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Banko P, Okimune KI, Nagy SK, Hamasaki A, Morishita R, Onouchi H, Takasuka TE. In vitro co-expression chromatin assembly and remodeling platform for plant histone variants. Sci Rep 2024; 14:936. [PMID: 38195981 PMCID: PMC10776871 DOI: 10.1038/s41598-024-51460-6] [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: 05/03/2023] [Accepted: 01/05/2024] [Indexed: 01/11/2024] Open
Abstract
Histone variants play a central role in shaping the chromatin landscape in plants, yet, how their distinct combinations affect nucleosome properties and dynamics is still largely elusive. To address this, we developed a novel chromatin assembly platform for Arabidopsis thaliana, using wheat germ cell-free protein expression. Four canonical histones and five reported histone variants were used to assemble twelve A. thaliana nucleosome combinations. Seven combinations were successfully reconstituted and confirmed by supercoiling and micrococcal nuclease (MNase) assays. The effect of the remodeling function of the CHR11-DDR4 complex on these seven combinations was evaluated based on the nucleosome repeat length and nucleosome spacing index obtained from the MNase ladders. Overall, the current study provides a novel method to elucidate the formation and function of a diverse range of nucleosomes in plants.
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Affiliation(s)
- Petra Banko
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Kei-Ichi Okimune
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
- Graduate School of Global Food Resources, Hokkaido University, Sapporo, 060-0809, Japan
| | - Szilvia K Nagy
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
- Department of Molecular Biology, Institute of Biochemistry and Molecular Biology, Semmelweis University, Budapest, 1094, Hungary
| | | | - Ryo Morishita
- CellFree Sciences Co., Ltd, Matsuyama, 790-8577, Japan
| | - Hitoshi Onouchi
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan
| | - Taichi E Takasuka
- Research Faculty of Agriculture, Hokkaido University, Sapporo, 060-8589, Japan.
- Graduate School of Global Food Resources, Hokkaido University, Sapporo, 060-0809, Japan.
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2
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Kadonaga JT. Perspectives on ATP-dependent chromatin remodeling. Enzymes 2023; 53:1-6. [PMID: 37748834 PMCID: PMC10552720 DOI: 10.1016/bs.enz.2023.03.002] [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] [Indexed: 09/27/2023]
Abstract
Nucleosomes are intrinsically immobile, and thus, ATP-dependent chromatin remodeling factors are needed to alter nucleosomes to facilitate DNA-directed processes such as transcription. More generally, chromatin remodeling factors mediate chromatin dynamics, which encompasses nucleosome assembly, movement, and disruption as well as histone exchange. Here, I present selected thoughts and perspectives on the past, present, and future of these fascinating ATP-driven motor proteins.
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Affiliation(s)
- James T Kadonaga
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA, United States.
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3
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Trujillo JT, Long J, Aboelnour E, Ogas J, Wisecaver JH. CHD chromatin remodeling protein diversification yields novel clades and domains absent in classic model organisms. Genome Biol Evol 2022; 14:6582301. [PMID: 35524943 PMCID: PMC9113485 DOI: 10.1093/gbe/evac066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2022] [Indexed: 11/20/2022] Open
Abstract
Chromatin remodelers play a fundamental role in the assembly of chromatin, regulation of transcription, and DNA repair. Biochemical and functional characterizations of the CHD family of chromatin remodelers from a variety of model organisms have shown that these remodelers participate in a wide range of activities. However, because the evolutionary history of CHD homologs is unclear, it is difficult to predict which of these activities are broadly conserved and which have evolved more recently in individual eukaryotic lineages. Here, we performed a comprehensive phylogenetic analysis of 8,042 CHD homologs from 1,894 species to create a model for the evolution of this family across eukaryotes with a particular focus on the timing of duplications that gave rise to the diverse copies observed in plants, animals, and fungi. Our analysis confirms that the three major subfamilies of CHD remodelers originated in the eukaryotic last common ancestor, and subsequent losses occurred independently in different lineages. Improved taxon sampling identified several subfamilies of CHD remodelers in plants that were absent or highly divergent in the model plant Arabidopsis thaliana. Whereas the timing of CHD subfamily expansions in vertebrates corresponds to whole genome duplication events, the mechanisms underlying CHD diversification in land plants appear more complicated. Analysis of protein domains reveals that CHD remodeler diversification has been accompanied by distinct transitions in domain architecture, contributing to the functional differences observed between these remodelers. This study demonstrates the importance of proper taxon sampling when studying ancient evolutionary events to prevent misinterpretation of subsequent lineage-specific changes and provides an evolutionary framework for functional and comparative analysis of this critical chromatin remodeler family across eukaryotes.
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Affiliation(s)
- Joshua T Trujillo
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jiaxin Long
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Erin Aboelnour
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA.,Helmholtz Pioneer Campus, Helmholtz Zentrum München, 85764 Neuherberg, Germany
| | - Joseph Ogas
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
| | - Jennifer H Wisecaver
- Center for Plant Biology and Department of Biochemistry, Purdue University, West Lafayette, Indiana 47907, USA
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4
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Okimune K, Hataya S, Matsumoto K, Ushirogata K, Banko P, Takeda S, Takasuka TE. Histone chaperone-mediated co-expression assembly of tetrasomes and nucleosomes. FEBS Open Bio 2021; 11:2912-2920. [PMID: 34614293 PMCID: PMC8564334 DOI: 10.1002/2211-5463.13311] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/16/2021] [Accepted: 10/05/2021] [Indexed: 11/07/2022] Open
Abstract
The nucleosome, a basic unit of chromatin found in all eukaryotes, is thought to be assembled through the orchestrated activity of several histone chaperones and chromatin assembly factors in a stepwise manner, proceeding from tetrasome assembly, to H2A/H2B deposition, and finally to formation of the mature nucleosome. In this study, we demonstrate chaperone-mediated assembly of both tetrasomes and nucleosomes on the well-defined Widom 601 positioning sequence using a co-expression/reconstitution wheat germ cell-free system. The purified tetrasomes and nucleosomes were positioned around the center of a given sequence. The heights and diameters were measured by atomic force microscopy. Together with the reported unmodified native histones produced by the wheat germ cell-free platform, our method is expected to be useful for downstream applications in the field of chromatin research.
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Affiliation(s)
- Kei‐ichi Okimune
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Shogo Hataya
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kazuki Matsumoto
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Kanako Ushirogata
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
| | - Petra Banko
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
| | - Seiji Takeda
- Faculty of Pharmaceutical SciencesHokkaido University of ScienceSapporoJapan
| | - Taichi E. Takasuka
- Research Faculty of AgricultureHokkaido UniversitySapporoJapan
- Graduate School of Global Food ResourcesHokkaido UniversitySapporoJapan
- Global Institute for Collaborative Research and EducationHokkaido UniversitySapporoJapan
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5
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Schoberleitner I, Bauer I, Huang A, Andreyeva EN, Sebald J, Pascher K, Rieder D, Brunner M, Podhraski V, Oemer G, Cázarez-García D, Rieder L, Keller MA, Winkler R, Fyodorov DV, Lusser A. CHD1 controls H3.3 incorporation in adult brain chromatin to maintain metabolic homeostasis and normal lifespan. Cell Rep 2021; 37:109769. [PMID: 34610319 PMCID: PMC8607513 DOI: 10.1016/j.celrep.2021.109769] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 07/26/2021] [Accepted: 09/08/2021] [Indexed: 01/31/2023] Open
Abstract
The ATP-dependent chromatin remodeling factor CHD1 is essential for the assembly of variant histone H3.3 into paternal chromatin during sperm chromatin remodeling in fertilized eggs. It remains unclear, however, if CHD1 has a similar role in normal diploid cells. Using a specifically tailored quantitative mass spectrometry approach, we show that Chd1 disruption results in reduced H3.3 levels in heads of Chd1 mutant flies. Chd1 deletion perturbs brain chromatin structure in a similar way as H3.3 deletion and leads to global de-repression of transcription. The physiological consequences are reduced food intake, metabolic alterations, and shortened lifespan. Notably, brain-specific CHD1 expression rescues these phenotypes. We further demonstrate a strong genetic interaction between Chd1 and H3.3 chaperone Hira. Thus, our findings establish CHD1 as a factor required for the assembly of H3.3-containing chromatin in adult cells and suggest a crucial role for CHD1 in the brain as a regulator of organismal health and longevity.
