromatin structure. A better understanding of these issues will be vital for further analyses of subunits of these chromatin remodelers, which are being identified as targets in human diseases by NGS (next-generation sequencing).
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Affiliation(s)
- Blaine Bartholomew
- University of Texas MD Anderson Cancer Center, Department of Molecular Carcinogenesis, Smithville, Texas 78957;
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12
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Pointner J, Persson J, Prasad P, Norman-Axelsson U, Strålfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K, Korber P. CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J 2012; 31:4388-403. [PMID: 23103765 DOI: 10.1038/emboj.2012.289] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 09/28/2012] [Indexed: 11/09/2022] Open
Abstract
Nucleosome positioning governs access to eukaryotic genomes. Many genes show a stereotypic organisation at their 5'end: a nucleosome free region just upstream of the transcription start site (TSS) followed by a regular nucleosomal array over the coding region. The determinants for this pattern are unclear, but nucleosome remodelers are likely critical. Here we study the role of remodelers in global nucleosome positioning in S. pombe and the corresponding changes in expression. We find a striking evolutionary shift in remodeler usage between budding and fission yeast. The S. pombe RSC complex does not seem to be involved in nucleosome positioning, despite its prominent role in S. cerevisiae. While S. pombe lacks ISWI-type remodelers, it has two CHD1-type ATPases, Hrp1 and Hrp3. We demonstrate nucleosome spacing activity for Hrp1 and Hrp3 in vitro, and that together they are essential for linking regular genic arrays to most TSSs in vivo. Impaired arrays in the absence of either or both remodelers may lead to increased cryptic antisense transcription, but overall gene expression levels are only mildly affected.
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Affiliation(s)
- Julia Pointner
- Adolf-Butenandt-Institut, University of Munich, Munich, Germany
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13
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Smolle M, Workman JL. Transcription-associated histone modifications and cryptic transcription. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2012; 1829:84-97. [PMID: 22982198 DOI: 10.1016/j.bbagrm.2012.08.008] [Citation(s) in RCA: 146] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Revised: 08/14/2012] [Accepted: 08/29/2012] [Indexed: 12/21/2022]
Abstract
Eukaryotic genomes are packaged into chromatin, a highly organized structure consisting of DNA and histone proteins. All nuclear processes take place in the context of chromatin. Modifications of either DNA or histone proteins have fundamental effects on chromatin structure and function, and thus influence processes such as transcription, replication or recombination. In this review we highlight histone modifications specifically associated with gene transcription by RNA polymerase II and summarize their genomic distributions. Finally, we discuss how (mis-)regulation of these histone modifications perturbs chromatin organization over coding regions and results in the appearance of aberrant, intragenic transcription. This article is part of a Special Issue entitled: RNA polymerase II Transcript Elongation.
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Affiliation(s)
- Michaela Smolle
- Stowers Institute for Medical Research, Kansas City, MO 64110, USA
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14
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Chromatin remodelers Isw1 and Chd1 maintain chromatin structure during transcription by preventing histone exchange. Nat Struct Mol Biol 2012; 19:884-92. [PMID: 22922743 PMCID: PMC3560298 DOI: 10.1038/nsmb.2312] [Citation(s) in RCA: 226] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2011] [Accepted: 05/31/2012] [Indexed: 12/25/2022]
Abstract
Set2-mediated methylation of histone H3 Lys36 (H3K36) is a mark associated with the coding sequences of actively transcribed genes, yet plays a negative role during transcription elongation. It prevents trans-histone exchange over coding regions and signals for histone deacetylation in the wake of RNA polymerase II (RNAPII) passage. We have found that in Saccharomyces cerevisiae the Isw1b chromatin-remodeling complex is specifically recruited to open reading frames (ORFs) by H3K36 methylation through the PWWP domain of its Ioc4 subunit in vivo and in vitro. Isw1b acts in conjunction with Chd1 to regulate chromatin structure by preventing trans-histone exchange from taking place over coding regions and thus maintains chromatin integrity during transcription elongation by RNA polymerase II.
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15
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Wang Z, Wang F, Tang T, Guo C. The role of PARP1 in the DNA damage response and its application in tumor therapy. Front Med 2012; 6:156-64. [PMID: 22660976 DOI: 10.1007/s11684-012-0197-3] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2011] [Accepted: 03/14/2012] [Indexed: 11/28/2022]
Abstract
Single-strand break repair protein poly(ADP-ribose) polymerase 1 (PARP1) catalyzes the poly(ADP-ribosyl)ation of many key proteins in vivo and thus plays important roles in multiple DNA damage response pathways, rendering it a promising target in cancer therapy. The tumor-suppressor effects of PARP inhibitors have attracted significant interest for development of novel cancer therapies. However, recent evidence indicated that the underlying mechanism of PARP inhibitors in tumor therapy is more complex than previously expected. The present review will focus on recent progress on the role of PARP1 in the DNA damage response and PARP inhibitors in cancer therapy. The emerging resistance of BRCA-deficient tumors to PARP inhibitors is also briefly discussed from the perspective of DNA damage and repair. These recent research advances will inform the selection of patient populations who can benefit from the PARP inhibitor treatment and development of effective drug combination strategies.
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Affiliation(s)
- Zhifeng Wang
- Laboratory of Disease Genomics and Individual Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 100029, China
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16
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Krietenstein N, Wippo CJ, Lieleg C, Korber P. Genome-wide in vitro reconstitution of yeast chromatin with in vivo-like nucleosome positioning. Methods Enzymol 2012; 513:205-32. [PMID: 22929771 DOI: 10.1016/b978-0-12-391938-0.00009-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Recent genome-wide mapping of nucleosome positions revealed that well-positioned nucleosomes are pervasive across eukaryotic genomes, especially in important regulatory regions such as promoters or origins of replication. As nucleosomes impede access to DNA, their positioning is a primary mode of genome regulation. In vivo studies, especially in yeast, shed some light on factors involved in nucleosome positioning, but there is an urgent need for a complementary biochemical approach in order to confirm their direct roles, identify missing factors, and study their mechanisms. Here we describe a method that allows the genome-wide in vitro reconstitution of nucleosomes with very in vivo-like positions by a combination of salt gradient dialysis reconstitution, yeast whole cell extracts, and ATP. This system provides a starting point and positive control for the biochemical dissection of nucleosome positioning mechanisms.
