1
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Bryll AR, Peterson CL. The circular logic of mRNA homeostasis. Transcription 2023; 14:18-26. [PMID: 36843061 PMCID: PMC10353332 DOI: 10.1080/21541264.2023.2183684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/28/2023] Open
Abstract
Eukaryotic cells rely upon dynamic, multifaceted regulation at each step of RNA biogenesis to maintain mRNA pools and ensure normal protein synthesis. Studies in budding yeast indicate a buffering phenomenon that preserves global mRNA levels through the reciprocal balancing of RNA synthesis rates and mRNA decay. In short, changes in transcription impact the efficiency of mRNA degradation and defects in either nuclear or cytoplasmic mRNA degradation are somehow sensed and relayed to control a compensatory change in mRNA transcription rates. Here, we review current views on molecular mechanisms that might explain this apparent bidirectional sensing process that ensures homeostasis of the stable mRNA pool.
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Affiliation(s)
- Alysia R. Bryll
- Program of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester
- Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester
| | - Craig L. Peterson
- Program of Molecular Medicine, University of Massachusetts Chan Medical School, Worcester
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2
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Baier AS, Gioacchini N, Eek P, Tan S, Peterson CL. Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C. Res Sq 2023:rs.3.rs-3050911. [PMID: 37546845 PMCID: PMC10402270 DOI: 10.21203/rs.3.rs-3050911/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
The SWR1C chromatin remodeling enzyme catalyzes the ATP-dependent exchange of nucleosomal histone H2A for the histone variant H2A.Z, a key variant involved in a multitude of nuclear functions. How the 14-subunit SWR1C engages the nucleosomal substrate remains largely unknown. Numerous studies on the ISWI, CHD1, and SWI/SNF families of chromatin remodeling enzymes have demonstrated key roles for the nucleosomal acidic patch for remodeling activity, however a role for this nucleosomal epitope in nucleosome editing by SWR1C has not been tested. Here, we employ a variety of biochemical assays to demonstrate an essential role for the acidic patch in the H2A.Z exchange reaction. Utilizing asymmetrically assembled nucleosomes, we demonstrate that the acidic patches on each face of the nucleosome are required for SWR1C-mediated dimer exchange, suggesting SWR1C engages the nucleosome in a "pincer-like" conformation, engaging both patches simultaneously. Loss of a single acidic patch results in loss of high affinity nucleosome binding and nucleosomal stimulation of ATPase activity. We identify a conserved arginine-rich motif within the Swc5 subunit that binds the acidic patch and is key for dimer exchange activity. In addition, our cryoEM structure of a Swc5-nucleosome complex suggests that promoter proximal, histone H2B ubiquitinylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.
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Affiliation(s)
- Alexander S. Baier
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605
- Medical Scientist Training Program, T.H. Chan School of Medicine, University of Massachusetts
| | - Nathan Gioacchini
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605
- Interdisciplinary Graduate Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical School, Worcester, MA, 01605
| | - Priit Eek
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 12618 Tallinn, Estonia
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA, 01605
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3
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Chio US, Rechiche O, Bryll AR, Zhu J, Leith EM, Feldman JL, Peterson CL, Tan S, Armache JP. Cryo-EM structure of the human Sirtuin 6-nucleosome complex. Sci Adv 2023; 9:eadf7586. [PMID: 37058572 PMCID: PMC10104460 DOI: 10.1126/sciadv.adf7586] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Accepted: 03/15/2023] [Indexed: 06/19/2023]
Abstract
Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56.
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Affiliation(s)
- Un Seng Chio
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94152, USA
| | - Othman Rechiche
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Alysia R. Bryll
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jiang Zhu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Erik M. Leith
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jessica L. Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jean-Paul Armache
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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4
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Chio US, Rechiche O, Bryll AR, Zhu J, Feldman JL, Peterson CL, Tan S, Armache JP. Cryo-EM structure of the human Sirtuin 6-nucleosome complex. bioRxiv 2023:2023.03.17.533206. [PMID: 36993468 PMCID: PMC10055229 DOI: 10.1101/2023.03.17.533206] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
UNLABELLED Sirtuin 6 (SIRT6) is a multifaceted protein deacetylase/deacylase and a major target for small-molecule modulators of longevity and cancer. In the context of chromatin, SIRT6 removes acetyl groups from histone H3 in nucleosomes, but the molecular basis for its nucleosomal substrate preference is unknown. Our cryo-electron microscopy structure of human SIRT6 in complex with the nucleosome shows that the catalytic domain of SIRT6 pries DNA from the nucleosomal entry-exit site and exposes the histone H3 N-terminal helix, while the SIRT6 zinc-binding domain binds to the histone acidic patch using an arginine anchor. In addition, SIRT6 forms an inhibitory interaction with the C-terminal tail of histone H2A. The structure provides insights into how SIRT6 can deacetylate both H3 K9 and H3 K56. TEASER The structure of the SIRT6 deacetylase/nucleosome complex suggests how the enzyme acts on both histone H3 K9 and K56 residues.
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Affiliation(s)
- Un Seng Chio
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94152, USA
| | - Othman Rechiche
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Alysia R. Bryll
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
- Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, MA 01605
| | - Jiang Zhu
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jessica L. Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jean-Paul Armache
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
- The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
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5
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Fan J, Moreno AT, Baier AS, Loparo JJ, Peterson CL. H2A.Z deposition by SWR1C involves multiple ATP-dependent steps. Nat Commun 2022; 13:7052. [PMID: 36396651 PMCID: PMC9672302 DOI: 10.1038/s41467-022-34861-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 11/09/2022] [Indexed: 11/18/2022] Open
Abstract
Histone variant H2A.Z is a conserved feature of nucleosomes flanking protein-coding genes. Deposition of H2A.Z requires ATP-dependent replacement of nucleosomal H2A by a chromatin remodeler related to the multi-subunit enzyme, yeast SWR1C. How these enzymes use ATP to promote this nucleosome editing reaction remains unclear. Here we use single-molecule and ensemble methodologies to identify three ATP-dependent phases in the H2A.Z deposition reaction. Real-time analysis of single nucleosome remodeling events reveals an initial priming step that occurs after ATP addition that involves a combination of both transient DNA unwrapping from the nucleosome and histone octamer deformations. Priming is followed by rapid loss of histone H2A, which is subsequently released from the H2A.Z nucleosomal product. Surprisingly, rates of both priming and the release of the H2A/H2B dimer are sensitive to ATP concentration. This complex reaction pathway provides multiple opportunities to regulate timely and accurate deposition of H2A.Z at key genomic locations.
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Affiliation(s)
- Jiayi Fan
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Interdisciplinary Graduate Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Andrew T. Moreno
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Alexander S. Baier
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA ,grid.168645.80000 0001 0742 0364Medical Scientist Training Program, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
| | - Joseph J. Loparo
- grid.38142.3c000000041936754XDepartment of Biological Chemistry and Molecular Pharmacology, Blavatnik Institute, Harvard Medical School, Boston, MA 02115 USA
| | - Craig L. Peterson
- grid.168645.80000 0001 0742 0364Program in Molecular Medicine, University of Massachusetts Chan Medical School, Worcester, MA 01605 USA
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6
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Gutierrez JI, Brittingham GP, Karadeniz YB, Tran KD, Dutta A, Holehouse AS, Peterson CL, Holt LJ. SWI/SNF senses carbon starvation with a pH-sensitive low complexity sequence. eLife 2022; 11:70344. [PMID: 35129437 PMCID: PMC8890752 DOI: 10.7554/elife.70344] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 02/06/2022] [Indexed: 11/16/2022] Open
Abstract
It is increasingly appreciated that intracellular pH changes are important biological signals. This motivates the elucidation of molecular mechanisms of pH sensing. We determined that a nucleocytoplasmic pH oscillation was required for the transcriptional response to carbon starvation in Saccharomyces cerevisiae. The SWI/SNF chromatin remodeling complex is a key mediator of this transcriptional response. A glutamine-rich low-complexity domain (QLC) in the SNF5 subunit of this complex, and histidines within this sequence, was required for efficient transcriptional reprogramming. Furthermore, the SNF5 QLC mediated pH-dependent recruitment of SWI/SNF to an acidic transcription factor in a reconstituted nucleosome remodeling assay. Simulations showed that protonation of histidines within the SNF5 QLC leads to conformational expansion, providing a potential biophysical mechanism for regulation of these interactions. Together, our results indicate that pH changes are a second messenger for transcriptional reprogramming during carbon starvation and that the SNF5 QLC acts as a pH sensor.