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Affiliation(s)
- Ines Schoberleitner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Ingo Bauer
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Anming Huang
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Evgeniya N Andreyeva
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Johanna Sebald
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Katharina Pascher
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Dietmar Rieder
- Institute of Bioinformatics, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Melanie Brunner
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Valerie Podhraski
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Gregor Oemer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Daniel Cázarez-García
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato 36824, Mexico
| | - Leila Rieder
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Markus A Keller
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck 6020, Austria
| | - Robert Winkler
- Department of Biotechnology and Biochemistry, Cinvestav Unidad Irapuato, Irapuato 36824, Mexico
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Alexandra Lusser
- Institute of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck 6020, Austria.
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6
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Oberbeckmann E, Niebauer V, Watanabe S, Farnung L, Moldt M, Schmid A, Cramer P, Peterson CL, Eustermann S, Hopfner KP, Korber P. Ruler elements in chromatin remodelers set nucleosome array spacing and phasing. Nat Commun 2021; 12:3232. [PMID: 34050140 PMCID: PMC8163753 DOI: 10.1038/s41467-021-23015-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 03/13/2021] [Indexed: 01/09/2023] Open
Abstract
Arrays of regularly spaced nucleosomes dominate chromatin and are often phased by alignment to reference sites like active promoters. How the distances between nucleosomes (spacing), and between phasing sites and nucleosomes are determined remains unclear, and specifically, how ATP-dependent chromatin remodelers impact these features. Here, we used genome-wide reconstitution to probe how Saccharomyces cerevisiae ATP-dependent remodelers generate phased arrays of regularly spaced nucleosomes. We find that remodelers bear a functional element named the 'ruler' that determines spacing and phasing in a remodeler-specific way. We use structure-based mutagenesis to identify and tune the ruler element residing in the Nhp10 and Arp8 modules of the INO80 remodeler complex. Generally, we propose that a remodeler ruler regulates nucleosome sliding direction bias in response to (epi)genetic information. This finally conceptualizes how remodeler-mediated nucleosome dynamics determine stable steady-state nucleosome positioning relative to other nucleosomes, DNA bound factors, DNA ends and DNA sequence elements.
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Affiliation(s)
- Elisa Oberbeckmann
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Vanessa Niebauer
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Shinya Watanabe
- Program of Molecular Medicine, University of Massachusetts, Worcester, MA, USA
| | - Lucas Farnung
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
- Department of Cell Biology, Blavatnik Institute, Harvard Medical School, Boston, USA
| | - Manuela Moldt
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Andrea Schmid
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany
| | - Patrick Cramer
- Department of Molecular Biology, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts, Worcester, MA, USA
| | - Sebastian Eustermann
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
- European Molecular Biology Laboratory (EMBL), Structural and Computational Biology Unit, Heidelberg, Germany.
| | - Karl-Peter Hopfner
- Gene Center, Ludwig-Maximilians-Universität München, Munich, Germany.
- Department of Biochemistry, Faculty of Chemistry and Pharmacy, Ludwig-Maximilians-Universität München, Munich, Germany.
| | - Philipp Korber
- Division of Molecular Biology, Biomedical Center (BMC), Faculty of Medicine, LMU Munich, Martinsried, Germany.
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7
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Clapier CR. Sophisticated Conversations between Chromatin and Chromatin Remodelers, and Dissonances in Cancer. Int J Mol Sci 2021; 22:5578. [PMID: 34070411 PMCID: PMC8197500 DOI: 10.3390/ijms22115578] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/18/2021] [Accepted: 05/18/2021] [Indexed: 01/13/2023] Open
Abstract
The establishment and maintenance of genome packaging into chromatin contribute to define specific cellular identity and function. Dynamic regulation of chromatin organization and nucleosome positioning are critical to all DNA transactions-in particular, the regulation of gene expression-and involve the cooperative action of sequence-specific DNA-binding factors, histone modifying enzymes, and remodelers. Remodelers are molecular machines that generate various chromatin landscapes, adjust nucleosome positioning, and alter DNA accessibility by using ATP binding and hydrolysis to perform DNA translocation, which is highly regulated through sophisticated structural and functional conversations with nucleosomes. In this review, I first present the functional and structural diversity of remodelers, while emphasizing the basic mechanism of DNA translocation, the common regulatory aspects, and the hand-in-hand progressive increase in complexity of the regulatory conversations between remodelers and nucleosomes that accompanies the increase in challenges of remodeling processes. Next, I examine how, through nucleosome positioning, remodelers guide the regulation of gene expression. Finally, I explore various aspects of how alterations/mutations in remodelers introduce dissonance into the conversations between remodelers and nucleosomes, modify chromatin organization, and contribute to oncogenesis.
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Affiliation(s)
- Cedric R Clapier
- Department of Oncological Sciences & Howard Hughes Medical Institute, Huntsman Cancer Institute, University of Utah School of Medicine, 2000 Circle of Hope, Salt Lake City, UT 84112, USA
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8
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Cruz-Becerra G, Kadonaga JT. Reconstitution of Chromatin by Stepwise Salt Dialysis. Bio Protoc 2021; 11:e3977. [PMID: 33889671 DOI: 10.21769/bioprotoc.3977] [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: 10/29/2020] [Revised: 02/05/2021] [Accepted: 02/24/2021] [Indexed: 11/02/2022] Open
Abstract
Chromatin, rather than plain DNA, is the natural substrate of the molecular machines that mediate DNA-directed processes in the nucleus. Chromatin can be reconstituted in vitro by using different methodologies. The salt dialysis method yields chromatin that consists of purified histones and DNA. This biochemically pure chromatin is well-suited for a wide range of applications. Here, we describe simple and straightforward protocols for the reconstitution of chromatin by stepwise salt dialysis and the analysis of the chromatin by the micrococcal nuclease (MNase) digestion assay. Chromatin that is reconstituted with this method can be used for efficient homology-directed repair (HDR)-mediated gene edited with the CRISPR-Cas9 system as well as for biochemical studies of chromatin dynamics and function.
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Affiliation(s)
- Grisel Cruz-Becerra
- Section of Molecular Biology, University of California San Diego, La Jolla, United States
| | - James T Kadonaga
- Section of Molecular Biology, University of California San Diego, La Jolla, United States
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9
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The yeast ISW1b ATP-dependent chromatin remodeler is critical for nucleosome spacing and dinucleosome resolution. Sci Rep 2021; 11:4195. [PMID: 33602956 PMCID: PMC7892562 DOI: 10.1038/s41598-021-82842-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/25/2021] [Indexed: 12/15/2022] Open
Abstract
Isw1 and Chd1 are ATP-dependent nucleosome-spacing enzymes required to establish regular arrays of phased nucleosomes near transcription start sites of yeast genes. Cells lacking both Isw1 and Chd1 have extremely disrupted chromatin, with weak phasing, irregular spacing and a propensity to form close-packed dinucleosomes. The Isw1 ATPase subunit occurs in two different remodeling complexes: ISW1a (composed of Isw1 and Ioc3) and ISW1b (composed of Isw1, Ioc2 and Ioc4). The Ioc4 subunit of ISW1b binds preferentially to the H3-K36me3 mark. Here we show that ISW1b is primarily responsible for setting nucleosome spacing and resolving close-packed dinucleosomes, whereas ISW1a plays only a minor role. ISW1b and Chd1 make additive contributions to dinucleosome resolution, such that neither enzyme is capable of resolving all dinucleosomes on its own. Loss of the Set2 H3-K36 methyltransferase partly phenocopies loss of Ioc4, resulting in increased dinucleosome levels with only a weak effect on nucleosome spacing, suggesting that Set2-mediated H3-K36 trimethylation contributes to ISW1b-mediated dinucleosome separation. The H4 tail domain is required for normal nucleosome spacing but not for dinucleosome resolution. We conclude that the nucleosome spacing and dinucleosome resolving activities of ISW1b and Chd1 are critical for normal global chromatin organisation.