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Affiliation(s)
- Nils Krietenstein
- Adolf-Butenandt-Institut, Molecular Biology Unit, University of Munich, Munich, Germany
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17
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Abstract
It is well established that ATP-dependent chromatin remodelers modulate DNA access of transcription factors and RNA polymerases by "opening" or "closing" chromatin structure. However, this view is far too simplistic. Recent findings have demonstrated that these enzymes not only set the stage for the transcription machinery to act but are actively involved at every step of the transcription process. As a consequence, they affect initiation, elongation, termination and RNA processing. In this review we will use the CHD family as a paradigm to illustrate the progress that has been made in revealing these new concepts.
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Affiliation(s)
- Magdalena Murawska
- Institute of Molecular Biology and Tumor Research, Philipps University Marburg, Marburg, Germany
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18
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Piatti P, Zeilner A, Lusser A. ATP-dependent chromatin remodeling factors and their roles in affecting nucleosome fiber composition. Int J Mol Sci 2011; 12:6544-65. [PMID: 22072904 PMCID: PMC3210995 DOI: 10.3390/ijms12106544] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2011] [Revised: 09/20/2011] [Accepted: 09/28/2011] [Indexed: 01/03/2023] Open
Abstract
ATP-dependent chromatin remodeling factors of the SNF2 family are key components of the cellular machineries that shape and regulate chromatin structure and function. Members of this group of proteins have broad and heterogeneous functions ranging from controlling gene activity, facilitating DNA damage repair, promoting homologous recombination to maintaining genomic stability. Several chromatin remodeling factors are critical components of nucleosome assembly processes, and recent reports have identified specific functions of distinct chromatin remodeling factors in the assembly of variant histones into chromatin. In this review we will discuss the specific roles of ATP-dependent chromatin remodeling factors in determining nucleosome composition and, thus, chromatin fiber properties.
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Affiliation(s)
- Paolo Piatti
- Division of Molecular Biology, Innsbruck Medical University, Biocenter, Fritz-Pregl Strasse 3, 6020 Innsbruck, Austria; E-Mails: (P.P.); (A.Z.)
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19
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Gkikopoulos T, Schofield P, Singh V, Pinskaya M, Mellor J, Smolle M, Workman JL, Barton G, Owen-Hughes T. A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization. Science 2011; 333:1758-60. [PMID: 21940898 PMCID: PMC3428865 DOI: 10.1126/science.1206097] [Citation(s) in RCA: 216] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The positioning of nucleosomes within the coding regions of eukaryotic genes is aligned with respect to transcriptional start sites. This organization is likely to influence many genetic processes, requiring access to the underlying DNA. Here, we show that the combined action of Isw1 and Chd1 nucleosome-spacing enzymes is required to maintain this organization. In the absence of these enzymes, regular positioning of the majority of nucleosomes is lost. Exceptions include the region upstream of the promoter, the +1 nucleosome, and a subset of locations distributed throughout coding regions where other factors are likely to be involved. These observations indicate that adenosine triphosphate-dependent remodeling enzymes are responsible for directing the positioning of the majority of nucleosomes within the Saccharomyces cerevisiae genome.
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Affiliation(s)
- Triantaffyllos Gkikopoulos
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Pieta Schofield
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Division of Biological Chemistry and Drug discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Vijender Singh
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Marina Pinskaya
- Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU
| | - Jane Mellor
- Department of Biochemistry University of Oxford South Parks Road Oxford OX1 3QU
| | - Michaela Smolle
- Stowers Institute for Medical Research, 1000E. 50 Street, Kansas City, MO 64110, USA
| | - Jerry L. Workman
- Stowers Institute for Medical Research, 1000E. 50 Street, Kansas City, MO 64110, USA
| | - Geoffrey Barton
- Division of Biological Chemistry and Drug discovery, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Tom Owen-Hughes
- Wellcome Trust Centre for Gene Regulation and Expression, College of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
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The DNA-binding domain of the Chd1 chromatin-remodelling enzyme contains SANT and SLIDE domains. EMBO J 2011; 30:2596-609. [PMID: 21623345 PMCID: PMC3155300 DOI: 10.1038/emboj.2011.166] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2011] [Accepted: 04/21/2011] [Indexed: 12/15/2022] Open
Abstract
The ATP-dependent chromatin-remodelling enzyme Chd1 is a 168-kDa protein consisting of a double chromodomain, Snf2-related ATPase domain, and a C-terminal DNA-binding domain. Here, we show the DNA-binding domain is required for Saccharomyces cerevisiae Chd1 to bind and remodel nucleosomes. The crystal structure of this domain reveals the presence of structural homology to SANT and SLIDE domains previously identified in ISWI remodelling enzymes. The presence of these domains in ISWI and Chd1 chromatin-remodelling enzymes may provide a means of efficiently harnessing the action of the Snf2-related ATPase domain for the purpose of nucleosome spacing and provide an explanation for partial redundancy between these proteins. Site directed mutagenesis was used to identify residues important for DNA binding and generate a model describing the interaction of this domain with DNA. Through inclusion of Chd1 sequences in homology searches SLIDE domains were identified in CHD6-9 proteins. Point mutations to conserved amino acids within the human CHD7 SLIDE domain have been identified in patients with CHARGE syndrome.