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Affiliation(s)
| | - Gregory P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, United States
| | - Yonca B Karadeniz
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Kathleen D Tran
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, United States
| | - Arnob Dutta
- Department of Cell and Molecular Biology, University of Rhode Island, South Kingstown, United States
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St. Louis, St Louis, United States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Liam J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, United States
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7
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Baier AS, Peterson CL. Fluorescence approaches for biochemical analysis of ATP-dependent chromatin remodeling enzymes. Methods Enzymol 2022; 673:1-17. [PMID: 35965003 PMCID: PMC10107425 DOI: 10.1016/bs.mie.2022.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The dynamic nature of chromatin is an essential mechanism by which gene expression is regulated. Chromatin is comprised of nucleosomes, an octamer of histone proteins wrapped by DNA, and manipulation of these structures is carried out by a family of proteins known as ATP-dependent chromatin remodeling enzymes. These enzymes carry out a diverse range of activities, from appropriately positioning and adjusting the density of nucleosomes on genes, to installation and removal of histones for sequence variants, to ejection from DNA. These activities have a critical role in the proper maintenance of chromatin architecture, and dysregulation of chromatin remodeling is directly linked to the pathophysiology of various diseases. Mechanistic understanding of chromatin remodeling enzymes is therefore desirable, both as the drivers of this essential cellular activity and as potentially novel therapeutic targets in disease. In this chapter we cover our current methods for characterization of remodeler substrate binding affinity and catalytic activity, leveraging fluorescence polarization and Förster resonance energy transfer assays.
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8
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Bryll AR, Peterson CL. Functional interaction between the RNA exosome and the sirtuin deacetylase Hst3 maintains transcriptional homeostasis. Genes Dev 2021; 36:17-22. [PMID: 34916303 PMCID: PMC8763048 DOI: 10.1101/gad.348923.121] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/22/2021] [Indexed: 11/24/2022]
Abstract
In this study, Bryll et al. found that inactivation of the RNA exosome leads to global reduction of nascent mRNA transcripts, and that this defect is accentuated by loss of deposition of histone variant H2A.Z. They identify the mRNA for the sirtuin deacetylase Hst3 as a key target for the RNA exosome that mediates communication between RNA degradation and transcription machineries. Eukaryotic cells maintain an optimal level of mRNAs through unknown mechanisms that balance RNA synthesis and degradation. We found that inactivation of the RNA exosome leads to global reduction of nascent mRNA transcripts, and that this defect is accentuated by loss of deposition of histone variant H2A.Z. We identify the mRNA for the sirtuin deacetylase Hst3 as a key target for the RNA exosome that mediates communication between RNA degradation and transcription machineries. These findings reveal how the RNA exosome and H2A.Z function together to control a deacetylase, ensuring proper levels of transcription in response to changes in RNA degradation.
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Affiliation(s)
- Alysia R Bryll
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Medical Scientist Training Program, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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9
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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: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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10
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Liu WH, Zheng J, Feldman JL, Klein MA, Kuznetsov VI, Peterson CL, Griffin PR, Denu JM. Multivalent interactions drive nucleosome binding and efficient chromatin deacetylation by SIRT6. Nat Commun 2020; 11:5244. [PMID: 33067423 PMCID: PMC7568541 DOI: 10.1038/s41467-020-19018-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 09/18/2020] [Indexed: 11/30/2022] Open
Abstract
The protein deacetylase SIRT6 maintains cellular homeostasis through multiple pathways that include the deacetylation of histone H3 and repression of transcription. Prior work suggests that SIRT6 is associated with chromatin and can substantially reduce global levels of H3 acetylation, but how SIRT6 is able to accomplish this feat is unknown. Here, we describe an exquisitely tight interaction between SIRT6 and nucleosome core particles, in which a 2:1 enzyme:nucleosome complex assembles via asymmetric binding with distinct affinities. While both SIRT6 molecules associate with the acidic patch on the nucleosome, we find that the intrinsically disordered SIRT6 C-terminus promotes binding at the higher affinity site through recognition of nucleosomal DNA. Together, multivalent interactions couple productive binding to efficient deacetylation of histones on endogenous chromatin. Unique among histone deacetylases, SIRT6 possesses the intrinsic capacity to tightly interact with nucleosomes for efficient activity.
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Affiliation(s)
- Wallace H Liu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Jie Zheng
- Department of Molecular Medicine, Scripps Research Florida, Jupiter, FL, 33458, USA
| | - Jessica L Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Mark A Klein
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Vyacheslav I Kuznetsov
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA
| | - Patrick R Griffin
- Department of Molecular Medicine, Scripps Research Florida, Jupiter, FL, 33458, USA
| | - John M Denu
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA.
- Wisconsin Institute for Discovery, University of Wisconsin-Madison, Madison, WI, 53715, USA.
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11
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Singh RK, Fan J, Gioacchini N, Watanabe S, Bilsel O, Peterson CL. Transient Kinetic Analysis of SWR1C-Catalyzed H2A.Z Deposition Unravels the Impact of Nucleosome Dynamics and the Asymmetry of Histone Exchange. Cell Rep 2020; 27:374-386.e4. [PMID: 30970243 PMCID: PMC6545893 DOI: 10.1016/j.celrep.2019.03.035] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 01/20/2019] [Accepted: 03/08/2019] [Indexed: 12/16/2022] Open
Abstract
The SWR1C chromatin remodeling enzyme catalyzes ATP-dependent replacement of nucleosomal H2A with the H2A.Z variant, regulating key DNA-mediated processes such as transcription and DNA repair. Here, we investigate the transient kinetic mechanism of the histone exchange reaction, employing ensemble FRET, fluorescence correlation spectroscopy (FCS), and the steady-state kinetics of ATP hydrolysis. Our studies indicate that SWR1C modulates nucleosome dynamics on both the millisecond and microsecond timescales, poising the nucleosome for the dimer exchange reaction. The transient kinetic analysis of the remodeling reaction performed under single turnover conditions unraveled a striking asymmetry in the ATP-dependent replacement of nucleosomal dimers, promoted by localized DNA unwrapping. Taken together, our transient kinetic studies identify intermediates and provide crucial insights into the SWR1C-catalyzed dimer exchange reaction and shed light on how the mechanics of H2A.Z deposition might contribute to transcriptional regulation in vivo. The SWR1C remodeling enzyme catalyzes ATP-dependent replacement of nucleosomal H2A with the H2A.Z variant at promoter-proximal nucleosomes. Singh et al. investigate the transient kinetic mechanism of this histone exchange reaction and show that SWR1C transiently unwraps nucleosomal DNA, promoting a concerted dimer eviction and replacement reaction.
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Affiliation(s)
- Raushan K Singh
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Jiayl Fan
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Nathan Gioacchini
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Osman Bilsel
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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12
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Wang A, Kolhe JA, Gioacchini N, Baade I, Brieher WM, Peterson CL, Freeman BC. Mechanism of Long-Range Chromosome Motion Triggered by Gene Activation. Dev Cell 2020; 52:309-320.e5. [PMID: 31902656 DOI: 10.1016/j.devcel.2019.12.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2018] [Revised: 11/18/2019] [Accepted: 12/12/2019] [Indexed: 12/18/2022]
Abstract
Movement of chromosome sites within interphase cells is critical for numerous pathways including RNA transcription and genome organization. Yet, a mechanism for reorganizing chromatin in response to these events had not been reported. Here, we delineate a molecular chaperone-dependent pathway for relocating activated gene loci in yeast. Our presented data support a model in which a two-authentication system mobilizes a gene promoter through a dynamic network of polymeric nuclear actin. Transcription factor-dependent nucleation of a myosin motor propels the gene locus through the actin matrix, and fidelity of the actin association was ensured by ARP-containing chromatin remodelers. Motor activity of nuclear myosin was dependent on the Hsp90 chaperone. Hsp90 further contributed by biasing the remodeler-actin interaction toward nucleosomes with the non-canonical histone H2A.Z, thereby focusing the pathway on select sites such as transcriptionally active genes. Together, the system provides a rapid and effective means to broadly yet selectively mobilize chromatin sites.
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Affiliation(s)
- Anqi Wang
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Janhavi A Kolhe
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Nate Gioacchini
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Imke Baade
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - William M Brieher
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA
| | - Craig L Peterson
- Program of Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Brian C Freeman
- Department of Cell and Developmental Biology, University of Illinois Urbana-Champaign, Urbana, IL 61801, USA.
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13
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Feldman JL, Peterson CL. Yeast Sirtuin Family Members Maintain Transcription Homeostasis to Ensure Genome Stability. Cell Rep 2019; 27:2978-2989.e5. [PMID: 31167142 PMCID: PMC6640630 DOI: 10.1016/j.celrep.2019.05.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 04/09/2019] [Accepted: 05/01/2019] [Indexed: 01/08/2023] Open
Abstract
The mammalian sirtuin, SIRT6, is a key tumor suppressor that maintains genome stability and regulates transcription, though how SIRT6 family members control genome stability is unclear. Here, we use multiple genome-wide approaches to demonstrate that the yeast SIRT6 homologs, Hst3 and Hst4, prevent genome instability by tuning levels of both coding and noncoding transcription. While nascent RNAs are elevated in the absence of Hst3 and Hst4, a global impact on steady-state mRNAs is masked by the nuclear exosome, indicating that sirtuins and the exosome provide two levels of regulation to maintain transcription homeostasis. We find that, in the absence of Hst3 and Hst4, increased transcription is associated with excessive DNA-RNA hybrids (R-loops) that appear to lead to new DNA double-strand breaks. Importantly, dissolution of R-loops suppresses the genome instability phenotypes of hst3 hst4 mutants, suggesting that the sirtuins maintain genome stability by acting as a rheostat to prevent promiscuous transcription.