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10
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The Role of Non-Catalytic Domains of Hrp3 in Nucleosome Remodeling. Int J Mol Sci 2021; 22:ijms22041793. [PMID: 33670267 PMCID: PMC7918567 DOI: 10.3390/ijms22041793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/23/2022] Open
Abstract
The Helicase-related protein 3 (Hrp3), an ATP-dependent chromatin remodeling enzyme from the CHD family, is crucial for maintaining global nucleosome occupancy in Schizosaccharomyces pombe (S. pombe). Although the ATPase domain of Hrp3 is essential for chromatin remodeling, the contribution of non-ATPase domains of Hrp3 is still unclear. Here, we investigated the role of non-ATPase domains using in vitro methods. In our study, we expressed and purified recombinant S. pombe histone proteins, reconstituted them into histone octamers, and assembled nucleosome core particles. Using reconstituted nucleosomes and affinity-purified wild type and mutant Hrp3 from S. pombe we created a homogeneous in vitro system to evaluate the ATP hydrolyzing capacity of truncated Hrp3 proteins. We found that all non-ATPase domain deletions (∆chromo, ∆SANT, ∆SLIDE, and ∆coupling region) lead to reduced ATP hydrolyzing activities in vitro with DNA or nucleosome substrates. Only the coupling region deletion showed moderate stimulation of ATPase activity with the nucleosome. Interestingly, affinity-purified Hrp3 showed co-purification with all core histones suggesting a strong association with the nucleosomes in vivo. However, affinity-purified Hrp3 mutant with SANT and coupling regions deletion showed complete loss of interactions with the nucleosomes, while SLIDE and chromodomain deletions reduced Hrp3 interactions with the nucleosomes. Taken together, nucleosome association and ATPase stimulation by DNA or nucleosomes substrate suggest that the enzymatic activity of Hrp3 is fine-tuned by unique contributions of all four non-catalytic domains.
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11
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Nucleosome Positioning and Spacing: From Mechanism to Function. J Mol Biol 2021; 433:166847. [PMID: 33539878 DOI: 10.1016/j.jmb.2021.166847] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Revised: 01/16/2021] [Accepted: 01/22/2021] [Indexed: 02/08/2023]
Abstract
Eukaryotes associate their genomes with histone proteins, forming nucleosome particles. Nucleosomes regulate and protect the genetic information. They often assemble into evenly spaced arrays of nucleosomes. These regular nucleosome arrays cover significant portions of the genome, in particular over genes. The presence of these evenly spaced nucleosome arrays is highly conserved throughout the entire eukaryotic domain. Here, we review the mechanisms behind the establishment of this primary structure of chromatin with special emphasis on the biogenesis of evenly spaced nucleosome arrays. We highlight the roles that transcription, nucleosome remodelers, DNA sequence, and histone density play towards the formation of evenly spaced nucleosome arrays and summarize our current understanding of their cellular functions. We end with key unanswered questions that remain to be explored to obtain an in-depth understanding of the biogenesis and function of the nucleosome landscape.
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12
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Interplay among ATP-Dependent Chromatin Remodelers Determines Chromatin Organisation in Yeast. BIOLOGY 2020; 9:biology9080190. [PMID: 32722483 PMCID: PMC7466152 DOI: 10.3390/biology9080190] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/15/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023]
Abstract
Cellular DNA is packaged into chromatin, which is composed of regularly-spaced nucleosomes with occasional gaps corresponding to active regulatory elements, such as promoters and enhancers, called nucleosome-depleted regions (NDRs). This chromatin organisation is primarily determined by the activities of a set of ATP-dependent remodeling enzymes that are capable of moving nucleosomes along DNA, or of evicting nucleosomes altogether. In yeast, the nucleosome-spacing enzymes are ISW1 (Imitation SWitch protein 1), Chromodomain-Helicase-DNA-binding (CHD)1, ISW2 (Imitation SWitch protein 2) and INOsitol-requiring 80 (INO80); the nucleosome eviction enzymes are the SWItching/Sucrose Non-Fermenting (SWI/SNF) family, the Remodeling the Structure of Chromatin (RSC) complexes and INO80. We discuss the contributions of each set of enzymes to chromatin organisation. ISW1 and CHD1 are the major spacing enzymes; loss of both enzymes results in major chromatin disruption, partly due to the appearance of close-packed di-nucleosomes. ISW1 and CHD1 compete to set nucleosome spacing on most genes. ISW1 is dominant, setting wild type spacing, whereas CHD1 sets short spacing and may dominate on highly-transcribed genes. We propose that the competing remodelers regulate spacing, which in turn controls the binding of linker histone (H1) and therefore the degree of chromatin folding. Thus, genes with long spacing bind more H1, resulting in increased chromatin compaction. RSC, SWI/SNF and INO80 are involved in NDR formation, either directly by nucleosome eviction or repositioning, or indirectly by affecting the size of the complex that resides in the NDR. The nature of this complex is controversial: some suggest that it is a RSC-bound “fragile nucleosome”, whereas we propose that it is a non-histone transcription complex. In either case, this complex appears to serve as a barrier to nucleosome formation, resulting in the formation of phased nucleosomal arrays on both sides.
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13
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Kang H, Wu D, Fan T, Zhu Y. Activities of Chromatin Remodeling Factors and Histone Chaperones and Their Effects in Root Apical Meristem Development. Int J Mol Sci 2020; 21:ijms21030771. [PMID: 31991579 PMCID: PMC7038114 DOI: 10.3390/ijms21030771] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/22/2020] [Accepted: 01/23/2020] [Indexed: 01/01/2023] Open
Abstract
Eukaryotic genes are packaged into dynamic but stable chromatin structures to deal with transcriptional reprogramming and inheritance during development. Chromatin remodeling factors and histone chaperones are epigenetic factors that target nucleosomes and/or histones to establish and maintain proper chromatin structures during critical physiological processes such as DNA replication and transcriptional modulation. Root apical meristems are vital for plant root development. Regarding the well-characterized transcription factors involved in stem cell proliferation and differentiation, there is increasing evidence of the functional implications of epigenetic regulation in root apical meristem development. In this review, we focus on the activities of chromatin remodeling factors and histone chaperones in the root apical meristems of the model plant species Arabidopsis and rice.
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14
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Xiong J, Chen S, Pang N, Deng X, Yang L, He F, Wu L, Chen C, Yin F, Peng J. Neurological Diseases With Autism Spectrum Disorder: Role of ASD Risk Genes. Front Neurosci 2019; 13:349. [PMID: 31031587 PMCID: PMC6470315 DOI: 10.3389/fnins.2019.00349] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 03/26/2019] [Indexed: 02/06/2023] Open
Abstract
Autism spectrum disorder (ASD) is frequently comorbid with other neurological disorders such as intellectual disability (ID) or global development delay (GDD) and epilepsy. The pathogenesis of ASD is complex. So far, studies have identified more than 1000 ASD risk genes. Most of them were also reported to relate with other neurological diseases, and only several of them have been confirmed as pathogenic genes for autism. Little is known about the roles of these risk genes in neurological diseases with ASD. In the present study, we recruited a cohort of 158 neurological disorder probands with 163 variants of 48 ASD risk genes. Of these, 50 individuals (31.6%) were diagnosed with ASD. In the ASD patient subset, we identified several rarely reported candidate genes including DOLK, USH2A, and HUWE1. In a comparison of patients with neurological disorders with and without ASD, we found that ID/GDD was frequently comorbid with ASD whereas epilepsy was more common in the non-ASD group. Statistical analyses of all possible risk factors implicated that variants in synaptic genes, especially non-voltage-gated ion channel genes and in transcriptional and chromosome genes were related to ASD, but none of the investigated environmental factors was. Our results are useful for the future diagnosis and prognosis of patients with neurological disorders and emphasize the utility of genetic screening.