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21
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De Benedetti A. Tousled kinase TLK1B mediates chromatin assembly in conjunction with Asf1 regardless of its kinase activity. BMC Res Notes 2010; 3:68. [PMID: 20222959 PMCID: PMC2845150 DOI: 10.1186/1756-0500-3-68] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2010] [Accepted: 03/11/2010] [Indexed: 11/12/2022] Open
Abstract
Background The Tousled Like Kinases (TLKs) are involved in chromatin dynamics, including DNA replication and repair, transcription, and chromosome segregation. Indeed, the first two TLK1 substrates were identified as the histone H3 and Asf1 (a histone H3/H4 chaperone), which immediately suggested a function in chromatin remodeling. However, despite the straightforward assumption that TLK1 acts simply by phosphorylating its substrates and hence modifying their activity, TLK1 also acts as a chaperone. In fact, a kinase-dead (KD) mutant of TLK1B is functional in stimulating chromatin assembly in vitro. However, subtle effects of Asf1 phosphorylation are more difficult to probe in chromatin assembly assays. Not until very recently was the Asf1 site phosphorylated by TLK1 identified. This has allowed for probing directly the functionality of a site-directed mutant of Asf1 in chromatin assembly assays. Findings Addition of either wt or non-phosphorylatable mutant Asf1 to nuclear extract stimulates chromatin assembly on a plasmid. Similarly, TLK1B-KD stimulates chromatin assembly and it synergizes in reactions with supplemental Asf1 (wt or non-phosphorylatable mutant). Conclusions Although the actual function of TLKs as mediators of Asf1 activity cannot be easily studied in vivo, particularly since in mammalian cells there are two TLK genes and two Asf1 genes, we were able to study specifically the stimulation of chromatin assembly in vitro. In such assays, clearly the TLK1 kinase activity was not critical, as neither a non-phosphorylatable Asf1 nor use of the TLK1B-KD impaired the stimulation of nucleosome formation.
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Affiliation(s)
- Arrigo De Benedetti
- Department of Biochemistry and Molecular Biology and the Feist-Weiller Cancer Center, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA.
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22
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Okuwaki M, Kato K, Nagata K. Functional characterization of human nucleosome assembly protein 1-like proteins as histone chaperones. Genes Cells 2010; 15:13-27. [DOI: 10.1111/j.1365-2443.2009.01361.x] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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23
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Histone H3K4 and K36 methylation, Chd1 and Rpd3S oppose the functions of Saccharomyces cerevisiae Spt4-Spt5 in transcription. Genetics 2009; 184:321-34. [PMID: 19948887 DOI: 10.1534/genetics.109.111526] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spt4-Spt5, a general transcription elongation factor for RNA polymerase II, also has roles in chromatin regulation. However, the relationships between these functions are not clear. Previously, we isolated suppressors of a Saccharomyces cerevisiae spt5 mutation in genes encoding members of the Paf1 complex, which regulates several cotranscriptional histone modifications, and Chd1, a chromatin remodeling enzyme. Here, we show that this suppression of spt5 can result from loss of histone H3 lysines 4 or 36 methylation, or reduced recruitment of Chd1 or the Rpd3S complex. These spt5 suppressors also rescue the synthetic growth defects observed in spt5 mutants that also lack elongation factor TFIIS. Using a FLO8 reporter gene, we found that a chd1 mutation caused cryptic initiation of transcription. We further observed enhancement of cryptic initiation in chd1 isw1 mutants and increased histone acetylation in a chd1 mutant. We suggest that, as previously proposed for H3 lysine 36 methylation and the Rpd3S complex, H3 lysine 4 methylation and Chd1 function to maintain normal chromatin structures over transcribed genes, and that one function of Spt4-Spt5 is to help RNA polymerase II overcome the repressive effects of these histone modifications and chromatin regulators on transcription.
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Abstract
Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.
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Affiliation(s)
- J Adam Hall
- Department of Biological Sciences, Marshall University, 1 John Marshall Drive, Huntington, WV 25755, USA
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25
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Armstrong JA. Negotiating the nucleosome: factors that allow RNA polymerase II to elongate through chromatin. Biochem Cell Biol 2008; 85:426-34. [PMID: 17713578 DOI: 10.1139/o07-054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Initiation by RNA polymerase II (Pol II) involves a host of enzymes, and the process of elongation appears similarly complex. Transcriptional elongation through chromatin requires the coordinated efforts of Pol II and its associated transcription factors: C-terminal domain kinases, elongation complexes, chromatin-modifying enzymes, chromatin remodeling factors, histone chaperones (nucleosome assembly factors), and histone variants. This review examines the following: (i) the consequences of the encounter between elongating Pol II and a nucleosome, and (ii) chromatin remodeling factors and nucleosome assembly factors that have recently been identified as important for the elongation stage of transcription.
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Affiliation(s)
- Jennifer A Armstrong
- Joint Science Department, The Claremont Colleges, 925 N. Mills Avenue, Claremont, CA 91711, USA.
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26
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Abstract
Chromodomain/helicase/DNA-binding domain (CHD) proteins have been identified in a variety of organisms. Despite common features, such as their chromodomain and helicase domain, they have been described as having multiple roles and interacting partners. However, a common theme for the main role of CHD proteins appears to be linked to their ATP-dependent chromatin-remodeling activity. Their actual activity as either repressor or activator, and their cell or gene specificity, is connected to their interacting partner(s). In this minireview, we attempt to match the members of the CHD family with the presence of structural domains, cofactors, and cellular roles in the regulation of gene expression, recombination, genome organization, and chromatin structure, as well as their potential activity in RNA processing.
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27
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Goodfellow H, Krejcí A, Moshkin Y, Verrijzer CP, Karch F, Bray SJ. Gene-specific targeting of the histone chaperone asf1 to mediate silencing. Dev Cell 2008; 13:593-600. [PMID: 17925233 DOI: 10.1016/j.devcel.2007.08.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 07/13/2007] [Accepted: 08/31/2007] [Indexed: 11/17/2022]
Abstract
The histone chaperone Asf1 assists in chromatin assembly and remodeling during replication, transcription activation, and gene silencing. However, it has been unclear to what extent Asf1 could be targeted to specific loci via interactions with sequence-specific DNA-binding proteins. Here, we show that Asf1 contributes to the repression of Notch target genes, as depletion of Asf1 in cells by RNAi causes derepression of the E(spl) Notch-inducible genes. Conversely, overexpression of Asf1 in vivo results in decreased expression of target genes and produces phenotypes that are strongly modified (enhanced and suppressed) by mutations affecting the Notch pathway, but not by mutations in other signaling pathways. Asf1 can be coprecipitated with the DNA-binding protein Su(H) and the corepressor Hairless and interacts directly with two components of this complex, Hairless and SKIP. Thus, in addition to playing more general roles in chromatin dynamics, Asf1 is directed via interactions with sequence-specific complexes to mediate silencing of specific target genes.