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Affiliation(s)
- Jessica L Feldman
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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14
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Abstract
Heterochromatin is a silenced chromatin region essential for maintaining genomic stability and driving developmental processes. The complicated structure and dynamics of heterochromatin have rendered it difficult to characterize. In budding yeast, heterochromatin assembly requires the SIR proteins-Sir3, believed to be the primary structural component of SIR heterochromatin, and the Sir2-4 complex, responsible for the targeted recruitment of SIR proteins and the deacetylation of lysine 16 of histone H4. Previously, we found that Sir3 binds but does not compact nucleosomal arrays. Here we reconstitute chromatin fibers with the complete complement of SIR proteins and use sedimentation velocity, molecular modeling, and atomic force microscopy to characterize the stoichiometry and conformation of SIR chromatin fibers. In contrast to fibers with Sir3 alone, our results demonstrate that SIR arrays are highly compact. Strikingly, the condensed structure of SIR heterochromatin fibers requires both the integrity of H4K16 and an interaction between Sir3 and Sir4. We propose a model in which a dimer of Sir3 bridges and stabilizes two adjacent nucleosomes, while a Sir2-4 heterotetramer interacts with Sir3 associated with a nucleosomal trimer, driving fiber compaction.
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Affiliation(s)
- Sarah G Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605
| | - Subhadip Senapati
- Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Mehmet F Bolukbasi
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Scot A Wolfe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01655
| | - Stuart Lindsay
- Center for Single Molecule Biophysics, Biodesign Institute, Arizona State University, Tempe, AZ 85287
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605;
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15
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Affiliation(s)
- Nathan Gioacchini
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
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16
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Xue Y, Pradhan SK, Sun F, Chronis C, Tran N, Su T, Van C, Vashisht A, Wohlschlegel J, Peterson CL, Timmers HTM, Kurdistani SK, Carey MF. Mot1, Ino80C, and NC2 Function Coordinately to Regulate Pervasive Transcription in Yeast and Mammals. Mol Cell 2017; 67:594-607.e4. [PMID: 28735899 DOI: 10.1016/j.molcel.2017.06.029] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 05/12/2017] [Accepted: 06/23/2017] [Indexed: 01/02/2023]
Abstract
Pervasive transcription initiates from cryptic promoters and is observed in eukaryotes ranging from yeast to mammals. The Set2-Rpd3 regulatory system prevents cryptic promoter function within expressed genes. However, conserved systems that control pervasive transcription within intergenic regions have not been well established. Here we show that Mot1, Ino80 chromatin remodeling complex (Ino80C), and NC2 co-localize on chromatin and coordinately suppress pervasive transcription in S. cerevisiae and murine embryonic stem cells (mESCs). In yeast, all three proteins bind subtelomeric heterochromatin through a Sir3-stimulated mechanism and to euchromatin via a TBP-stimulated mechanism. In mESCs, the proteins bind to active and poised TBP-bound promoters along with promoters of polycomb-silenced genes apparently lacking TBP. Depletion of Mot1, Ino80C, or NC2 by anchor away in yeast or RNAi in mESCs leads to near-identical transcriptome phenotypes, with new subtelomeric transcription in yeast, and greatly increased pervasive transcription in both yeast and mESCs.
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Affiliation(s)
- Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Fei Sun
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Constantinos Chronis
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Nancy Tran
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Christopher Van
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - H T Marc Timmers
- Regenerative Medicine Center and Center for Molecular Medicine, University Medical Center Utrecht, 3584 CT Utrecht, the Netherlands
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine, UCLA, Los Angeles, CA 90095, USA.
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17
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Clapier CR, Iwasa J, Cairns BR, Peterson CL. Mechanisms of action and regulation of ATP-dependent chromatin-remodelling complexes. Nat Rev Mol Cell Biol 2017; 18:407-422. [PMID: 28512350 DOI: 10.1038/nrm.2017.26] [Citation(s) in RCA: 658] [Impact Index Per Article: 94.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cells utilize diverse ATP-dependent nucleosome-remodelling complexes to carry out histone sliding, ejection or the incorporation of histone variants, suggesting that different mechanisms of action are used by the various chromatin-remodelling complex subfamilies. However, all chromatin-remodelling complex subfamilies contain an ATPase-translocase 'motor' that translocates DNA from a common location within the nucleosome. In this Review, we discuss (and illustrate with animations) an alternative, unifying mechanism of chromatin remodelling, which is based on the regulation of DNA translocation. We propose the 'hourglass' model of remodeller function, in which each remodeller subfamily utilizes diverse specialized proteins and protein domains to assist in nucleosome targeting or to differentially detect nucleosome epitopes. These modules converge to regulate a common DNA translocation mechanism, to inform the conserved ATPase 'motor' on whether and how to apply DNA translocation, which together achieve the various outcomes of chromatin remodelling: nucleosome assembly, chromatin access and nucleosome editing.
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Affiliation(s)
- Cedric R Clapier
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Janet Iwasa
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Bradley R Cairns
- Howard Hughes Medical Institute and Department of Oncological Sciences, Huntsman Cancer Institute, University of Utah School of Medicine, Salt Lake City, Utah 84112, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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18
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Azmi IF, Watanabe S, Maloney MF, Kang S, Belsky JA, MacAlpine DM, Peterson CL, Bell SP. Nucleosomes influence multiple steps during replication initiation. eLife 2017; 6. [PMID: 28322723 PMCID: PMC5400510 DOI: 10.7554/elife.22512] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 03/20/2017] [Indexed: 12/20/2022] Open
Abstract
Eukaryotic replication origin licensing, activation and timing are influenced by chromatin but a mechanistic understanding is lacking. Using reconstituted nucleosomal DNA replication assays, we assessed the impact of nucleosomes on replication initiation. To generate distinct nucleosomal landscapes, different chromatin-remodeling enzymes (CREs) were used to remodel nucleosomes on origin-DNA templates. Nucleosomal organization influenced two steps of replication initiation: origin licensing and helicase activation. Origin licensing assays showed that local nucleosome positioning enhanced origin specificity and modulated helicase loading by influencing ORC DNA binding. Interestingly, SWI/SNF- and RSC-remodeled nucleosomes were permissive for origin licensing but showed reduced helicase activation. Specific CREs rescued replication of these templates if added prior to helicase activation, indicating a permissive chromatin state must be established during origin licensing to allow efficient origin activation. Our studies show nucleosomes directly modulate origin licensing and activation through distinct mechanisms and provide insights into the regulation of replication initiation by chromatin.
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Affiliation(s)
- Ishara F Azmi
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Michael F Maloney
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
| | - Sukhyun Kang
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States.,Center for Genomic Integrity, Institute for Basic Science, Ulsan, South Korea
| | - Jason A Belsky
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, United States.,Program in Computational Biology and Bioinformatics, Duke University, Durham, United States
| | - David M MacAlpine
- Department of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, United States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, United States
| | - Stephen P Bell
- Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, United States
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19
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Adkins NL, Swygert SG, Kaur P, Niu H, Grigoryev SA, Sung P, Wang H, Peterson CL. Nucleosome-like, Single-stranded DNA (ssDNA)-Histone Octamer Complexes and the Implication for DNA Double Strand Break Repair. J Biol Chem 2017; 292:5271-5281. [PMID: 28202543 DOI: 10.1074/jbc.m117.776369] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 02/13/2017] [Indexed: 11/06/2022] Open
Abstract
Repair of DNA double strand breaks (DSBs) is key for maintenance of genome integrity. When DSBs are repaired by homologous recombination, DNA ends can undergo extensive processing, producing long stretches of single-stranded DNA (ssDNA). In vivo, DSB processing occurs in the context of chromatin, and studies indicate that histones may remain associated with processed DSBs. Here we demonstrate that histones are not evicted from ssDNA after in vitro chromatin resection. In addition, we reconstitute histone-ssDNA complexes (termed ssNucs) with ssDNA and recombinant histones and analyze these particles by a combination of native gel electrophoresis, sedimentation velocity, electron microscopy, and a recently developed electrostatic force microscopy technique, DREEM (dual-resonance frequency-enhanced electrostatic force microscopy). The reconstituted ssNucs are homogenous and relatively stable, and DREEM reveals ssDNA wrapping around histones. We also find that histone octamers are easily transferred in trans from ssNucs to either double-stranded DNA or ssDNA. Furthermore, the Fun30 remodeling enzyme, which has been implicated in DNA repair, binds ssNucs preferentially over nucleosomes, and ssNucs are effective at activating Fun30 ATPase activity. Our results indicate that ssNucs may be a hallmark of processes that generate ssDNA, and that posttranslational modification of ssNucs may generate novel signaling platforms involved in genome stability.