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Affiliation(s)
- Juan Xiong
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Shimeng Chen
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Nan Pang
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Xiaolu Deng
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Lifen Yang
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fang He
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Liwen Wu
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Chen Chen
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Fei Yin
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
| | - Jing Peng
- Departmen of Pediatrics, Xiangya Hospital, Central South University, Changsha, China.,Hunan Intellectual and Developmental Disabilities Research Center, Changsha, China
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15
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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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16
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Schoberleitner I, Mutti A, Sah A, Wille A, Gimeno-Valiente F, Piatti P, Kharitonova M, Torres L, López-Rodas G, Liu JJ, Singewald N, Schwarzer C, Lusser A. Role for Chromatin Remodeling Factor Chd1 in Learning and Memory. Front Mol Neurosci 2019; 12:3. [PMID: 30728766 PMCID: PMC6351481 DOI: 10.3389/fnmol.2019.00003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/08/2019] [Indexed: 12/21/2022] Open
Abstract
Precise temporal and spatial regulation of gene expression in the brain is a prerequisite for cognitive processes such as learning and memory. Epigenetic mechanisms that modulate the chromatin structure have emerged as important regulators in this context. While posttranslational modification of histones or the modification of DNA bases have been examined in detail in many studies, the role of ATP-dependent chromatin remodeling factors (ChRFs) in learning- and memory-associated gene regulation has largely remained obscure. Here we present data that implicate the highly conserved chromatin assembly and remodeling factor Chd1 in memory formation and the control of immediate early gene (IEG) response in the hippocampus. We used various paradigms to assess short-and long-term memory in mice bearing a mutated Chd1 gene that gives rise to an N-terminally truncated protein. Our data demonstrate that the Chd1 mutation negatively affects long-term object recognition and short- and long-term spatial memory. We found that Chd1 regulates hippocampal expression of the IEG early growth response 1 (Egr1) and activity-regulated cytoskeleton-associated (Arc) but not cFos and brain derived neurotrophic factor (Bdnf), because the Chd1-mutation led to dysregulation of Egr1 and Arc expression in naive mice and in mice analyzed at different stages of object location memory (OLM) testing. Of note, Chd1 likely regulates Egr1 in a direct manner, because chromatin immunoprecipitation (ChIP) assays revealed enrichment of Chd1 upon stimulation at the Egr1 genomic locus in the hippocampus and in cultured cells. Together these data support a role for Chd1 as a critical regulator of molecular mechanisms governing memory-related processes, and they show that this function involves the N-terminal serine-rich region of the protein.
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Affiliation(s)
- Ines Schoberleitner
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Anna Mutti
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Anupam Sah
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Alexandra Wille
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Francisco Gimeno-Valiente
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Paolo Piatti
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
| | - Maria Kharitonova
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Luis Torres
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Gerardo López-Rodas
- Institute of Health Research, INCLIVA, and Department of Biochemistry and Molecular Biology, University of Valencia, Valencia, Spain
| | - Jeffrey J. Liu
- Department of Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Munich, Germany
| | - Nicolas Singewald
- Department of Pharmacology and Toxicology, Institute of Pharmacy and Centre for Molecular Biosciences (CMBI), Leopold-Franzens University of Innsbruck, Innsbruck, Austria
| | - Christoph Schwarzer
- Department of Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexandra Lusser
- Division of Molecular Biology, Biocenter, Medical University of Innsbruck, Innsbruck, Austria
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17
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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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18
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Abstract
Chromatin is a mighty consumer of cellular energy generated by metabolism. Metabolic status is efficiently coordinated with transcription and translation, which also feed back to regulate metabolism. Conversely, suppression of energy utilization by chromatin processes may serve to preserve energy resources for cell survival. Most of the reactions involved in chromatin modification require metabolites as their cofactors or coenzymes. Therefore, the metabolic status of the cell can influence the spectra of posttranslational histone modifications and the structure, density and location of nucleosomes, impacting epigenetic processes. Thus, transcription, translation, and DNA/RNA biogenesis adapt to cellular metabolism. In addition to dysfunctions of metabolic enzymes, imbalances between metabolism and chromatin activities trigger metabolic disease and life span alteration. Here, we review the synthesis of the metabolites and the relationships between metabolism and chromatin function. Furthermore, we discuss how the chromatin response feeds back to metabolic regulation in biological processes.
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Affiliation(s)
- Tamaki Suganuma
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;,
| | - Jerry L. Workman
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA;,
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19
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Fei J, Ishii H, Hoeksema MA, Meitinger F, Kassavetis GA, Glass CK, Ren B, Kadonaga JT. NDF, a nucleosome-destabilizing factor that facilitates transcription through nucleosomes. Genes Dev 2018; 32:682-694. [PMID: 29759984 PMCID: PMC6004073 DOI: 10.1101/gad.313973.118] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 04/11/2018] [Indexed: 12/22/2022]
Abstract
Our understanding of transcription by RNA polymerase II (Pol II) is limited by our knowledge of the factors that mediate this critically important process. Here we describe the identification of NDF, a nucleosome-destabilizing factor that facilitates Pol II transcription in chromatin. NDF has a PWWP motif, interacts with nucleosomes near the dyad, destabilizes nucleosomes in an ATP-independent manner, and facilitates transcription by Pol II through nucleosomes in a purified and defined transcription system as well as in cell nuclei. Upon transcriptional induction, NDF is recruited to the transcribed regions of thousands of genes and colocalizes with a subset of H3K36me3-enriched regions. Notably, the recruitment of NDF to gene bodies is accompanied by an increase in the transcript levels of many of the NDF-enriched genes. In addition, the global loss of NDF results in a decrease in the RNA levels of many genes. In humans, NDF is present at high levels in all tested tissue types, is essential in stem cells, and is frequently overexpressed in breast cancer. These findings indicate that NDF is a nucleosome-destabilizing factor that is recruited to gene bodies during transcriptional activation and facilitates Pol II transcription through nucleosomes.
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Affiliation(s)
- Jia Fei
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Haruhiko Ishii
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
| | - Marten A Hoeksema
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Franz Meitinger
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Christopher K Glass
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Department of Medicine, University of California at San Diego, La Jolla, California 92093, USA
| | - Bing Ren
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093, USA
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, California 92093, USA
- Center for Epigenomics, Institute of Genome Medicine, Moores Cancer Center, University of California at San Diego, La Jolla, California 92093, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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20
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Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nat Rev Mol Cell Biol 2017; 18:548-562. [PMID: 28537572 DOI: 10.1038/nrm.2017.47] [Citation(s) in RCA: 289] [Impact Index Per Article: 41.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in genomics technology have provided the means to probe myriad chromatin interactions at unprecedented spatial and temporal resolution. This has led to a profound understanding of nucleosome organization within the genome, revealing that nucleosomes are highly dynamic. Nucleosome dynamics are governed by a complex interplay of histone composition, histone post-translational modifications, nucleosome occupancy and positioning within chromatin, which are influenced by numerous regulatory factors, including general regulatory factors, chromatin remodellers, chaperones and polymerases. It is now known that these dynamics regulate diverse cellular processes ranging from gene transcription to DNA replication and repair.