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Affiliation(s)
- Henry Goodfellow
- Department of Physiology, Development and Neuroscience, University of Cambridge, Downing Street, Cambridge CB2 3DY, United Kingdom
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28
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CHD8 associates with human Staf and contributes to efficient U6 RNA polymerase III transcription. Mol Cell Biol 2007; 27:8729-38. [PMID: 17938208 DOI: 10.1128/mcb.00846-07] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Chromatin remodeling and histone modification are essential for eukaryotic transcription regulation, but little is known about chromatin-modifying activities acting on RNA polymerase III (Pol III)-transcribed genes. The human U6 small nuclear RNA promoter, located 5' of the transcription start site, consists of a core region directing basal transcription and an activating region that recruits the transcription factors Oct-1 and Staf (ZNF143). Oct-1 activates transcription in part by helping recruit core binding factors, but nothing is known about the mechanisms of transcription activation by Staf. We show that Staf activates U6 transcription from a preassembled chromatin template in vitro and associates with several proteins linked to chromatin modification, among them chromodomain-helicase-DNA binding protein 8 (CHD8). CHD8 binds to histone H3 di- and trimethylated on lysine 4. It resides on the human U6 promoter as well as the mRNA IRF3 promoter in vivo and contributes to efficient transcription from both these promoters. Thus, Pol III transcription from type 3 promoters uses some of the same factors used for chromatin remodeling at Pol II promoters.
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29
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Abstract
Histone acetylation regulates many cellular processes, and specific acetylation marks, either singly or in combination, produce distinct outcomes. For example, the acetylation pattern on newly synthesized histones is important for their assembly into nucleosomes by histone chaperones. Additionally, the degree of chromatin compaction and folding may be regulated by acetylation of histone H4 at lysine 16. Histone acetylation also regulates the formation of heterochromatin; deacetylation of H4 lysine 16 is important for spreading of heterochromatin components, whereas acetylation of this site serves as a barrier to this spreading. Finally, histone acetylation is critical for gene transcription, but recent results suggest that deacetylation of certain sites also plays an important role. There are many histone acetyltransferases (HATs) and deacetylases, with differing preferences for the various histone proteins and for specific sites on individual histones. Determining how these enzymes create distinct acetylation patterns and regulate the functional outcome is an important challenge.
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Affiliation(s)
- Mona D Shahbazian
- Department of Biological Chemistry, Geffen School of Medicine and the Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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30
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Rufiange A, Jacques PE, Bhat W, Robert F, Nourani A. Genome-wide replication-independent histone H3 exchange occurs predominantly at promoters and implicates H3 K56 acetylation and Asf1. Mol Cell 2007; 27:393-405. [PMID: 17679090 DOI: 10.1016/j.molcel.2007.07.011] [Citation(s) in RCA: 258] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2007] [Revised: 05/28/2007] [Accepted: 07/10/2007] [Indexed: 10/23/2022]
Abstract
In yeast, histone H3/H4 exchange independent of replication is poorly understood. Here, we analyzed the deposition of histone H3 molecules, synthesized during G1, using a high-density microarray histone exchange assay. While we found that H3 exchange in coding regions requires high levels of transcription, promoters exchange H3 molecules in the absence of transcription. In inactive promoters, H3 is deposited predominantly in well-positioned nucleosomes surrounding nucleosome-free regions, indicating that some nucleosomes in promoters are dynamic. This could facilitate induction of repressed genes. Importantly, we show that histone H3 K56 acetylation, a replication-associated mark, is also present in replication-independent newly assembled nucleosomes and correlates perfectly with the deposition of new H3. Finally, we found that transcription-dependent incorporation of H3 at promoters is highly dependent on Asf1. Taken together, our data underline the dynamic nature of replication-independent nucleosome assembly/disassembly, specify a link to transcription, and implicate Asf1 and H3 K56 acetylation.
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Affiliation(s)
- Anne Rufiange
- Centre de Recherche en Cancérologie de l'Université Laval, L'Hôtel-Dieu de Québec (CHUQ), Québec, Canada
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31
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Biswas D, Dutta-Biswas R, Stillman DJ. Chd1 and yFACT act in opposition in regulating transcription. Mol Cell Biol 2007; 27:6279-87. [PMID: 17620414 PMCID: PMC2099615 DOI: 10.1128/mcb.00978-07] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
CHD1 encodes an ATP-dependent chromatin remodeler with two chromodomains. Deletion of CHD1 suppresses the temperature-sensitive growth defect caused by mutations in either SPT16 or POB3, which encode subunits of the yFACT chromatin-reorganizing complex. chd1 also suppresses synthetic defects caused by combining an spt16 mutation with other transcription factor mutations, including the synthetic lethality caused by combining an spt16 mutation with TATA binding protein (TBP) or TFIIA defects. Binding of TBP and RNA polymerase II to the GAL1 promoter is reduced in a pob3 mutant, resulting in low levels of GAL1 expression, and all three defects are suppressed by removing Chd1. These results suggest that Chd1 and yFACT have opposing roles in regulating TBP binding at promoters. Additionally, overexpression of Chd1 is tolerated in wild-type cells but is toxic in spt16 mutants. Further, both the ATPase and chromodomain are required for Chd1 activity in opposing yFACT function. Similar to the suppression by chd1, mutations in the SET2 histone methyltransferase also suppress defects caused by yFACT mutations. chd1 and set2 are additive in suppressing pob3, suggesting that Chd1 and Set2 act in distinct pathways. Although human Chd1 has been shown to bind to H3-K4-Me, we discuss evidence arguing that yeast Chd1 binds to neither H3-K4-Me nor H3-K36-Me.
