1
|
Baier AS, Gioacchini N, Eek P, Leith EM, Tan S, Peterson CL. Dual engagement of the nucleosomal acidic patches is essential for deposition of histone H2A.Z by SWR1C. eLife 2024; 13:RP94869. [PMID: 38809771 PMCID: PMC11139478 DOI: 10.7554/elife.94869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024] Open
Abstract
The yeast 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. 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 ubiquitylation may regulate H2A.Z deposition. Together these findings provide new insights into how SWR1C engages its nucleosomal substrate to promote efficient H2A.Z deposition.
Collapse
Affiliation(s)
- Alexander S Baier
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Medical Scientist Training Program, T.H. Chan School of Medicine, University of MassachusettsBostonUnited States
| | - Nathan Gioacchini
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
- Interdisciplinary Graduate Program, Morningside Graduate School of Biomedical Sciences, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| | - Priit Eek
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
- Department of Chemistry and Biotechnology, Tallinn University of TechnologyTallinnEstonia
| | - Erik M Leith
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Song Tan
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, Pennsylvania State UniversityUniversity ParkUnited States
| | - Craig L Peterson
- Program in Molecular Medicine, University of Massachusetts Chan Medical SchoolWorcesterUnited States
| |
Collapse
|
2
|
Sánchez H, Liu Z, van Veen E, van Laar T, Diffley JFX, Dekker NH. A chromatinized origin reduces the mobility of ORC and MCM through interactions and spatial constraint. Nat Commun 2023; 14:6735. [PMID: 37872142 PMCID: PMC10593741 DOI: 10.1038/s41467-023-42524-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 10/13/2023] [Indexed: 10/25/2023] Open
Abstract
Chromatin replication involves the assembly and activity of the replisome within the nucleosomal landscape. At the core of the replisome is the Mcm2-7 complex (MCM), which is loaded onto DNA after binding to the Origin Recognition Complex (ORC). In yeast, ORC is a dynamic protein that diffuses rapidly along DNA, unless halted by origin recognition sequences. However, less is known about the dynamics of ORC proteins in the presence of nucleosomes and attendant consequences for MCM loading. To address this, we harnessed an in vitro single-molecule approach to interrogate a chromatinized origin of replication. We find that ORC binds the origin of replication with similar efficiency independently of whether the origin is chromatinized, despite ORC mobility being reduced by the presence of nucleosomes. Recruitment of MCM also proceeds efficiently on a chromatinized origin, but subsequent movement of MCM away from the origin is severely constrained. These findings suggest that chromatinized origins in yeast are essential for the local retention of MCM, which may facilitate subsequent assembly of the replisome.
Collapse
Affiliation(s)
- Humberto Sánchez
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Zhaowei Liu
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Edo van Veen
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - Theo van Laar
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
| | - John F X Diffley
- Chromosome Replication Laboratory, Francis Crick Institute, London, United Kingdom
| | - Nynke H Dekker
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands.
| |
Collapse
|
3
|
Börner GV, Hochwagen A, MacQueen AJ. Meiosis in budding yeast. Genetics 2023; 225:iyad125. [PMID: 37616582 PMCID: PMC10550323 DOI: 10.1093/genetics/iyad125] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 06/13/2023] [Indexed: 08/26/2023] Open
Abstract
Meiosis is a specialized cell division program that is essential for sexual reproduction. The two meiotic divisions reduce chromosome number by half, typically generating haploid genomes that are packaged into gametes. To achieve this ploidy reduction, meiosis relies on highly unusual chromosomal processes including the pairing of homologous chromosomes, assembly of the synaptonemal complex, programmed formation of DNA breaks followed by their processing into crossovers, and the segregation of homologous chromosomes during the first meiotic division. These processes are embedded in a carefully orchestrated cell differentiation program with multiple interdependencies between DNA metabolism, chromosome morphogenesis, and waves of gene expression that together ensure the correct number of chromosomes is delivered to the next generation. Studies in the budding yeast Saccharomyces cerevisiae have established essentially all fundamental paradigms of meiosis-specific chromosome metabolism and have uncovered components and molecular mechanisms that underlie these conserved processes. Here, we provide an overview of all stages of meiosis in this key model system and highlight how basic mechanisms of genome stability, chromosome architecture, and cell cycle control have been adapted to achieve the unique outcome of meiosis.