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21
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Kubik S, Bruzzone MJ, Shore D. Establishing nucleosome architecture and stability at promoters: Roles of pioneer transcription factors and the RSC chromatin remodeler. Bioessays 2017; 39. [PMID: 28345796 DOI: 10.1002/bies.201600237] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Improvements in deep sequencing, together with methods to rapidly deplete essential transcription factors (TFs) and chromatin remodelers, have recently led to a more detailed picture of promoter nucleosome architecture in yeast and its relationship to transcriptional regulation. These studies revealed that ∼40% of all budding yeast protein-coding genes possess a unique promoter structure, where we propose that an unusually unstable nucleosome forms immediately upstream of the transcription start site (TSS). This "fragile" nucleosome (FN) promoter architecture relies on the combined action of the essential RSC (Remodels Structure of Chromatin) nucleosome remodeler and pioneer transcription factors (PTFs). FNs are associated with genes whose expression is high, coupled to cell growth, and characterized by low cell-to-cell variability (noise), suggesting that they may promote these features. Recent studies in metazoans suggest that the presence of dynamic nucleosomes upstream of the TSS at highly expressed genes may be conserved throughout evolution.
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Affiliation(s)
- Slawomir Kubik
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - Maria Jessica Bruzzone
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
| | - David Shore
- Department of Molecular Biology and Institute of Genetics and Genomics in Geneva (iGE3), University of Geneva, Geneva, Switzerland
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22
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Nodelman IM, Bleichert F, Patel A, Ren R, Horvath KC, Berger JM, Bowman GD. Interdomain Communication of the Chd1 Chromatin Remodeler across the DNA Gyres of the Nucleosome. Mol Cell 2017; 65:447-459.e6. [PMID: 28111016 DOI: 10.1016/j.molcel.2016.12.011] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/24/2016] [Accepted: 12/15/2016] [Indexed: 12/13/2022]
Abstract
Chromatin remodelers use a helicase-like ATPase motor to reposition and reorganize nucleosomes along genomic DNA. Yet, how the ATPase motor communicates with other remodeler domains in the context of the nucleosome has so far been elusive. Here, we report for the Chd1 remodeler a unique organization of domains on the nucleosome that reveals direct domain-domain communication. Site-specific cross-linking shows that the chromodomains and ATPase motor bind to adjacent SHL1 and SHL2 sites, respectively, on nucleosomal DNA and pack against the DNA-binding domain on DNA exiting the nucleosome. This domain arrangement spans the two DNA gyres of the nucleosome and bridges both ends of a wrapped, ∼90-bp nucleosomal loop of DNA, suggesting a means for nucleosome assembly. This architecture illustrates how Chd1 senses DNA outside the nucleosome core and provides a basis for nucleosome spacing and directional sliding away from transcription factor barriers.
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Affiliation(s)
- Ilana M Nodelman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Franziska Bleichert
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Ashok Patel
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Ren Ren
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - Kyle C Horvath
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA
| | - James M Berger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Gregory D Bowman
- T.C. Jenkins Department of Biophysics, Johns Hopkins University, 302 Jenkins Hall, 3400 N. Charles Street, Baltimore, MD 21218, USA.
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23
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Mohanty B, Helder S, Silva APG, Mackay JP, Ryan DP. The Chromatin Remodelling Protein CHD1 Contains a Previously Unrecognised C-Terminal Helical Domain. J Mol Biol 2016; 428:4298-4314. [PMID: 27591891 DOI: 10.1016/j.jmb.2016.08.028] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 08/25/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022]
Abstract
The packaging of eukaryotic DNA into nucleosomes, and the organisation of these nucleosomes into chromatin, plays a critical role in regulating all DNA-associated processes. Chromodomain helicase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodelling protein that is conserved throughout eukaryotes and has an ability to assemble and organise nucleosomes both in vitro and in vivo. This activity is involved in the regulation of transcription and is implicated in mammalian development and stem cell biology. CHD1 is classically depicted as possessing a pair of tandem chromodomains that directly precede a core catalytic helicase-like domain that is then followed by a SANT-SLIDE DNA-binding domain. Here, we have identified an additional conserved domain C-terminal to the SANT-SLIDE domain and determined its structure by multidimensional heteronuclear NMR spectroscopy. We have termed this domain the CHD1 helical C-terminal (CHCT) domain as it is comprised of five α-helices arranged in a variant helical bundle topology. CHCT has a conserved, positively charged surface and is able to bind DNA and nucleosomes. In addition, we have identified another group of proteins, the as yet uncharacterised C17orf64 proteins, as also containing a conserved CHCT domain. Our data provide new structural insights into the CHD1 enzyme family.
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Affiliation(s)
- Biswaranjan Mohanty
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia; Faculty of Pharmacy and Pharmaceutical Sciences, Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, Victoria, 3052, Australia
| | - Stephanie Helder
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia
| | - Ana P G Silva
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia
| | - Joel P Mackay
- School of Life and Environmental Sciences, The University of Sydney, Building G08, Corner Butlin Avenue and Maze Crescent, Sydney, New South Wales, 2006, Australia.
| | - Daniel P Ryan
- Department of Genome Sciences, The John Curtin School of Medical Research, Building 131, Garran Road, The Australian National University, Canberra, Australian Capital Territory, 2601, Australia.
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24
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Fei J, Torigoe SE, Brown CR, Khuong MT, Kassavetis GA, Boeger H, Kadonaga JT. The prenucleosome, a stable conformational isomer of the nucleosome. Genes Dev 2016; 29:2563-75. [PMID: 26680301 PMCID: PMC4699385 DOI: 10.1101/gad.272633.115] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Fei et al. show that the prenucleosome is a stable alternate conformational isomer of the nucleosome. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. Chromatin comprises nucleosomes as well as nonnucleosomal histone–DNA particles. Prenucleosomes are rapidly formed histone–DNA particles that can be converted into canonical nucleosomes by a motor protein such as ACF. Here we show that the prenucleosome is a stable conformational isomer of the nucleosome. It consists of a histone octamer associated with ∼80 base pair (bp) of DNA, which is located at a position that corresponds to the central 80 bp of a nucleosome core particle. Monomeric prenucleosomes with free flanking DNA do not spontaneously fold into nucleosomes but can be converted into canonical nucleosomes by an ATP-driven motor protein such as ACF or Chd1. In addition, histone H3K56, which is located at the DNA entry and exit points of a canonical nucleosome, is specifically acetylated by p300 in prenucleosomes relative to nucleosomes. Prenucleosomes assembled in vitro exhibit properties that are strikingly similar to those of nonnucleosomal histone–DNA particles in the upstream region of active promoters in vivo. These findings suggest that the prenucleosome, the only known stable conformational isomer of the nucleosome, is related to nonnucleosomal histone–DNA species in the cell.
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Affiliation(s)
- Jia Fei
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Sharon E Torigoe
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Christopher R Brown
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - Mai T Khuong
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - George A Kassavetis
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
| | - Hinrich Boeger
- Department of Molecular, Cell, and Developmental Biology, University of California at Santa Cruz, Santa Cruz, California 95064, USA
| | - James T Kadonaga
- Section of Molecular Biology, University of California at San Diego, La Jolla, California 92093, USA
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25
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Yadav T, Whitehouse I. Replication-Coupled Nucleosome Assembly and Positioning by ATP-Dependent Chromatin-Remodeling Enzymes. Cell Rep 2016; 15:715-723. [PMID: 27149855 DOI: 10.1016/j.celrep.2016.03.059] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 02/05/2016] [Accepted: 03/15/2016] [Indexed: 12/27/2022] Open
Abstract
During DNA replication, chromatin must be disassembled and faithfully reassembled on newly synthesized genomes. The mechanisms that govern the assembly of chromatin structures following DNA replication are poorly understood. Here, we exploited Okazaki fragment synthesis and other assays to study how nucleosomes are deposited and become organized in S. cerevisiae. We observe that global nucleosome positioning is quickly established on newly synthesized DNA in vivo. Importantly, we find that ATP-dependent chromatin-remodeling enzymes, Isw1 and Chd1, collaborate with histone chaperones to remodel nucleosomes as they are loaded behind a replication fork. Using a whole-genome sequencing approach, we determine that the positioning of newly deposited nucleosomes in vivo is specified by the combined actions of ATP-dependent chromatin-remodeling enzymes and select DNA-binding proteins. Altogether, our data provide in vivo evidence for coordinated "loading and remodeling" of nucleosomes behind the replication fork, allowing for rapid organization of chromatin during S phase.