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Affiliation(s)
- Debabrata Biswas
- Department of Pathology, University of Utah, 15 N. Medical Drive East, Salt Lake City, UT 84112, USA
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32
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Abstract
Chromatin remodeling enzymes contribute to the dynamic changes that occur in chromatin structure during cellular processes such as transcription, recombination, repair, and replication. Members of the chromodomain helicase DNA-binding (Chd) family of enzymes belong to the SNF2 superfamily of ATP-dependent chromatin remodelers. The Chd proteins are distinguished by the presence of two N-terminal chromodomains that function as interaction surfaces for a variety of chromatin components. Genetic, biochemical, and structural studies demonstrate that Chd proteins are important regulators of transcription and play critical roles during developmental processes. Numerous Chd proteins are also implicated in human disease.
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Affiliation(s)
- Concetta G A Marfella
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
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33
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Marfella CGA, Ohkawa Y, Coles AH, Garlick DS, Jones SN, Imbalzano AN. Mutation of the SNF2 family member Chd2 affects mouse development and survival. J Cell Physiol 2006; 209:162-71. [PMID: 16810678 DOI: 10.1002/jcp.20718] [Citation(s) in RCA: 69] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The chromodomain helicase DNA-binding domain (Chd) proteins belong to the SNF2-like family of ATPases that function in chromatin remodeling and assembly. These proteins are characterized by the presence of tandem chromodomains and are further subdivided based on the presence or absence of additional structural motifs. The Chd1-Chd2 subfamily is distinguished by the presence of a DNA-binding domain that recognizes AT-rich sequence. Currently, there are no reports addressing the function of the Chd2 family member. Embryonic stem cells containing a retroviral gene-trap inserted at the Chd2 locus were utilized to generate mice expressing a Chd2 protein lacking the DNA-binding domain. This mutation in Chd2 resulted in a general growth delay in homozygous mutants late in embryogenesis and in perinatal lethality. Animals heterozygous for the mutation showed decreased neonatal viability and increased susceptibility to non-neoplastic lesions affecting most primary organs. In particular, approximately 85% of the heterozygotes showed gross kidney abnormalities. Our results demonstrate that mutation of Chd2 dramatically affects mammalian development and long-term survival.
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Affiliation(s)
- Concetta G A Marfella
- Department of Cell Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01655, USA
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34
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Okuda M, Horikoshi M, Nishimura Y. Structural polymorphism of chromodomains in Chd1. J Mol Biol 2006; 365:1047-62. [PMID: 17098252 DOI: 10.1016/j.jmb.2006.10.039] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2006] [Revised: 09/11/2006] [Accepted: 10/11/2006] [Indexed: 10/24/2022]
Abstract
Chromodomain from heterochromatin protein 1 and polycomb protein is known to be a lysine-methylated histone H3 tail-binding module. Chromo-helicase/ATPase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodeling factor, containing two tandem chromodomains. In human CHD1, both chromodomains are essential for specific binding to a K4 methylated histone H3 (H3 MeK4) peptide and are found to bind cooperatively in the crystal structure. For the budding yeast homologue, Chd1, the second but not the first chromodomain was once reported to bind to an H3 MeK4 peptide. Here, we reveal that neither the second chromodomain nor a region containing tandem chromodomains from yeast Chd1 bind to any lysine-methylated or arginine-methylated histone peptides that we examined. In addition, we examined the structures of the chromodomains from Chd1 by NMR. Although the tertiary structure of the region containing tandem chromodomains could not be obtained, the secondary structure deduced from NMR is well conserved in the tertiary structures of the corresponding first and second chromodomains determined individually by NMR. Both chromodomains of Chd1 demonstrate a structure similar to that of the corresponding part of CHD1, consisting of a three-stranded beta-sheet followed by a C-terminal alpha-helix. However, an additional helix between the first and second beta-strands, which is found in both of the first chromodomains of Chd1 and CHD1, is positioned in an entirely different manner in Chd1 and CHD1. In human CHD1 this helix forms the peptide-binding site. The amino acid sequences of the chromodomains could be well aligned on the basis of these structures. The alignment showed that yeast Chd1 lacks several key functional residues, which are responsible for specific binding to a methylated lysine residue in other chromodomains. Chd1 is likely to have no binding affinity for any H3 MeK peptide, as found in other chromodomain proteins.
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Affiliation(s)
- Masahiko Okuda
- Graduate School of Supramolecular Biology, Yokohama City University, Tsurumi-ku, Yokohama 230-0045, Japan
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35
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Ishihara K, Oshimura M, Nakao M. CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol Cell 2006; 23:733-42. [PMID: 16949368 DOI: 10.1016/j.molcel.2006.08.008] [Citation(s) in RCA: 182] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2006] [Revised: 06/17/2006] [Accepted: 08/10/2006] [Indexed: 10/24/2022]
Abstract
Chromatin insulators are boundary elements between distinctly regulated, neighboring chromosomal domains, and they function by blocking the effects of nearby enhancers in a position-dependent manner. Here, we show that the SNF2-like chromodomain helicase protein CHD8 interacts with the insulator binding protein CTCF. Chromatin immunoprecipitation analysis revealed that CHD8 was present at known CTCF target sites, such as the differentially methylated region (DMR) of H19, the locus control region of beta-globin, and the promoter region of BRCA1 and c-myc genes. RNA interference-mediated knockdown of CHD8 significantly abolished the H19 DMR insulator activity that depends highly on CTCF, leading to reactivation of imprinted IGF2 from chromosome of maternal origin. Further, the lack of CHD8 affected CpG methylation and histone acetylation around the CTCF binding sites, adjacent to heterochromatin, of BRCA1 and c-myc genes. These findings provide insight into the role of CTCF-CHD8 complex in insulation and epigenetic regulation at active insulator sites.