Collapse
Affiliation(s)
- G Valentin Börner
- Center for Gene Regulation in Health and Disease (GRHD), Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA
| | | | - Amy J MacQueen
- Department of Molecular Biology and Biochemistry, Wesleyan University, Middletown, CT 06459, USA
| |
Collapse
|
4
|
Huang L, Wang Y, Long H, Zhu H, Wen Z, Zhang L, Zhang W, Guo Z, Wang L, Tang F, Hu J, Bao K, Zhu P, Li G, Zhou Z. Structural insight into H4K20 methylation on H2A.Z-nucleosome by SUV420H1. Mol Cell 2023; 83:2884-2895.e7. [PMID: 37536340 DOI: 10.1016/j.molcel.2023.07.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 08/05/2023]
Abstract
DNA replication ensures the accurate transmission of genetic information during the cell cycle. Histone variant H2A.Z is crucial for early replication origins licensing and activation in which SUV420H1 preferentially recognizes H2A.Z-nucleosome and deposits H4 lysine 20 dimethylation (H4K20me2) on replication origins. Here, we report the cryo-EM structures of SUV420H1 bound to H2A.Z-nucleosome or H2A-nucleosome and demonstrate that SUV420H1 directly interacts with H4 N-terminal tail, the DNA, and the acidic patch in the nucleosome. The H4 (1-24) forms a lasso-shaped structure that stabilizes the SUV420H1-nucleosome complex and precisely projects the H4K20 residue into the SUV420H1 catalytic center. In vitro and in vivo analyses reveal a crucial role of the SUV420H1 KR loop (residues 214-223), which lies close to the H2A.Z-specific residues D97/S98, in H2A.Z-nucleosome preferential recognition. Together, our findings elucidate how SUV420H1 recognizes nucleosomes to ensure site-specific H4K20me2 modification and provide insights into how SUV420H1 preferentially recognizes H2A.Z nucleosome.
Collapse
Affiliation(s)
- Li Huang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Youwang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Haizhen Long
- Institute of Molecular Physiology, Shenzhen Bay Laboratory, Shenzhen 518132, China.
| | - Haoqiang Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zengqi Wen
- School of Medicine, Sun Yat-sen University, Shenzhen 518107, China
| | - Liwei Zhang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Wenhao Zhang
- Ministry of Education (MOE) Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Zhenqian Guo
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Longge Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangyi Tang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jie Hu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keyan Bao
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ping Zhu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| | - Guohong Li
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430072, China.
| | - Zheng Zhou
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China.
| |
Collapse
|
5
|
Wang S, Fairall L, Pham TK, Ragan TJ, Vashi D, Collins M, Dominguez C, Schwabe JR. A potential histone-chaperone activity for the MIER1 histone deacetylase complex. Nucleic Acids Res 2023; 51:6006-6019. [PMID: 37099381 PMCID: PMC10325919 DOI: 10.1093/nar/gkad294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 03/10/2023] [Accepted: 04/19/2023] [Indexed: 04/27/2023] Open
Abstract
Histone deacetylases 1 and 2 (HDAC1/2) serve as the catalytic subunit of six distinct families of nuclear complexes. These complexes repress gene transcription through removing acetyl groups from lysine residues in histone tails. In addition to the deacetylase subunit, these complexes typically contain transcription factor and/or chromatin binding activities. The MIER:HDAC complex has hitherto been poorly characterized. Here, we show that MIER1 unexpectedly co-purifies with an H2A:H2B histone dimer. We show that MIER1 is also able to bind a complete histone octamer. Intriguingly, we found that a larger MIER1:HDAC1:BAHD1:C1QBP complex additionally co-purifies with an intact nucleosome on which H3K27 is either di- or tri-methylated. Together this suggests that the MIER1 complex acts downstream of PRC2 to expand regions of repressed chromatin and could potentially deposit histone octamer onto nucleosome-depleted regions of DNA.