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Affiliation(s)
- Nicholas L Adkins
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Sarah G Swygert
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605
| | - Parminder Kaur
- the Department of Physics.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
| | - Hengyao Niu
- the Department Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
| | - Sergei A Grigoryev
- the Department of Biochemistry and Molecular Biology, Pennsylvania State University College of Medicine, Hershey, Pennsylvania 17033
| | - Patrick Sung
- the Department Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, and
| | - Hong Wang
- the Department of Physics.,Center for Human Health and the Environment, North Carolina State University, Raleigh, North Carolina 27695
| | - Craig L Peterson
- From the Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605,
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20
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Krietenstein N, Wal M, Watanabe S, Park B, Peterson CL, Pugh BF, Korber P. Genomic Nucleosome Organization Reconstituted with Pure Proteins. Cell 2016; 167:709-721.e12. [PMID: 27768892 DOI: 10.1016/j.cell.2016.09.045] [Citation(s) in RCA: 166] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 07/04/2016] [Accepted: 09/22/2016] [Indexed: 12/20/2022]
Abstract
Chromatin remodelers regulate genes by organizing nucleosomes around promoters, but their individual contributions are obfuscated by the complex in vivo milieu of factor redundancy and indirect effects. Genome-wide reconstitution of promoter nucleosome organization with purified proteins resolves this problem and is therefore a critical goal. Here, we reconstitute four stages of nucleosome architecture using purified components: yeast genomic DNA, histones, sequence-specific Abf1/Reb1, and remodelers RSC, ISW2, INO80, and ISW1a. We identify direct, specific, and sufficient contributions that in vivo observations validate. First, RSC clears promoters by translating poly(dA:dT) into directional nucleosome removal. Second, partial redundancy is recapitulated where INO80 alone, or ISW2 at Abf1/Reb1sites, positions +1 nucleosomes. Third, INO80 and ISW2 each align downstream nucleosomal arrays. Fourth, ISW1a tightens the spacing to canonical repeat lengths. Such a minimal set of rules and proteins establishes core mechanisms by which promoter chromatin architecture arises through a blend of redundancy and specialization.
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Affiliation(s)
- Nils Krietenstein
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried near Munich, Germany
| | - Megha Wal
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Bongsoo Park
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - B Franklin Pugh
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.
| | - Philipp Korber
- Molecular Biology Division, Biomedical Center, LMU Munich, 82152 Planegg-Martinsried near Munich, Germany.
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21
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Yu L, Rege M, Peterson CL, Volkert MR. RNA polymerase II depletion promotes transcription of alternative mRNA species. BMC Mol Biol 2016; 17:20. [PMID: 27578267 PMCID: PMC5004267 DOI: 10.1186/s12867-016-0074-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Accepted: 08/18/2016] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Cells respond to numerous internal and external stresses, such as heat, cold, oxidative stress, DNA damage, and osmotic pressure changes. In most cases, the primary response to stress is transcriptional induction of genes that assist the cells in tolerating the stress and facilitate the repair of the cellular damage. However, when the transcription machinery itself is stressed, responding by such standard mechanisms may not be possible. RESULTS In this study, we demonstrate that depletion or inactivation of RNA polymerase II (RNAPII) changes the preferred polyadenylation site usage for several transcripts, and leads to increased transcription of a specific subset of genes. Surprisingly, depletion of RNA polymerase I (RNAPI) also promotes altered polyadenylation site usage, while depletion of RNA polymerase III (RNAPIII) does not appear to have an impact. CONCLUSIONS Our results demonstrate that stressing the transcription machinery by depleting either RNAPI or RNAPII leads to a novel transcriptional response that results in induction of specific mRNAs and altered polyadenylation of many of the induced transcripts.
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Affiliation(s)
- Lijian Yu
- Microbiological and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA
| | - Mayuri Rege
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA, 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA, 01605, USA.
| | - Michael R Volkert
- Microbiological and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester, MA, 01655, USA.
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22
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Watanabe S, Peterson CL. Response to Comment on "A histone acetylation switch regulates H2A.Z deposition by the SWR-C remodeling enzyme". Science 2016; 353:358. [PMID: 27463666 DOI: 10.1126/science.aad6398] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 06/02/2016] [Indexed: 12/29/2022]
Abstract
Wang et al report a failure to reproduce our biochemical observation that the INO80C and SWR1C/SWR1/SWR-C chromatin remodeling enzymes catalyze replacement of nucleosomal H2A.Z with H2A when the substrate contains H3-K56Q. They point to technical problems with our dimer exchange assay. In response, we have recapitulated our findings using a mobility shift assay that was developed and employed by Wang and colleagues.
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Affiliation(s)
- Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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23
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Rege M, Subramanian V, Zhu C, Hsieh THS, Weiner A, Friedman N, Clauder-Münster S, Steinmetz LM, Rando OJ, Boyer LA, Peterson CL. Chromatin Dynamics and the RNA Exosome Function in Concert to Regulate Transcriptional Homeostasis. Cell Rep 2015; 13:1610-22. [PMID: 26586442 PMCID: PMC4662874 DOI: 10.1016/j.celrep.2015.10.030] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Revised: 09/02/2015] [Accepted: 10/09/2015] [Indexed: 12/12/2022] Open
Abstract
The histone variant H2A.Z is a hallmark of nucleosomes flanking promoters of protein-coding genes and is often found in nucleosomes that carry lysine 56-acetylated histone H3 (H3-K56Ac), a mark that promotes replication-independent nucleosome turnover. Here, we find that H3-K56Ac promotes RNA polymerase II occupancy at many protein-coding and noncoding loci, yet neither H3-K56Ac nor H2A.Z has a significant impact on steady-state mRNA levels in yeast. Instead, broad effects of H3-K56Ac or H2A.Z on RNA levels are revealed only in the absence of the nuclear RNA exosome. H2A.Z is also necessary for the expression of divergent, promoter-proximal non-coding RNAs (ncRNAs) in mouse embryonic stem cells. Finally, we show that H2A.Z functions with H3-K56Ac to facilitate formation of chromosome interaction domains (CIDs). Our study suggests that H2A.Z and H3-K56Ac work in concert with the RNA exosome to control mRNA and ncRNA expression, perhaps in part by regulating higher-order chromatin structures.
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Affiliation(s)
- Mayuri Rege
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Vidya Subramanian
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Chenchen Zhu
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
| | - Tsung-Han S Hsieh
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Assaf Weiner
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | - Nir Friedman
- School of Computer Science and Engineering, The Hebrew University, Jerusalem 91904, Israel; Alexander Silberman Institute of Life Sciences, The Hebrew University, Jerusalem 91904, Israel
| | | | - Lars M Steinmetz
- Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany; Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Laurie A Boyer
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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24
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Zhao H, Ghirlando R, Alfonso C, Arisaka F, Attali I, Bain DL, Bakhtina MM, Becker DF, Bedwell GJ, Bekdemir A, Besong TMD, Birck C, Brautigam CA, Brennerman W, Byron O, Bzowska A, Chaires JB, Chaton CT, Cölfen H, Connaghan KD, Crowley KA, Curth U, Daviter T, Dean WL, Díez AI, Ebel C, Eckert DM, Eisele LE, Eisenstein E, England P, Escalante C, Fagan JA, Fairman R, Finn RM, Fischle W, de la Torre JG, Gor J, Gustafsson H, Hall D, Harding SE, Cifre JGH, Herr AB, Howell EE, Isaac RS, Jao SC, Jose D, Kim SJ, Kokona B, Kornblatt JA, Kosek D, Krayukhina E, Krzizike D, Kusznir EA, Kwon H, Larson A, Laue TM, Le Roy A, Leech AP, Lilie H, Luger K, Luque-Ortega JR, Ma J, May CA, Maynard EL, Modrak-Wojcik A, Mok YF, Mücke N, Nagel-Steger L, Narlikar GJ, Noda M, Nourse A, Obsil T, Park CK, Park JK, Pawelek PD, Perdue EE, Perkins SJ, Perugini MA, Peterson CL, Peverelli MG, Piszczek G, Prag G, Prevelige PE, Raynal BDE, Rezabkova L, Richter K, Ringel AE, Rosenberg R, Rowe AJ, Rufer AC, Scott DJ, Seravalli JG, Solovyova AS, Song R, Staunton D, Stoddard C, Stott K, Strauss HM, Streicher WW, Sumida JP, Swygert SG, Szczepanowski RH, Tessmer I, Toth RT, Tripathy A, Uchiyama S, Uebel SFW, Unzai S, Gruber AV, von Hippel PH, Wandrey C, Wang SH, Weitzel SE, Wielgus-Kutrowska B, Wolberger C, Wolff M, Wright E, Wu YS, Wubben JM, Schuck P. A multilaboratory comparison of calibration accuracy and the performance of external references in analytical ultracentrifugation. PLoS One 2015; 10:e0126420. [PMID: 25997164 PMCID: PMC4440767 DOI: 10.1371/journal.pone.0126420] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2015] [Accepted: 04/02/2015] [Indexed: 12/21/2022] Open
Abstract
Analytical ultracentrifugation (AUC) is a first principles based method to determine absolute sedimentation coefficients and buoyant molar masses of macromolecules and their complexes, reporting on their size and shape in free solution. The purpose of this multi-laboratory study was to establish the precision and accuracy of basic data dimensions in AUC and validate previously proposed calibration techniques. Three kits of AUC cell assemblies containing radial and temperature calibration tools and a bovine serum albumin (BSA) reference sample were shared among 67 laboratories, generating 129 comprehensive data sets. These allowed for an assessment of many parameters of instrument performance, including accuracy of the reported scan time after the start of centrifugation, the accuracy of the temperature calibration, and the accuracy of the radial magnification. The range of sedimentation coefficients obtained for BSA monomer in different instruments and using different optical systems was from 3.655 S to 4.949 S, with a mean and standard deviation of (4.304 ± 0.188) S (4.4%). After the combined application of correction factors derived from the external calibration references for elapsed time, scan velocity, temperature, and radial magnification, the range of s-values was reduced 7-fold with a mean of 4.325 S and a 6-fold reduced standard deviation of ± 0.030 S (0.7%). In addition, the large data set provided an opportunity to determine the instrument-to-instrument variation of the absolute radial positions reported in the scan files, the precision of photometric or refractometric signal magnitudes, and the precision of the calculated apparent molar mass of BSA monomer and the fraction of BSA dimers. These results highlight the necessity and effectiveness of independent calibration of basic AUC data dimensions for reliable quantitative studies.