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Affiliation(s)
- Ko Ishihara
- Department of Regeneration Medicine, Institute of Molecular Embryology and Genetics, Kumamoto University, 2-2-1 Honjo, Kumamoto 860-0811, Japan
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36
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Schwabish MA, Struhl K. Asf1 mediates histone eviction and deposition during elongation by RNA polymerase II. Mol Cell 2006; 22:415-22. [PMID: 16678113 DOI: 10.1016/j.molcel.2006.03.014] [Citation(s) in RCA: 197] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2006] [Revised: 02/23/2006] [Accepted: 03/08/2006] [Indexed: 11/29/2022]
Abstract
Histones are rapidly evicted and deposited during transcription by RNA polymerase (Pol) II, but a factor that mediates histone eviction in vivo has not yet been identified. Here, we show that the histone chaperone Asf1 associates with promoters and coding regions of transcriptionally active genes. Asf1 mediates histone H3, but not H2B, eviction and deposition during Pol II elongation, suggesting that nucleosome assembly and disassembly occur in a stepwise fashion. Lastly, Asf1 inhibits internal initiation from cryptic promoters within coding regions. These results strongly suggest that Asf1 functions as an elongation factor to disassemble and reassemble histones during Pol II elongation.
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Affiliation(s)
- Marc A Schwabish
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts 02115, USA
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37
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Abstract
Nucleosome assembly protein 1 (NAP-1) is an integral component in the establishment, maintenance, and dynamics of eukaryotic chromatin. It shuttles histones into the nucleus, assembles nucleosomes, and promotes chromatin fluidity, thereby affecting the transcription of many genes. The 3.0 A crystal structure of yeast NAP-1 reveals a previously uncharacterized fold with implications for histone binding and shuttling. A long alpha-helix is responsible for homodimerization via a previously uncharacterized antiparallel non-coiled-coil, and an alpha/beta domain is implicated in protein-protein interaction. A nuclear export sequence that is embedded in the dimerization helix is almost completely masked by an accessory domain that contains several target sites for casein kinase II. The four-stranded antiparallel beta-sheet that characterizes the alpha/beta domain is found in all histone chaperones, despite the absence of homology in sequence, structural context, or quaternary structure. To our knowledge, this is the first structure of a member of the large NAP family of proteins and suggests a mechanism by which the shuttling of histones to and from the nucleus is regulated.
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Affiliation(s)
- Young-Jun Park
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA
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38
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Abstract
There has been remarkable progress in the last 20 years in defining the molecular mechanisms that regulate initiation of DNA synthesis in eukaryotic cells. Replication origins in the DNA nucleate the ordered assembly of protein factors to form a prereplication complex (preRC) that is poised for DNA synthesis. Transition of the preRC to an active initiation complex is regulated by cyclin-dependent kinases and other signaling molecules, which promote further protein assembly and activate the mini chromosome maintenance helicase. We will review these mechanisms and describe the state of knowledge about the proteins involved. However, we will also consider an additional layer of complexity. The DNA in the cell is packaged with histone proteins into chromatin. Chromatin structure provides an additional layer of heritable information with associated epigenetic modifications. Thus, we will begin by describing chromatin structure, and how the cell generally controls access to the DNA. Access to the DNA requires active chromatin remodeling, specific histone modifications, and regulated histone deposition. Studies in transcription have revealed a variety of mechanisms that regulate DNA access, and some of these are likely to be shared with DNA replication. We will briefly describe heterochromatin as a model for an epigenetically inherited chromatin state. Next, we will describe the mechanisms of replication initiation and how these are affected by constraints of chromatin. Finally, chromatin must be reassembled with appropriate modifications following passage of the replication fork, and our third major topic will be the reassembly of chromatin and its associated epigenetic marks. Thus, in this chapter, we seek to bring together the studies of replication initiation and the studies of chromatin into a single holistic narrative.
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Affiliation(s)
- Angel P Tabancay
- Molecular and Computational Biology Section University of Southern California Los Angeles, California 90089, USA
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39
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Radchuk VV, Sreenivasulu N, Radchuk RI, Wobus U, Weschke W. The methylation cycle and its possible functions in barley endosperm development. PLANT MOLECULAR BIOLOGY 2005; 59:289-307. [PMID: 16247558 DOI: 10.1007/s11103-005-8881-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2005] [Accepted: 06/16/2005] [Indexed: 05/05/2023]
Abstract
Barley endosperm development can be subdivided into the pre-storage, intermediate, storage and desiccation phase. Nothing is known about DNA methylation events involved in different endosperm-specific developmental programmes. A complete set of methylation cycle enzyme genes was identified and investigated by mRNA expression analysis. During the pre-storage phase, methionine synthase and S-adenosylmethionine (AdoMet) synthase genes are expressed at high levels, mainly to produce AdoMet, which might be used for methylation processes as indicated by high expression of methyltransferases HvMET1, HvCMT1 and HvDnmt3-1 as well as AdoHcy hydrolase genes. The methyltransferases, core histones and DNA-unwinding ATPases are co-expressed at the mRNA level. On the contrary, storage protein (prolamin) gene expression is repressed due to CpG methylation. Expression of genes responsible for starch biosynthesis is also developmentally regulated but not methylation-dependent. Thus, during pre-storage phase, activity of HvMET1 and HvCMT1 possibly maintains DNA replication and suppresses specific pathways of maturation. Besides, HvDnmt3-1 might be responsible for differentiation-specific de novo methylation. Expression of methyltransferases HvDnmt3-2 and HvCMT2 peaks during the onset of massive starch accumulation. The enzymes are likely responsible for DNA methylation involved in determining plastid division and amyloplast differentiation as concluded from the patterns of co-expressed genes. Levels of AdoMet decarboxylase mRNA, but not methyltransferase- and AdoHcy mRNA, increase at the beginning of desiccation together with methionine synthase and AdoMet synthase levels. This increase may be indicative for utilization of AdoMet in polyamine production protecting aleuron and embryo cell membranes during desiccation.