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Affiliation(s)
- Tejas Yadav
- Weill Cornell Graduate School of Medical Sciences, 1300 York Avenue, New York, NY 10065, USA; Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10065, USA.
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26
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Horlbeck MA, Witkowsky LB, Guglielmi B, Replogle JM, Gilbert LA, Villalta JE, Torigoe SE, Tjian R, Weissman JS. Nucleosomes impede Cas9 access to DNA in vivo and in vitro. eLife 2016; 5. [PMID: 26987018 PMCID: PMC4861601 DOI: 10.7554/elife.12677] [Citation(s) in RCA: 254] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/16/2016] [Indexed: 12/23/2022] Open
Abstract
The prokaryotic CRISPR (clustered regularly interspaced palindromic repeats)-associated protein, Cas9, has been widely adopted as a tool for editing, imaging, and regulating eukaryotic genomes. However, our understanding of how to select single-guide RNAs (sgRNAs) that mediate efficient Cas9 activity is incomplete, as we lack insight into how chromatin impacts Cas9 targeting. To address this gap, we analyzed large-scale genetic screens performed in human cell lines using either nuclease-active or nuclease-dead Cas9 (dCas9). We observed that highly active sgRNAs for Cas9 and dCas9 were found almost exclusively in regions of low nucleosome occupancy. In vitro experiments demonstrated that nucleosomes in fact directly impede Cas9 binding and cleavage, while chromatin remodeling can restore Cas9 access. Our results reveal a critical role of eukaryotic chromatin in dictating the targeting specificity of this transplanted bacterial enzyme, and provide rules for selecting Cas9 target sites distinct from and complementary to those based on sequence properties. DOI:http://dx.doi.org/10.7554/eLife.12677.001 Many bacteria have a type of immune system known as CRISPR that can target and cut foreign DNA to protect it against viruses. Recently, the CRISPR system was adapted to allow scientists to easily manipulate the genome of humans and many other organisms. However, unlike the loosely organized DNA found in bacteria, the DNA that makes up the human genome is tightly packed and wrapped around complexes of proteins to form structures called nucleosomes. It was not clear whether the CRISPR system was able to effectively target the stretches of DNA in a nucleosome. In 2013, researchers developed a modified version of CRISPR, known as CRISPR interference, to block gene activity and in 2014 used it to systematically repress many of the genes in the human genome. Now, Horlbeck, Witkowsky et al. – who include several of the researchers from the 2014 work – have analyzed existing data for a specific type of human cell grown in the laboratory and found that CRISPR interference activity was strongest in certain areas around the start of each gene. However, CRISPR interference was much weaker in other areas of genes that coincided well with stretches of DNA that are known to often be bound by nucleosomes. Nucleosomes also appeared to block CRISPR editing, although the effects were less pronounced. Horlbeck, Witkowsky et al. then directly tested whether nucleosomes could prevent the CRISPR system from binding or modifying the DNA. When the individual components were mixed in test tubes, the CRISPR system could readily target “naked” DNA. However, it could not access nucleosome-bound DNA, unless an enzyme that can move nucleosomes along the DNA in the human genome was also added to the mix. These findings suggest one way that CRISPR can manipulate much of the human genome despite the widespread presence of nucleosomes. Future work will now aim to develop computational methods that take the positions of nucleosomes into account when picking DNA sites to target with CRISPR. DOI:http://dx.doi.org/10.7554/eLife.12677.002
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Affiliation(s)
- Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Lea B Witkowsky
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Benjamin Guglielmi
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Joseph M Replogle
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Jacqueline E Villalta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Sharon E Torigoe
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Robert Tjian
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,CIRM Center of Excellence, University of California, Berkeley, Berkeley, United States
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States.,California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States.,Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.,Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
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27
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Ocampo J, Chereji RV, Eriksson PR, Clark DJ. The ISW1 and CHD1 ATP-dependent chromatin remodelers compete to set nucleosome spacing in vivo. Nucleic Acids Res 2016; 44:4625-35. [PMID: 26861626 PMCID: PMC4889916 DOI: 10.1093/nar/gkw068] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/28/2016] [Indexed: 12/17/2022] Open
Abstract
Adenosine triphosphate-dependent chromatin remodeling machines play a central role in gene regulation by manipulating chromatin structure. Most genes have a nucleosome-depleted region at the promoter and an array of regularly spaced nucleosomes phased relative to the transcription start site. In vitro, the three known yeast nucleosome spacing enzymes (CHD1, ISW1 and ISW2) form arrays with different spacing. We used genome-wide nucleosome sequencing to determine whether these enzymes space nucleosomes differently in vivo We find that CHD1 and ISW1 compete to set the spacing on most genes, such that CHD1 dominates genes with shorter spacing and ISW1 dominates genes with longer spacing. In contrast, ISW2 plays a minor role, limited to transcriptionally inactive genes. Heavily transcribed genes show weak phasing and extreme spacing, either very short or very long, and are depleted of linker histone (H1). Genes with longer spacing are enriched in H1, which directs chromatin folding. We propose that CHD1 directs short spacing, resulting in eviction of H1 and chromatin unfolding, whereas ISW1 directs longer spacing, allowing H1 to bind and condense the chromatin. Thus, competition between the two remodelers to set the spacing on each gene may result in a highly dynamic chromatin structure.
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Affiliation(s)
- Josefina Ocampo
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Răzvan V Chereji
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter R Eriksson
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - David J Clark
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute for Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
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28
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Khuong MT, Fei J, Ishii H, Kadonaga JT. Prenucleosomes and Active Chromatin. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2016; 80:65-72. [PMID: 26767995 PMCID: PMC4915978 DOI: 10.1101/sqb.2015.80.027300] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Chromatin consists of nucleosomes as well as nonnucleosomal histone-containing particles. Here we describe the prenucleosome, which is a stable conformational isomer of the nucleosome that associates with ∼80 bp DNA. Prenucleosomes are formed rapidly upon the deposition of histones onto DNA and can be converted into canonical nucleosomes by an ATP-driven chromatin assembly factor such as ACF. Different lines of evidence reveal that there are prenucleosome-sized DNA-containing particles with histones in the upstream region of active promoters. Moreover, p300 acetylates histone H3K56 in prenucleosomes but not in nucleosomes, and H3K56 acetylation is found at active promoters and enhancers. These findings therefore suggest that there may be prenucleosomes or prenucleosome-like particles in the upstream region of active promoters. More generally, we postulate that prenucleosomes or prenucleosome-like particles are present at dynamic chromatin, whereas canonical nucleosomes are at static chromatin.
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Affiliation(s)
- Mai T Khuong
- Section of Molecular Biology, University of California, San Diego, La Jolla, California 92093-0347
| | - Jia Fei
- Section of Molecular Biology, University of California, San Diego, La Jolla, California 92093-0347
| | - Haruhiko Ishii
- Ludwig Institute for Cancer Research, San Diego Branch, La Jolla, California 92093-0653
| | - James T Kadonaga
- Section of Molecular Biology, University of California, San Diego, La Jolla, California 92093-0347
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29
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Abstract
Base Excision Repair (BER) is a conserved, intracellular DNA repair system that recognizes and removes chemically modified bases to insure genomic integrity and prevent mutagenesis. Aberrant BER has been tightly linked with a broad spectrum of human pathologies, such as several types of cancer, neurological degeneration, developmental abnormalities, immune dysfunction and aging. In the cell, BER must recognize and remove DNA lesions from the tightly condensed, protein-coated chromatin. Because chromatin is necessarily refractory to DNA metabolic processes, like transcription and replication, the compaction of the genomic material is also inhibitory to the repair systems necessary for its upkeep. Multiple ATP-dependent chromatin remodelling (ACR) complexes play essential roles in modulating the protein-DNA interactions within chromatin, regulating transcription and promoting activities of some DNA repair systems, including double-strand break repair and nucleotide excision repair. However, it remains unclear how BER operates in the context of chromatin, and if the chromatin remodelling processes that govern transcription and replication also actively regulate the efficiency of BER. In this review we highlight the emerging role of ACR in regulation of BER.