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Affiliation(s)
- Huaying Zhao
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carlos Alfonso
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Fumio Arisaka
- Life Science Research Center, Nihon University, College of Bioresource Science, Fujisawa, 252–0880, Japan
| | - Ilan Attali
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - David L. Bain
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Marina M. Bakhtina
- Department of Chemistry and Biochemistry, Center for Retrovirus Research, and Center for RNA Biology, The Ohio State University, Columbus, Ohio, 43210, United States of America
| | - Donald F. Becker
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Gregory J. Bedwell
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Ahmet Bekdemir
- Supramolecular Nanomaterials and Interfaces Laboratory, Institute of Materials, École Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Tabot M. D. Besong
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Chad A. Brautigam
- Department of Biophysics, The University of Texas Southwestern Medical Center, Dallas, Texas, 75390, United States of America
| | - William Brennerman
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G37TT, United Kingdom
| | - Agnieszka Bzowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Jonathan B. Chaires
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Catherine T. Chaton
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Helmut Cölfen
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Keith D. Connaghan
- Department of Pharmaceutical Sciences, University of Colorado Denver Anschutz Medical Campus, Aurora, Colorado, 80045, United States of America
| | - Kimberly A. Crowley
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Ute Curth
- Institute for Biophysical Chemistry, Hannover Medical School, 30625, Hannover, Germany
| | - Tina Daviter
- Institute of Structural and Molecular Biology Biophysics Centre, Birkbeck, University of London and University College London, London, WC1E 7HX, United Kingdom
| | - William L. Dean
- JG Brown Cancer Center, University of Louisville, Louisville, Kentucky, 40202, United States of America
| | - Ana I. Díez
- Department of Physical Chemistry, University of Murcia, Murcia, 30071, Spain
| | - Christine Ebel
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Debra M. Eckert
- Protein Interactions Core, Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, 84112, United States of America
| | - Leslie E. Eisele
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - Edward Eisenstein
- Institute for Bioscience and Biotechnology Research, Fischell Department of Bioengineering, University of Maryland, Rockville, Maryland, 20850, United States of America
| | - Patrick England
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Carlos Escalante
- Department of Physiology and Biophysics, School of Medicine, Virginia Commonwealth University, Richmond, Virginia, 23220, United States of America
| | - Jeffrey A. Fagan
- Materials Science and Engineering Laboratory, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899, United States of America
| | - Robert Fairman
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Ron M. Finn
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Wolfgang Fischle
- Laboratory of Chromatin Biochemistry, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | | | - Jayesh Gor
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | | | - Damien Hall
- Research School of Chemistry, Section on Biological Chemistry, The Australian National University, Acton, ACT 0200, Australia
| | - Stephen E. Harding
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | | | - Andrew B. Herr
- Department of Molecular Genetics, Biochemistry and Microbiology, University of Cincinnati College of Medicine, Cincinnati, Ohio, 45267, United States of America
| | - Elizabeth E. Howell
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Richard S. Isaac
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Shu-Chuan Jao
- Institute of Biological Chemistry, Academia Sinica, Taipei, 115, Taiwan
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Davis Jose
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Soon-Jong Kim
- Department of Chemistry, Mokpo National University, Muan, 534–729, Korea
| | - Bashkim Kokona
- Department of Biology, Haverford College, Haverford, Pennsylvania, 19041, United States of America
| | - Jack A. Kornblatt
- Enzyme Research Group, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Dalibor Kosek
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Elena Krayukhina
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Daniel Krzizike
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Eric A. Kusznir
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - Hyewon Kwon
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Adam Larson
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Thomas M. Laue
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Aline Le Roy
- Univ. Grenoble Alpes, IBS, F-38044, Grenoble, France
- CNRS, IBS, F-38044, Grenoble, France
- CEA, IBS, F-38044, Grenoble, France
| | - Andrew P. Leech
- Technology Facility, Department of Biology, University of York, York, YO10 5DD, United Kingdom
| | - Hauke Lilie
- Institute of Biochemistry and Biotechnology, Martin-Luther University Halle-Wittenberg, 06120, Halle, Germany
| | - Karolin Luger
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, United States of America
| | - Juan R. Luque-Ortega
- Analytical Ultracentrifugacion and Light Scattering Facility, Centro de Investigaciones Biológicas, CSIC, Madrid, 28040, Spain
| | - Jia Ma
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Carrie A. May
- Department of Biochemistry, University of New Hampshire, Durham, New Hampshire, 03824, United States of America
| | - Ernest L. Maynard
- Department of Biochemistry, Uniformed Services University of the Health Sciences, Bethesda, Maryland, 20814, United States of America
| | - Anna Modrak-Wojcik
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, Bio21 Instute of Molecular Science and Biotechnology, University of Melbourne, Parkville, 3010, Victoria, Australia
| | - Norbert Mücke
- Biophysics of Macromolecules, German Cancer Research Center, Heidelberg, 69120, Germany
| | | | - Geeta J. Narlikar
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Masanori Noda
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Amanda Nourse
- Molecular Interaction Analysis Shared Resource, St. Jude Children’s Research Hospital, Memphis, Tennessee, 38105, United States of America
| | - Tomas Obsil
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague, Prague, 12843, Czech Republic
| | - Chad K. Park
- Analytical Biophysics & Materials Characterization, Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, 85721, United States of America
| | - Jin-Ku Park
- Central Instrument Center, Mokpo National University, Muan, 534–729, Korea
| | - Peter D. Pawelek
- Department of Chemistry and Biochemistry, Concordia University, Montreal, Quebec, H4B 1R6, Canada
| | - Erby E. Perdue
- Beckman Coulter, Inc., Life Science Division, Indianapolis, Indiana, 46268, United States of America
| | - Stephen J. Perkins
- Department of Structural and Molecular Biology, Darwin Building, University College London, London, WC1E 6BT, United Kingdom
| | - Matthew A. Perugini
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Craig L. Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Martin G. Peverelli
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Grzegorz Piszczek
- Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
| | - Gali Prag
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter E. Prevelige
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, Alabama, 35294, United States of America
| | - Bertrand D. E. Raynal
- Institut Pasteur, Centre of Biophysics of Macromolecules and Their Interactions, Paris, 75724, France
| | - Lenka Rezabkova
- Laboratory of Biomolecular Research, Department of Biology and Chemistry, Paul Scherrer Institute, 5232, Villigen PSI, Switzerland
| | - Klaus Richter
- Department of Chemistry and Center for Integrated Protein Science, Technische Universität München, 85748, Garching, Germany
| | - Alison E. Ringel
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Rose Rosenberg
- Physical Chemistry, University of Konstanz, 78457, Konstanz, Germany
| | - Arthur J. Rowe
- National Centre for Macromolecular Hydrodynamics, University of Nottingham, School of Biosciences, Sutton Bonington, LE12 5RD, United Kingdom
| | - Arne C. Rufer
- Pharma Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-LaRoche Ltd., Basel, 4070, Switzerland
| | - David J. Scott
- Research Complex at Harwell, Rutherford Appleton Laboratory, Oxfordshire, OX11 0FA, United Kingdom
| | - Javier G. Seravalli