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Affiliation(s)
- Volodymyr V Radchuk
- Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK), Molecular Genetics, Corrensstrasse 3, Gatersleben, 06466, Saxoinia-Anhalt, Germany
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40
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Zhang L, Schroeder S, Fong N, Bentley DL. Altered nucleosome occupancy and histone H3K4 methylation in response to 'transcriptional stress'. EMBO J 2005; 24:2379-90. [PMID: 15944735 PMCID: PMC1173152 DOI: 10.1038/sj.emboj.7600711] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2004] [Accepted: 05/18/2005] [Indexed: 11/09/2022] Open
Abstract
We report that under 'transcriptional stress' in budding yeast, when most pol II activity is acutely inhibited, rapid deposition of nucleosomes occurs within genes, particularly at 3' positions. Whereas histone H3K4 trimethylation normally marks 5' ends of highly transcribed genes, under 'transcriptional stress' induced by 6-azauracil (6-AU) and inactivation of pol II, TFIIE or CTD kinases Kin28 and Ctk1, this mark shifted to the 3' end of the TEF1 gene. H3K4Me3 at 3' positions was dynamic and could be rapidly removed when transcription recovered. Set1 and Chd1 are required for H3K4 trimethylation at 3' positions when transcription is inhibited by 6-AU. Furthermore, Deltachd1 suppressed the growth defect of Deltaset1. We suggest that a 'transcriptional stress' signal sensed through Set1, Chd1, and possibly other factors, causes H3K4 hypermethylation of newly deposited nucleosomes at downstream positions within a gene. This response identifies a new role for H3K4 trimethylation at the 3' end of the gene, as a chromatin mark associated with impaired pol II transcription.
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Affiliation(s)
- Lian Zhang
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Aurora, CO, USA
| | - Stephanie Schroeder
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Aurora, CO, USA
| | - Nova Fong
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Aurora, CO, USA
| | - David L Bentley
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Aurora, CO, USA
- Department of Biochemistry and Molecular Genetics, University of Colorado School of Medicine, UCHSC at Fitzsimons, Mail Stop 8101, PO Box 6511, Aurora, CO 80045, USA. Tel.: +1 303 724 3238; Fax: +1 303 724 3215; E-mail:
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Gunjan A, Paik J, Verreault A. Regulation of histone synthesis and nucleosome assembly. Biochimie 2005; 87:625-35. [PMID: 15989979 DOI: 10.1016/j.biochi.2005.02.008] [Citation(s) in RCA: 86] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2004] [Accepted: 02/10/2005] [Indexed: 11/25/2022]
Abstract
Histone deposition onto nascent DNA is the first step in the process of chromatin assembly during DNA replication. The process of nucleosome assembly represents a daunting task for S-phase cells, partly because cells need to rapidly package nascent DNA into nucleosomes while avoiding the generation of excess histones. Consequently, cells have evolved a number of nucleosome assembly factors and regulatory mechanisms that collectively function to coordinate the rates of histone and DNA synthesis during both normal cell cycle progression and in response to conditions that interfere with DNA replication.
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Affiliation(s)
- Akash Gunjan
- Cancer Research UK, London Research Institute, Clare Hall Laboratories, Blanche Lane, South Mimms, Hertfordshire EN6 3LD, United Kingdom
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42
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Lusser A, Urwin DL, Kadonaga JT. Distinct activities of CHD1 and ACF in ATP-dependent chromatin assembly. Nat Struct Mol Biol 2005; 12:160-6. [PMID: 15643425 DOI: 10.1038/nsmb884] [Citation(s) in RCA: 225] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2004] [Accepted: 11/22/2004] [Indexed: 11/09/2022]
Abstract
CHD1 is a chromodomain-containing protein in the SNF2-like family of ATPases. Here we show that CHD1 exists predominantly as a monomer and functions as an ATP-utilizing chromatin assembly factor. This reaction involves purified CHD1, NAP1 chaperone, core histones and relaxed DNA. CHD1 catalyzes the ATP-dependent transfer of histones from the NAP1 chaperone to the DNA by a processive mechanism that yields regularly spaced nucleosomes. The comparative analysis of CHD1 and ACF revealed that CHD1 assembles chromatin with a shorter nucleosome repeat length than ACF. In addition, ACF, but not CHD1, can assemble chromatin containing histone H1, which is involved in the formation of higher-order chromatin structure and transcriptional repression. These results suggest a role for CHD1 in the assembly of active chromatin and a function of ACF in the assembly of repressive chromatin.
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Affiliation(s)
- Alexandra Lusser
- Section of Molecular Biology, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0347, USA
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Glowczewski L, Waterborg JH, Berman JG. Yeast chromatin assembly complex 1 protein excludes nonacetylatable forms of histone H4 from chromatin and the nucleus. Mol Cell Biol 2005; 24:10180-92. [PMID: 15542829 PMCID: PMC529027 DOI: 10.1128/mcb.24.23.10180-10192.2004] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In yeast, the establishment and maintenance of a transcriptionally silent chromatin state are dependent upon the acetylation state of the N terminus of histone proteins. Histone H4 proteins that contain mutations in N-terminal lysines disrupt heterochromatin and result in yeast that cannot mate. Introduction of a wild-type copy of histone H4 restores mating, despite the presence of the mutant protein, suggesting that mutant H4 protein is either excluded from, or tolerated in, chromatin. To understand how the cell differentiates wild-type histone and mutant histone in which the four N-terminal lysines were replaced with alanine (H4-4A), we analyzed silencing, growth phenotypes, and the histone composition of chromatin in yeast strains coexpressing equal amounts of wild-type and mutant H4 proteins (histone H4 heterozygote). We found that histone H4 heterozygotes have defects in heterochromatin silencing and growth, implying that mutations in H4 are not completely recessive. Nuclear preparations from histone H4 heterozygotes contained less mutant H4 than wild-type H4, consistent with the idea that cells exclude some of the mutant histone. Surprisingly, the N-terminal nuclear localization signal of H4-4A fused to green fluorescent protein was defective in nuclear localization, while a mutant in which the four lysines were replaced with arginine (H4-4R) appeared to have normal nuclear import, implying a role for the charged state of the acetylatable lysines in the nuclear import of histones. The biased partial exclusion of H4-4A was dependent upon Cac1p, the largest subunit of yeast chromatin assembly factor 1 (CAF-1), as well as upon the karyopherin Kap123p, but was independent of Cac2p, another CAF-1 component, and other chromatin assembly proteins (Hir3p, Nap1p, and Asf1p). We conclude that N-terminal lysines of histone H4 are important for efficient histone nuclear import. In addition, our data support a model whereby Cac1p and Kap123 cooperate to ensure that only appropriately acetylated histone H4 proteins are imported into the nucleus.