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Affiliation(s)
- John M Hinz
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164-7520, USA.
| | - Wioletta Czaja
- Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602-7229, USA
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30
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Shen Y, Devic M, Lepiniec L, Zhou DX. Chromodomain, Helicase and DNA-binding CHD1 protein, CHR5, are involved in establishing active chromatin state of seed maturation genes. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:811-20. [PMID: 25581843 DOI: 10.1111/pbi.12315] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Revised: 11/01/2014] [Accepted: 11/19/2014] [Indexed: 05/17/2023]
Abstract
Chromatin modification and remodelling are the basis for epigenetic regulation of gene expression. LEAFY COTYLEDON 1 (LEC1), LEAFY COTYLEDON 2 (LEC2), ABSCISIC ACID-INSENSITIVE 3 (ABI3) and FUSCA3 (FUS3) are key regulators of embryo development and are repressed after seed maturation. The chromatin remodelling CHD3 protein PICKLE (PKL) is involved in the epigenetic silencing of the genes. However, the chromatin mechanism that establishes the active state of these genes during early embryo development is not clear. We show that the Arabidopsis CHD1-related gene, CHR5, is activated during embryo development. Mutation of the gene reduced expression of LEC1, ABI3 and FUS3 in developing embryo and accumulation of seed storage proteins. Analysis of double mutants revealed an antagonistic function between CHR5 and PKL in embryo gene expression and seed storage protein accumulation, which likely acted on the promoter region of the genes. CHR5 was shown to be associated with the promoters of ABI3 and FUS3 and to be required to reduce nucleosome occupancy near the transcriptional start site. The results suggest that CHR5 is involved in establishing the active state of embryo regulatory genes by reducing nucleosomal barrier, which may be exploited to enhance seed protein production.
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Affiliation(s)
- Yuan Shen
- Université Paris-sud 11, Institut de Biologie des Plantes, CNRS, UMR8618, Saclay Plant Science, Orsay, France
| | - Martine Devic
- Régulation Epigénétique et Développement de la Graine, ERL 3500 CNRS-IRD UMR DIADE, IRD centre de Montpellier, Montpellier, France
| | - Loïc Lepiniec
- INRA, Institut Jean-Pierre Bourgin, Saclay Plant Science, Versailles, France
| | - Dao-Xiu Zhou
- Université Paris-sud 11, Institut de Biologie des Plantes, CNRS, UMR8618, Saclay Plant Science, Orsay, France
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31
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Han SK, Wu MF, Cui S, Wagner D. Roles and activities of chromatin remodeling ATPases in plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2015; 83:62-77. [PMID: 25977075 DOI: 10.1111/tpj.12877] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 05/04/2015] [Accepted: 05/06/2015] [Indexed: 05/18/2023]
Abstract
Chromatin remodeling ATPases and their associated complexes can alter the accessibility of the genome in the context of chromatin by using energy derived from the hydrolysis of ATP to change the positioning, occupancy and composition of nucleosomes. In animals and plants, these remodelers have been implicated in diverse processes ranging from stem cell maintenance and differentiation to developmental phase transitions and stress responses. Detailed investigation of their roles in individual processes has suggested a higher level of selectivity of chromatin remodeling ATPase activity than previously anticipated, and diverse mechanisms have been uncovered that can contribute to the selectivity. This review summarizes recent advances in understanding the roles and activities of chromatin remodeling ATPases in plants.
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Affiliation(s)
- Soon-Ki Han
- Howard Hughes Medical Institute and Department of Biology, University of Washington, Seattle, WA, 98195, USA
| | - Miin-Feng Wu
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Sujuan Cui
- Hebei Key Laboratory of Molecular Cell Biology, College of Life Science, Hebei Normal University, Shijiazhuang, 050024, China
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, PA, 19104, USA
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32
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MPE-seq, a new method for the genome-wide analysis of chromatin structure. Proc Natl Acad Sci U S A 2015; 112:E3457-65. [PMID: 26080409 DOI: 10.1073/pnas.1424804112] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
The analysis of chromatin structure is essential for the understanding of transcriptional regulation in eukaryotes. Here we describe methidiumpropyl-EDTA sequencing (MPE-seq), a method for the genome-wide characterization of chromatin that involves the digestion of nuclei withMPE-Fe(II) followed by massively parallel sequencing. Like micrococcal nuclease (MNase), MPE-Fe(II) preferentially cleaves the linker DNA between nucleosomes. However, there are differences in the cleavage of nuclear chromatin by MPE-Fe(II) relative to MNase. Most notably, immediately upstream of the transcription start site of active promoters, we frequently observed nucleosome-sized (141-190 bp) and subnucleosome-sized (such as 101-140 bp) peaks of digested chromatin fragments with MPE-seq but not with MNase-seq. These peaks also correlate with the presence of core histones and could thus be due, at least in part, to noncanonical chromatin structures such as labile nucleosome-like particles that have been observed in other contexts. The subnucleosome-sized MPE-seq peaks exhibit a particularly distinct association with active promoters. In addition, unlike MNase, MPE-Fe(II) cleaves nuclear DNA with little sequence bias. In this regard, we found that DNA sequences at RNA splice sites are hypersensitive to digestion by MNase but not by MPE-Fe(II). This phenomenon may have affected the analysis of nucleosome occupancy over exons. These findings collectively indicate that MPE-seq provides a unique and straightforward means for the genome-wide analysis of chromatin structure with minimal DNA sequence bias. In particular, the combined use of MPE-seq and MNase-seq enables the identification of noncanonical chromatin structures that are likely to be important for the regulation of gene expression.
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33
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Nucleosome spacing generated by ISWI and CHD1 remodelers is constant regardless of nucleosome density. Mol Cell Biol 2015; 35:1588-605. [PMID: 25733687 DOI: 10.1128/mcb.01070-14] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Accepted: 02/14/2015] [Indexed: 12/14/2022] Open
Abstract
Arrays of regularly spaced nucleosomes are a hallmark of chromatin, but it remains unclear how they are generated. Recent genome-wide studies, in vitro and in vivo, showed constant nucleosome spacing even if the histone concentration was experimentally reduced. This counters the long-held assumption that nucleosome density determines spacing and calls for factors keeping spacing constant regardless of nucleosome density. We call this a clamping activity. Here, we show in a purified system that ISWI- and CHD1-type nucleosome remodelers have a clamping activity such that they not only generate regularly spaced nucleosome arrays but also generate constant spacing regardless of nucleosome density. This points to a functionally attractive nucleosome interaction that could be mediated either directly by nucleosome-nucleosome contacts or indirectly through the remodelers. Mutant Drosophila melanogaster ISWI without the Hand-Sant-Slide (HSS) domain had no detectable spacing activity even though it is known to remodel and slide nucleosomes. This suggests that the role of ISWI remodelers in generating constant spacing is not just to mediate nucleosome sliding; they actively contribute to the attractive interaction. Additional factors are necessary to set physiological spacing in absolute terms.