- Redox Biology Center, University of Nebraska-Lincoln, Lincoln, Nebraska, 68588, United States of America
| | - Alexandra S. Solovyova
- Proteome and Protein Analysis, University of Newcastle, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Renjie Song
- Wadsworth Center, New York State Department of Health, Albany, New York, 12208, United States of America
| | - David Staunton
- Molecular Biophysics Suite, Department of Biochemistry, Oxford, Oxon, OX1 3QU, United Kingdom
| | - Caitlin Stoddard
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, California, 94158, United States of America
- Tetrad Graduate Program, University of California San Francisco, San Francisco, California, 94158, United States of America
| | - Katherine Stott
- Biochemistry Department, University of Cambridge, Cambridge, CB2 1GA, United Kingdom
| | | | - Werner W. Streicher
- Protein Function and Interactions, Novo Nordisk Foundation Center for Protein Research, Copenhagen, 2200, Denmark
| | - John P. Sumida
- Analytical Biopharmacy Core, University of Washington, Seattle, Washington, 98195, United States of America
| | - Sarah G. Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts, 01605, United States of America
| | - Roman H. Szczepanowski
- Core Facility, International Institute of Molecular and Cell Biology, Warsaw, 02–109, Poland
| | - Ingrid Tessmer
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg, 97080, Würzburg, Germany
| | - Ronald T. Toth
- Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047, United States of America
| | - Ashutosh Tripathy
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, 27599, United States of America
| | - Susumu Uchiyama
- Department of Biotechnology, Graduate School of Engineering, Osaka University, Suita, Osaka, 565–0871, Japan
| | - Stephan F. W. Uebel
- Biochemistry Core Facility, Max Planck Institute of Biochemistry, 82152, Martinsried, Germany
| | - Satoru Unzai
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, Yokohama, 230–0045, Japan
| | - Anna Vitlin Gruber
- Department of Biochemistry and Molecular Biology, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Peter H. von Hippel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Christine Wandrey
- Laboratoire de Médecine Régénérative et de Pharmacobiologie, Ecole Polytechnique Fédérale de Lausanne, Lausanne, CH-1015, Switzerland
| | - Szu-Huan Wang
- Biophysics Core Facility, Scientific Instrument Center, Academia Sinica, Taipei, 115, Taiwan
| | - Steven E. Weitzel
- Institute of Molecular Biology and Department of Chemistry and Biochemistry, University of Oregon, Eugene, Oregon, 97403, United States of America
| | - Beata Wielgus-Kutrowska
- Division of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Warsaw, 02–089, Poland
| | - Cynthia Wolberger
- Department of Biophysics and Biophysical Chemistry, Johns Hopkins University School of Medicine, Baltimore, Maryland, 21205, United States of America
| | - Martin Wolff
- ICS-6, Structural Biochemistry, Research Center Juelich, 52428, Juelich, Germany
| | - Edward Wright
- Biochemistry, Cell and Molecular Biology Department, University of Tennessee, Knoxville, Tennessee, 37996–0840, United States of America
| | - Yu-Sung Wu
- Department of Chemical & Biomolecular Engineering, University of Delaware, Newark, Delaware, 19716, United States of America
| | - Jacinta M. Wubben
- Department of Biochemistry, La Trobe Institute for Molecular Science, La Trobe University, Melbourne, Victoria, 3086, Australia
| | - Peter Schuck
- Dynamics of Macromolecular Assembly Section, Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, 20892, United States of America
- * E-mail:
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Xue Y, Van C, Pradhan SK, Su T, Gehrke J, Kuryan BG, Kitada T, Vashisht A, Tran N, Wohlschlegel J, Peterson CL, Kurdistani SK, Carey MF. The Ino80 complex prevents invasion of euchromatin into silent chromatin. Genes Dev 2015; 29:350-5. [PMID: 25691465 PMCID: PMC4335291 DOI: 10.1101/gad.256255.114] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Here we show that the Ino80 chromatin remodeling complex (Ino80C) directly prevents euchromatin from invading transcriptionally silent chromatin within intergenic regions and at the border of euchromatin and heterochromatin. Deletion of Ino80C subunits leads to increased H3K79 methylation and noncoding RNA polymerase II (Pol II) transcription centered at the Ino80C-binding sites. The effect of Ino80C is direct, as it blocks H3K79 methylation by Dot1 in vitro. Heterochromatin stimulates the binding of Ino80C in vitro and in vivo. Our data reveal that Ino80C serves as a general silencing complex that restricts transcription to gene units in euchromatin.
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Affiliation(s)
- Yong Xue
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Christopher Van
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Suman K Pradhan
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Trent Su
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Jason Gehrke
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Benjamin G Kuryan
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Tasuku Kitada
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Ajay Vashisht
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Nancy Tran
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - James Wohlschlegel
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
| | - Siavash K Kurdistani
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Michael F Carey
- Department of Biological Chemistry, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, California 90095, USA;
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Bennett G, Peterson CL. SWI/SNF recruitment to a DNA double-strand break by the NuA4 and Gcn5 histone acetyltransferases. DNA Repair (Amst) 2015; 30:38-45. [PMID: 25869823 DOI: 10.1016/j.dnarep.2015.03.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2015] [Revised: 03/16/2015] [Accepted: 03/18/2015] [Indexed: 12/19/2022]
Abstract
The DNA damage response to double-strand breaks (DSBs) is critical for cellular viability. Recent work has shown that a host of chromatin regulators are recruited to a DSB, and that they are important for the DNA damage response. However, the functional relationships between different chromatin regulators at DSBs remain unclear. Here we describe a conserved functional interaction among the chromatin remodeling enzyme, SWI/SNF, the NuA4 and Gcn5 histone acetyltransferases, and phosphorylation of histone H2A.X (γH2AX). Specifically, we find that the NuA4 and Gcn5 enzymes are both required for the robust recruitment of SWI/SNF to a DSB, which in turn promotes the phosphorylation of H2A.X.
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Affiliation(s)
- Gwendolyn Bennett
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01606, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01606, USA.
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Van C, Williams JS, Kunkel TA, Peterson CL. Deposition of histone H2A.Z by the SWR-C remodeling enzyme prevents genome instability. DNA Repair (Amst) 2014; 25:9-14. [PMID: 25463393 DOI: 10.1016/j.dnarep.2014.10.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Revised: 10/27/2014] [Accepted: 10/31/2014] [Indexed: 10/24/2022]
Abstract
The yeast SWR-C chromatin remodeling enzyme catalyzes chromatin incorporation of the histone variant H2A.Z which plays roles in transcription, DNA repair, and chromosome segregation. Dynamic incorporation of H2A.Z by SWR-C also enhances the ability of exonuclease I (Exo1) to process DNA ends during repair of double strand breaks. Given that Exo1 also participates in DNA replication and mismatch repair, here we test whether SWR-C influences DNA replication fidelity. We find that inactivation of SWR-C elevates the spontaneous mutation rate of a strain encoding a L612M variant of DNA polymerase (Pol) δ, with a single base mutation signature characteristic of lagging strand replication errors. However, this genomic instability does not solely result from reduced Exo1 function, because single base mutator effects are seen in both Exo1-proficient and Exo1-deficient pol3-L612M swr1Δ strains. The data are consistent with the possibility that incorporation of the H2A.Z variant by SWR-C may stimulate Exo1 activity, as well as enhance the fidelity of replication by Pol δ, the repair of mismatches generated by Pol δ, or both.
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Affiliation(s)
- Christopher Van
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, United States
| | - Jessica S Williams
- Laboratory of Structural Biology and Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
| | - Thomas A Kunkel
- Laboratory of Structural Biology and Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, United States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, United States.