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Affiliation(s)
- Lynn Glowczewski
- Department of Genetics, Cell Biology and Development, University of Minnesota, 6-170 MCB Building, 420 Washington Ave. SE, Minneapolis, MN 55455, USA
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Schwabish MA, Struhl K. Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol Cell Biol 2005; 24:10111-7. [PMID: 15542822 PMCID: PMC529037 DOI: 10.1128/mcb.24.23.10111-10117.2004] [Citation(s) in RCA: 301] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Biochemical experiments indicate that transcriptional elongation by RNA polymerase II (Pol II) is inhibited by nucleosomes and hence requires chromatin-modifying activities. Here, we examine the fate of histones upon passage of elongating Pol II in vivo. Histone density throughout the entire Saccharomyces cerevisiae GAL10 coding region is inversely correlated with Pol II association and transcriptional activity, suggesting that the elongating Pol II machinery efficiently evicts core histones from the DNA. Furthermore, new histones appear to be deposited onto DNA less than 1 min after passage of Pol II. Transcription-dependent deposition of histones requires the FACT complex that travels with elongating Pol II. Our results suggest that Pol II transcription generates a highly dynamic equilibrium of histone eviction and histone deposition and that there is significant histone exchange throughout most of the yeast genome within a single cell cycle.
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Affiliation(s)
- Marc A Schwabish
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
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Rodríguez-Campos A, Koop R, Faraudo S, Beato M. Transcriptionally competent chromatin assembled with exogenous histones in a yeast whole cell extract. Nucleic Acids Res 2004; 32:e111. [PMID: 15282330 PMCID: PMC506827 DOI: 10.1093/nar/gnh107] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We describe a cell-free chromatin assembly system derived from the yeast Saccharomyces cerevisiae, which efficiently packages DNA into minichromosomes in a reaction dependent on exogenous core histones and an ATP-regenerating system. Both supercoiled and relaxed plasmid DNA serve as templates for nucleosomal loading in a gradual process that takes at least 6 h for completion at 30 degrees C. Micrococcal nuclease digestion of the assembled minichromosomes displays an extended nucleosomal ladder with a repeat length of 165 bp. The purified minichromosomes contain the four core histones in stoichiometric proportion and exhibit phased nucleosomes over the mouse mammary tumour virus (MMTV) promoter. The progesterone receptor and NF1 synergize on these minichromosomes resulting in efficient cell-free transcription. The ease of manipulation and the potential use of yeast strains carrying mutations in the chromatin handling machinery make this system suitable for detailed mechanistic studies.
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Affiliation(s)
- Antonio Rodríguez-Campos
- CRG, Centre de Regulació Genòmica, Universitat Pompeu Fabra (UPF), Passeig Marítim, 37-49, 08003 Barcelona, Spain
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Korber P, Hörz W. In vitro assembly of the characteristic chromatin organization at the yeast PHO5 promoter by a replication-independent extract system. J Biol Chem 2004; 279:35113-20. [PMID: 15192097 DOI: 10.1074/jbc.m405446200] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
An extensive set of analyses of the yeast PHO5 gene, mostly performed in vivo, has made this gene a model for the role of chromatin structure in gene regulation. In the repressed state, the PHO5 promoter shows a characteristic chromatin organization with four positioned nucleosomes and a short hypersensitive site. So far the basis for this nucleosome positioning has remained unresolved. We have therefore decided to complement the in vivo studies by an in vitro approach. As a first step, we have asked whether the characteristic PHO5 promoter chromatin structure depends on the cellular context including replication or higher order nuclear chromatin organization or whether it can be reconstituted in vitro in a cell-free system. To this end we have established an in vitro chromatin assembly system based on yeast extracts. It is capable of generating extensive regular nucleosomal arrays with physiological spacing. Assembly requires supplementation with exogenous histones and is dependent on energy leading to chromatin with dynamic properties due to ATP-dependent activities of the extract. Using the PHO5 promoter sequence as template in this replication independent system, we obtain a nucleosomal pattern over the PHO5 promoter region that is very similar to the in vivo pattern of the repressed state. This shows that the chromatin structure at the PHO5 promoter represents a self-organizing system in cell-free yeast extracts and provides a promising substrate for in vitro studies with a direct in vivo correlate.
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Affiliation(s)
- Philipp Korber
- Adolf-Butenandt-Institut, University of Munich, Schillerstrasse 44, 80336 Munich, Germany
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47
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Abstract
The regulation of transcription elongation within the context of chromatin is a topic of great interest. Even though chromatin presents a barrier to transcription by the PolII machinery in vitro, this process is rather efficient in vivo. Importantly, the chromatin structure of the actively transcribed genes is altered as part of this process. A large number of factors implicated in the control of transcript elongation have been identified through genetics, biochemistry and targeted proteomics approaches. However the precise roles and mechanisms of action of these factors remain obscure. A significant advance came about this past year with the elucidation of the roles of FACT and Spt6 in transcription elongation. These factors facilitate PolII passage through chromatin by destabilizing the nucleosome structure as well as reassemble nucleosomes traversed by PolII.
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Affiliation(s)
- Rimma Belotserkovskaya
- Howard Hughes Medical Institute, Division of Nucleic Acids Enzymology, Department of Biochemistry, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, Piscataway, New Jersey 08854, USA
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