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34
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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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35
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Emelyanov AV, Rabbani J, Mehta M, Vershilova E, Keogh MC, Fyodorov DV. Drosophila TAP/p32 is a core histone chaperone that cooperates with NAP-1, NLP, and nucleophosmin in sperm chromatin remodeling during fertilization. Genes Dev 2014; 28:2027-40. [PMID: 25228646 PMCID: PMC4173154 DOI: 10.1101/gad.248583.114] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Accepted: 08/20/2014] [Indexed: 12/21/2022]
Abstract
Nuclear DNA in the male gamete of sexually reproducing animals is organized as sperm chromatin compacted primarily by sperm-specific protamines. Fertilization leads to sperm chromatin remodeling, during which protamines are expelled and replaced by histones. Despite our increased understanding of the factors that mediate nucleosome assembly in the nascent male pronucleus, the machinery for protamine removal remains largely unknown. Here we identify four Drosophila protamine chaperones that mediate the dissociation of protamine-DNA complexes: NAP-1, NLP, and nucleophosmin are previously characterized histone chaperones, and TAP/p32 has no known function in chromatin metabolism. We show that TAP/p32 is required for the removal of Drosophila protamine B in vitro, whereas NAP-1, NLP, and Nph share roles in the removal of protamine A. Embryos from P32-null females show defective formation of the male pronucleus in vivo. TAP/p32, similar to NAP-1, NLP, and Nph, facilitates nucleosome assembly in vitro and is therefore a histone chaperone. Furthermore, mutants of P32, Nlp, and Nph exhibit synthetic-lethal genetic interactions. In summary, we identified factors mediating protamine removal from DNA and reconstituted in a defined system the process of sperm chromatin remodeling that exchanges protamines for histones to form the nucleosome-based chromatin characteristic of somatic cells.
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Affiliation(s)
- Alexander V Emelyanov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Joshua Rabbani
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Monika Mehta
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Elena Vershilova
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Michael C Keogh
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Dmitry V Fyodorov
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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36
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Lake RJ, Boetefuer EL, Tsai PF, Jeong J, Choi I, Won KJ, Fan HY. The sequence-specific transcription factor c-Jun targets Cockayne syndrome protein B to regulate transcription and chromatin structure. PLoS Genet 2014; 10:e1004284. [PMID: 24743307 PMCID: PMC3990521 DOI: 10.1371/journal.pgen.1004284] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2013] [Accepted: 02/20/2014] [Indexed: 11/19/2022] Open
Abstract
Cockayne syndrome is an inherited premature aging disease associated with numerous developmental and neurological defects, and mutations in the gene encoding the CSB protein account for the majority of Cockayne syndrome cases. Accumulating evidence suggests that CSB functions in transcription regulation, in addition to its roles in DNA repair, and those defects in this transcriptional activity might contribute to the clinical features of Cockayne syndrome. Transcription profiling studies have so far uncovered CSB-dependent effects on gene expression; however, the direct targets of CSB's transcriptional activity remain largely unknown. In this paper, we report the first comprehensive analysis of CSB genomic occupancy during replicative cell growth. We found that CSB occupancy sites display a high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, we found that CSB occupancy is enriched at sites containing the TPA-response element. Consistent with this binding site preference, we show that CSB and the transcription factor c-Jun can be found in the same protein-DNA complex, suggesting that c-Jun can target CSB to specific genomic regions. In support of this notion, we observed decreased CSB occupancy of TPA-response elements when c-Jun levels were diminished. By modulating CSB abundance, we found that CSB can influence the expression of nearby genes and impact nucleosome positioning in the vicinity of its binding site. These results indicate that CSB can be targeted to specific genomic loci by sequence-specific transcription factors to regulate transcription and local chromatin structure. Additionally, comparison of CSB occupancy sites with the MSigDB Pathways database suggests that CSB might function in peroxisome proliferation, EGF receptor transactivation, G protein signaling and NF-κB activation, shedding new light on the possible causes and mechanisms of Cockayne syndrome. Cockayne syndrome is a devastating inherited disease, in which patients appear to age prematurely, have sun sensitivity and suffer from profound neurological and developmental defects. Mutations in the CSB gene account for the majority of Cockayne syndrome cases. CSB is an ATP-dependent chromatin remodeler, and these proteins can use energy from ATP-hydrolysis to alter contacts between DNA and histones of a nucleosome, the basic units of chromatin structure. CSB functions in DNA repair, but accumulating evidence reveals that CSB also functions in transcription regulation. Here, we determined the genomic localization of CSB to identify its gene targets and found that CSB occupancy displays high correlation to regions with epigenetic features of promoters and enhancers. Furthermore, CSB is enriched at genomic regions containing the binding site for the c-Jun transcription factor, and we found that these two proteins interact, uncovering a new targeting mechanism for CSB. We also demonstrate that CSB can influence gene expression in the vicinity of its binding sites and alter local chromatin structure. Together, this study supports the hypothesis that defects in the regulation of gene expression and chromatin structure by CSB might contribute to the diverse clinical features of Cockayne syndrome.
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Affiliation(s)
- Robert J. Lake
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Erica L. Boetefuer
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Biology Graduate Program, Graduate School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Pei-Fang Tsai
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jieun Jeong
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Inchan Choi
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Kyoung-Jae Won
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Hua-Ying Fan
- Epigenetics Program, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Institute for Diabetes Obesity and Metabolism, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
- * E-mail:
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37
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Skene PJ, Hernandez AE, Groudine M, Henikoff S. The nucleosomal barrier to promoter escape by RNA polymerase II is overcome by the chromatin remodeler Chd1. eLife 2014; 3:e02042. [PMID: 24737864 PMCID: PMC3983905 DOI: 10.7554/elife.02042] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
RNA polymerase II (PolII) transcribes RNA within a chromatin context, with nucleosomes acting as barriers to transcription. Despite these barriers, transcription through chromatin in vivo is highly efficient, suggesting the existence of factors that overcome this obstacle. To increase the resolution obtained by standard chromatin immunoprecipitation, we developed a novel strategy using micrococcal nuclease digestion of cross-linked chromatin. We find that the chromatin remodeler Chd1 is recruited to promoter proximal nucleosomes of genes undergoing active transcription, where Chd1 is responsible for the vast majority of PolII-directed nucleosome turnover. The expression of a dominant negative form of Chd1 results in increased stalling of PolII past the entry site of the promoter proximal nucleosomes. We find that Chd1 evicts nucleosomes downstream of the promoter in order to overcome the nucleosomal barrier and enable PolII promoter escape, thus providing mechanistic insight into the role of Chd1 in transcription and pluripotency. DOI:http://dx.doi.org/10.7554/eLife.02042.001 DNA is tightly packaged in a material called chromatin inside the cell nucleus. To produce proteins this DNA must first be transcribed to produce a molecule of messenger RNA, which is then translated to make a protein. To assist with this process cells ‘unpack’ certain regions of the DNA so that enzymes that catalyze the different steps in this process can have access to the DNA. A protein called Chd1 is involved in the unpacking process in yeast, but its role in more complex animals is not clear. Now, Skene et al. have shown that this protein is needed to allow the enzyme that catalyzes the transcription of DNA—an enzyme called RNA polymerase II—to do its job. Chd1 acts to unpack the tightly packaged DNA from chromatin, thus allowing the transcription of the DNA to proceed. In the absence of Chd1 activity, RNA polymerase II stalls at the gene promoter—the region of DNA that starts the transcription of a particular gene. This work highlights how the packaging of DNA in the cell is highly dynamic and controls fundamental biological processes. Skene et al. modified a well-known genetic technique called ChIP-seq. Previous ChIP-seq protocols typically provided a blurry, low-resolution map of where proteins bound to chromatin. Skene et al. used an enzyme to ‘chew back’ the DNA to reveal the exact ‘footprints’ of the Chd1 protein and the RNA polymerase II enzyme on the chromatin in mice. It will be possible to adapt this new protocol to map the positions of other proteins, which will help to improve our understanding of the ways in which chromatin regulates access to DNA. DOI:http://dx.doi.org/10.7554/eLife.02042.002
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Affiliation(s)
- Peter J Skene
- Basic Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, United States
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Abstract
Biochemical assays reveal that nucleosome maturation and chromatin remodelling by the motor protein Chd1 are distinct, separable enzymatic activities.
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Affiliation(s)
- Karim Bouazoune
- is in the Department of Molecular Biology and the Department of Genetics , Massachusetts General Hospital, Harvard Medical School , Boston , United States
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