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Swygert SG, Peterson CL. Chromatin dynamics: interplay between remodeling enzymes and histone modifications. Biochim Biophys Acta 2014; 1839:728-36. [PMID: 24583555 DOI: 10.1016/j.bbagrm.2014.02.013] [Citation(s) in RCA: 165] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Revised: 02/13/2014] [Accepted: 02/20/2014] [Indexed: 01/08/2023]
Abstract
Chromatin dynamics play an essential role in regulating the accessibility of genomic DNA for a variety of nuclear processes, including gene transcription and DNA repair. The posttranslational modification of the core histones and the action of ATP-dependent chromatin remodeling enzymes represent two primary mechanisms by which chromatin dynamics are controlled and linked to nuclear events. Although there are examples in which a histone modification or a remodeling enzyme may be sufficient to drive a chromatin transition, these mechanisms typically work in concert to integrate regulatory inputs, leading to a coordinated alteration in chromatin structure and function. Indeed, site-specific histone modifications can facilitate the recruitment of chromatin remodeling enzymes to particular genomic regions, or they can regulate the efficiency or the outcome of a chromatin remodeling reaction. Conversely, chromatin remodeling enzymes can also influence, and sometimes directly modulate, the modification state of histones. These functional interactions are generally complex, frequently transient, and often require the association of myriad additional factors. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
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Affiliation(s)
- Sarah G Swygert
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Bennett G, Papamichos-Chronakis M, Peterson CL. DNA repair choice defines a common pathway for recruitment of chromatin regulators. Nat Commun 2013; 4:2084. [PMID: 23811932 PMCID: PMC3731036 DOI: 10.1038/ncomms3084] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Accepted: 05/30/2013] [Indexed: 12/31/2022] Open
Abstract
DNA double-strand break (DSB) repair is essential for maintenance of genome stability. Recent work has implicated a host of chromatin regulators in the DNA damage response, and although several functional roles have been defined, the mechanisms that control their recruitment to DNA lesions remain unclear. Here, we find that efficient DSB recruitment of the INO80, SWR-C, NuA4, SWI/SNF, and RSC enzymes is inhibited by the non-homologous end joining machinery, and that their recruitment is controlled by early steps of homologous recombination. Strikingly, we find no significant role for H2A.X phosphorylation (γH2AX) in the recruitment of chromatin regulators, but rather their recruitment coincides with reduced levels of γH2AX. Our work indicates that cell cycle position plays a key role in DNA repair pathway choice and that recruitment of chromatin regulators is tightly coupled to homologous recombination.
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Affiliation(s)
- Gwendolyn Bennett
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01606, USA
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Abstract
By some estimates, a eukaryotic cell must repair up to 10,000 DNA lesions per cell cycle to counteract endogenous sources of DNA damage. Exposure to environmental toxins, UV sources, or other radiations only increases this enormous number. Failure to repair such lesions can lead to a deleterious mutation rate, genomic instability, or cell death. The timely and efficient repair of eukaryotic DNA damage is further complicated by the realization that DNA lesions must be detected and repaired in the context of chromatin with its complex organization within the nucleus. Numerous studies have shown that chromatin packaging can inhibit nearly all repair pathways, and recent work has defined specific mechanisms that facilitate DNA repair within the chromatin context. In this review, we provide a broad overview of chromatin regulatory mechanisms, mainly at the nucleosomal level, and then focus on recent work that elucidates the role of chromatin structure in regulating the timely and efficient repair of DNA double-strand breaks (DSBs).
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Affiliation(s)
- Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
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31
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Abstract
Unlike traditional site-directed mutagenesis, this protocol requires only a single PCR step using full plasmid amplification to generate point mutants. The method can introduce small mutations into promoter sites and is even better suited for introducing single or double mutations into proteins. It is elegant in its simplicity and can be applied quite easily in any laboratory using standard protein expression vectors and commercially available reagents.
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32
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Affiliation(s)
- Shinya Watanabe
- Program in Molecular Medicine; University of Massachusetts Medical School; Worcester, MA USA
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33
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Abstract
The repair of DNA double strand breaks (DSBs) is critical for the maintenance of genome integrity. The first step in DSB repair by homologous recombination is processing of the ends by one of two resection pathways, exemplified by Saccharomyces cerevisiae Exo1 and Sgs1–Dna2. Here we report in vitro and in vivo studies that characterize the impact of chromatin on each resection pathway. We find that efficient resection by the Sgs1-Dna2 -dependent machinery requires a nucleosome-free gap adjacent to the DSB. Resection by Exo1 is blocked by nucleosomes, and processing activity can be partially restored by removal of the H2A-H2B dimers. Our study also supports a role for the dynamic incorporation of the H2A.Z histone variant in Exo1 processing, and it further suggests that the two resection pathways require distinct chromatin remodeling events in order to navigate chromatin structure.
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Affiliation(s)
- Nicholas L Adkins
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
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34
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Abstract
DNase I footprinting has found a wide following for both identifying and characterizing DNA-protein interactions, particularly because of its simplicity. The concept is that a partial digestion by DNase I of a uniquely (32)P-end-labeled fragment will generate a ladder of fragments, whose mobilities on a denaturing acrylamide gel and whose positions in a subsequent autoradiograph will represent the distance from the end label to the points of cleavage. Bound protein prevents binding of DNase I in and around its binding site and thus generates a "footprint" in the cleavage ladder. The distance from the end label to the edges of the footprint represents the position of the protein-binding site on the DNA fragment. The position of the binding site can be determined by electrophoresing a DNA sequencing ladder alongside the footprint. DNase I cannot bind directly adjacent to a DNA-bound protein because of steric hindrance. Hence, the footprint gives a broad indication of the binding site, generally 8-10 base pairs (bp) larger than the site itself.
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35
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Carey MF, Peterson CL, Smale ST. Preparation of (32)P-end-labeled DNA fragments for performing DNA-binding experiments. Cold Spring Harb Protoc 2013; 2013:464-8. [PMID: 23637369 DOI: 10.1101/pdb.prot074336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
The generation of a uniquely (32)P-end-labeled DNA fragment is essential for DNA-binding experiments such as DNase I footprinting and ethylation interference. We describe here a protocol for end-labeling a restriction fragment. For a plasmid DNA bearing a region containing the binding site of interest, cleaving with a single restriction endonuclease generates a 5' overhang containing a phosphate. This is generally necessary for both common forms of fragment end-labeling: phosphorylation with polynucleotide kinase and "filling in the end" with DNA polymerases (e.g., Klenow fragment). For the phosphorylation reaction, as described here, the phosphate is removed with calf intestinal phosphatase or bacterial alkaline phosphatase, and the resulting free 5'-OH is phosphorylated with polynucleotide kinase and [γ-(32)P]ATP. This generates a plasmid labeled at each end with γ-(32)P. The molar amount of plasmid DNA must be below the amount of ATP added to the reaction and the ATP must be of sufficiently high specific activity to generate a fragment labeled to the extent necessary for many DNA-binding experiments. To generate a uniquely end-labeled DNA fragment, the labeled plasmid is heat-treated to inactivate any remaining kinase and recleaved with a second endonuclease, releasing a short DNA fragment and a longer vector fragment. The DNA fragment is purified from the labeled vector on a 5%-8% native polyacrylamide gel. The preparation and labeling of DNA restriction fragments typically takes 1-2 d.
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36
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Abstract
The histone variant H2A.Z plays key roles in gene expression, DNA repair, and centromere function. H2A.Z deposition is controlled by SWR-C chromatin remodeling enzymes that catalyze the nucleosomal exchange of canonical H2A with H2A.Z. Here we report that acetylation of histone H3 on lysine 56 (H3-K56Ac) alters the substrate specificity of SWR-C, leading to promiscuous dimer exchange in which either H2A.Z or H2A can be exchanged from nucleosomes. This result was confirmed in vivo, where genome-wide analysis demonstrated widespread decreases in H2A.Z levels in yeast mutants with hyperacetylated H3K56. Our work also suggests that a conserved SWR-C subunit may function as a "lock" that prevents removal of H2A.Z from nucleosomes. Our study identifies a histone modification that regulates a chromatin remodeling reaction and provides insights into how histone variants and nucleosome turnover can be controlled by chromatin regulators.
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Affiliation(s)
- Shinya Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA 01605, USA
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37
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Rege MM, Peterson CL. SWI/SNF
remodels
SIR3
heterochromatin during transcription. FASEB J 2013. [DOI: 10.1096/fasebj.27.1_supplement.770.6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Mayuri M Rege
- Program in Molecular MedicineUniversity of Massachusetts Medical SchoolWorcesterMA
| | - Craig L. Peterson
- Program in Molecular MedicineUniversity of Massachusetts Medical SchoolWorcesterMA
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38
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Abstract
The RNase protection assay is a sensitive method for transcription start-site localization. It begins with an RNA probe that is uniformly labeled by incorporation of one [α-(32)P]NTP, usually [α-(32)P]UTP. The RNA probe is synthesized by bacteriophage RNA polymerase (SP6, T7, or T3), which initiates transcription from specific phage promoters that have been engineered into a number of common plasmid vectors. The plasmid template contains a genomic DNA fragment spanning the region thought to contain the transcription start site for the gene of interest. This genomic fragment is subcloned into the plasmid downstream of the phage promoter in the antisense orientation, so that a portion of the 5' end of the resulting RNA probe will be complementary to the mRNA of interest. The radiolabeled probe is annealed to cytoplasmic or total cellular mRNA purified from the cells of interest, with the hybridization reaction proceeding for several hours or overnight. RNase A and/or RNase T1 is then added to the hybridization reactions. These nucleases digest the single-stranded overhang regions of RNA molecules, but RNA-RNA hybrids are resistant to cleavage. This resistance forms the conceptual basis for the procedure; the region of the probe that anneals to the specific mRNA will be resistant to digestion. The length of the resistant region of the probe will correspond to the distance from the 5' end of the probe to the transcription start site. The size of the resistant fragment can be determined by electrophoresis on a high-resolution, denaturing polyacrylamide gel.
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Abstract
Chromatin-remodeling enzymes use the energy from ATP hydrolysis to mobilize, disrupt or change the histone composition of nucleosomes, facilitating nearly every nuclear event. Two recent studies indicate that remodeling enzymes harness the power of an ancient constitutively active DNA translocase and that different remodeling enzymes may use specialized coupling domains that communicate the presence of nucleosomal epitopes to regulate translocase and remodeling activity.
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Affiliation(s)
- Benjamin J Manning
- University of Massachusetts Medical School, Worcester, Massachusetts, USA
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40
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Abstract
Identifying DNA-binding proteins that interact with a control region of interest has become quite straightforward. However, the functional relevance of a given protein-DNA interaction is difficult to establish. The hypothesis that an interaction is relevant can be tested by several different experiments, 12 of which are outlined in this article. It must be remembered that none of these experiments by itself is conclusive. The information gained from each approach is described and explanations are given for why each yields useful but inconclusive results. The approaches vary widely with respect to the amount of effort required and the quality of information obtained.
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Sanz AB, García R, Rodríguez-Peña JM, Díez-Muñiz S, Nombela C, Peterson CL, Arroyo J. Chromatin remodeling by the SWI/SNF complex is essential for transcription mediated by the yeast cell wall integrity MAPK pathway. Mol Biol Cell 2012; 23:2805-17. [PMID: 22621902 PMCID: PMC3395667 DOI: 10.1091/mbc.e12-04-0278] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In Saccharomyces cerevisiae, the transcriptional program triggered by cell wall stress is coordinated by Slt2/Mpk1, the mitogen-activated protein kinase (MAPK) of the cell wall integrity (CWI) pathway, and is mostly mediated by the transcription factor Rlm1. Here we show that the SWI/SNF chromatin-remodeling complex plays a critical role in orchestrating the transcriptional response regulated by Rlm1. swi/snf mutants show drastically reduced expression of cell wall stress-responsive genes and hypersensitivity to cell wall-interfering compounds. On stress, binding of RNA Pol II to the promoters of these genes depends on Rlm1, Slt2, and SWI/SNF. Rlm1 physically interacts with SWI/SNF to direct its association to target promoters. Finally, we observe nucleosome displacement at the CWI-responsive gene MLP1/KDX1, which relies on the SWI/SNF complex. Taken together, our results identify the SWI/SNF complex as a key element of the CWI MAPK pathway that mediates the chromatin remodeling necessary for adequate transcriptional response to cell wall stress.
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Affiliation(s)
- A Belén Sanz
- Departamento de Microbiología II, Facultad de Farmacia, Universidad Complutense de Madrid, Madrid, Spain
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42
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Abstract
The integrity of a eukaryotic genome is often challenged by DNA double-strand breaks (DSBs). Even a single, unrepaired DSB can be a lethal event, or such unrepaired damage can result in chromosomal instability and loss of genetic information. Furthermore, defects in the pathways that respond to and repair DSBs can lead to the onset of several human pathologic disorders with pleiotropic clinical features, including age-related diseases and cancer. For decades, studies have focused on elucidating the enzymatic mechanisms involved in recognizing, signaling and repairing DSBs within eukaryotic cells. The majority of biochemical and genetic studies have used simple, DNA substrates, whereas only recently efforts have been geared towards understanding how the repair machinery deals with DSBs within chromatin fibers, the nucleoprotein complex that packages DNA within the eukaryotic nucleus. The aim of this review is to discuss our recent understanding of the relationship between chromatin structure and the repair of DSBs by homologous recombination. In particular, we discuss recent studies implicating specialized roles for several, distinct ATP-dependent chromatin remodeling enzymes in facilitating multiple steps within the homologous recombination process.
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Affiliation(s)
- Manisha Sinha
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
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43
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Abstract
Computational methods can be used to identify DNA sequence motifs that have been conserved through evolution, as well as motifs that correspond to recognition sites for known DNA-binding proteins. These computational methods, when combined with chromatin immunoprecipitation and other basic experiments, can provide preliminary insight into the elements and factors that regulate a gene of interest. When pursuing a more complete understanding of a control region of interest, a comprehensive mutant analysis should generally be performed as a critical step toward more advanced functional studies. This article describes strategies for such a comprehensive analysis. It also summarizes the insights provided by a comprehensive mutant analysis versus a phylogenetic analysis.
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Carey MF, Peterson CL, Smale ST. Experimental strategies for cloning or identifying genes encoding DNA-binding proteins. Cold Spring Harb Protoc 2012; 2012:183-92. [PMID: 22301659 DOI: 10.1101/pdb.top067900] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
This article describes experimental strategies for cloning or identifying genes encoding DNA-binding proteins. DNA-binding proteins are most commonly identified by electrophoretic mobility-shift assay (EMSA) or DNase I footprinting. To identify the gene encoding a protein detected by EMSA or DNase footprinting, the protein often needs to be purified and its sequence analyzed, as described here. Other methods are also available which do not resort to protein purification, including the one-hybrid screen, in vitro expression library screen, and mammalian expression cloning. These methods are outlined, and their advantages and disadvantages are discussed.
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45
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Abstract
This article describes approaches for identifying proteins that bind conserved or functional DNA motifs. It discusses the use of consensus sequence databases to identify candidate proteins capable of binding a DNA motif of interest and then explains the potential uses of sophisticated mass spectrometry technology. DNA-binding proteins are most commonly identified by electrophoretic mobility-shift assay (EMSA) or DNase I footprinting. Each of these methods is described, and their advantages and limitations are outlined. It is important to stress that each of the strategies discussed in this article may identify one or more proteins that bind a DNA element of interest. However, none of the strategies will necessarily lead to the protein that is the functionally relevant regulator of the control element in the context of the endogenous locus. Regardless of how a DNA-binding protein is isolated and identified, it merely becomes a candidate regulator of the gene of interest.
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46
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Abstract
Repetitive DNA is often packaged into heterochromatin structures that prevent illicit recombination events that cause genomic instability. A recent study by Chiolo et al. (2011) published in Cell finds that DNA double-strand breaks formed within heterochromatin are shuttled to adjacent sites that are "safe" to complete repair by recombination.
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Affiliation(s)
- Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Medical School, 373 Plantation Street, Worcester, MA 01605, USA.
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47
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Abstract
The evolutionarily conserved INO80 family of ATP-dependent chromatin-remodeling enzymes has roles in many nuclear processes, including transcription, DNA repair, and DNA replication. Here, we discuss the in vivo and in vitro properties of these enzymes, focusing on recent studies which suggest that members of this family govern the deposition and removal of the histone variant H2A.Z.
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Affiliation(s)
- S Watanabe
- Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA
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48
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49
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Carey MF, Peterson CL, Smale ST. Magnesium-agarose electrophoretic mobility shift assay (EMSA) of transcription factor IID binding to DNA. Cold Spring Harb Protoc 2010; 2010:pdb.prot5514. [PMID: 21041387 DOI: 10.1101/pdb.prot5514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The general transcription factor IID (TFIID) is a key target for regulation because its binding to a core promoter is the nucleating step in transcription complex assembly. Many eukaryotic activators stimulate recruitment of the TFIID when its concentration is made limiting at a promoter in vitro. Magnesium-agarose gels can separate large complexes containing TFIID, TFIIA (the DA complex), and TFIIB (the DAB complex) and permit a quantitative measurement of how activators stimulate assembly of such complexes. The advantage of the electrophoretic mobility shift assay (EMSA) is that the reactions can be performed under subsaturating conditions where a TFIID footprint might not be observed. Typically, the activator is incubated with a 32P-labeled DNA template, recombinant TFIIA purified from Escherichia coli, and immunopurified TFIID. After incubation, the samples are electrophoresed on magnesium-containing agarose gels, dried onto DEAE-cellulose paper, and autoradiographed. The DNA-protein complexes containing TFIID migrate with reduced mobility on magnesium-agarose gels both because of the large size of the complex and because the TATA-binding protein (TBP) subunit induces a sharp bend in the DNA, causing altered mobility. By comparing the binding of TFIID over a wide concentration range, with and without activator, one can assess whether the activator interacts with TBP or with one of the TBP-associated factors (TAFIIs). Additional factors such as TFIIA and TFIIB can be added subsequently to quantify their contributions to assembly of the transcription complex.
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50
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Carey MF, Peterson CL, Smale ST. Protein complex binding to promoter DNA: immobilized template assay. Cold Spring Harb Protoc 2010; 2010:pdb.prot5465. [PMID: 20679374 DOI: 10.1101/pdb.prot5465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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