Collapse
Affiliation(s)
- Siyu Wang
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Trong Khoa Pham
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Timothy J Ragan
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Dipti Vashi
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Mark O Collins
- School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
- biOMICS facility, Mass Spectrometry Centre, University of Sheffield, Sheffield S10 2TN, UK
| | - Cyril Dominguez
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- Institute for Structural and Chemical Biology & Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| |
Collapse
|
6
|
Liu D, Sonalkar J, Prasanth SG. ORChestra coordinates the replication and repair music. Bioessays 2023; 45:e2200229. [PMID: 36811379 PMCID: PMC10023367 DOI: 10.1002/bies.202200229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/03/2023] [Accepted: 02/06/2023] [Indexed: 02/24/2023]
Abstract
Error-free genome duplication and accurate cell division are critical for cell survival. In all three domains of life, bacteria, archaea, and eukaryotes, initiator proteins bind replication origins in an ATP-dependent manner, play critical roles in replisome assembly, and coordinate cell-cycle regulation. We discuss how the eukaryotic initiator, Origin recognition complex (ORC), coordinates different events during the cell cycle. We propose that ORC is the maestro driving the orchestra to coordinately perform the musical pieces of replication, chromatin organization, and repair.
Collapse
Affiliation(s)
- Dazhen Liu
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
| | - Jay Sonalkar
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
| | - Supriya G. Prasanth
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, 601S Goodwin Avenue, Urbana, IL 61801 USA
- Cancer center at Illinois, UIUC
| |
Collapse
|
7
|
Chacin E, Reusswig KU, Furtmeier J, Bansal P, Karl LA, Pfander B, Straub T, Korber P, Kurat CF. Establishment and function of chromatin organization at replication origins. Nature 2023; 616:836-842. [PMID: 37020028 DOI: 10.1038/s41586-023-05926-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 03/03/2023] [Indexed: 04/07/2023]
Abstract
The origin recognition complex (ORC) is essential for initiation of eukaryotic chromosome replication as it loads the replicative helicase-the minichromosome maintenance (MCM) complex-at replication origins1. Replication origins display a stereotypic nucleosome organization with nucleosome depletion at ORC-binding sites and flanking arrays of regularly spaced nucleosomes2-4. However, how this nucleosome organization is established and whether this organization is required for replication remain unknown. Here, using genome-scale biochemical reconstitution with approximately 300 replication origins, we screened 17 purified chromatin factors from budding yeast and found that the ORC established nucleosome depletion over replication origins and flanking nucleosome arrays by orchestrating the chromatin remodellers INO80, ISW1a, ISW2 and Chd1. The functional importance of the nucleosome-organizing activity of the ORC was demonstrated by orc1 mutations that maintained classical MCM-loader activity but abrogated the array-generation activity of ORC. These mutations impaired replication through chromatin in vitro and were lethal in vivo. Our results establish that ORC, in addition to its canonical role as the MCM loader, has a second crucial function as a master regulator of nucleosome organization at the replication origin, a crucial prerequisite for efficient chromosome replication.
Collapse
Affiliation(s)
- Erika Chacin
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Karl-Uwe Reusswig
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jessica Furtmeier
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Priyanka Bansal
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Leonhard A Karl
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
| | - Boris Pfander
- Max Planck Institute of Biochemistry, DNA Replication and Genome Integrity, Martinsried, Germany
- Genome Maintenance Mechanisms in Health and Disease, Institute of Aerospace Medicine, German Aerospace Center (DLR), Cologne, Germany
- Institute of Genome Stability in Aging and Disease, CECAD, University of Cologne, Medical Faculty, Cologne, Germany
| | - Tobias Straub
- Core Facility Bioinformatics, BMC, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Philipp Korber
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany
| | - Christoph F Kurat
- Biomedical Center Munich (BMC), Division of Molecular Biology, Faculty of Medicine, Ludwig-Maximilians-Universität in Munich, Martinsried, Germany.
| |
Collapse
|
8
|
Origin recognition complex harbors an intrinsic nucleosome remodeling activity. Proc Natl Acad Sci U S A 2022; 119:e2211568119. [PMID: 36215487 PMCID: PMC9586268 DOI: 10.1073/pnas.2211568119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Nucleosomes package the entire eukaryotic genome, yet enzymes need access to the DNA for numerous metabolic activities, such as replication and transcription. Eukaryotic origins of replication in Saccharomyces cerevisiae are AT rich and are generally nucleosome free for the binding of ORC (origin recognition complex). However, the nucleosome-free region often undergoes expansion during G1/S phase, presumably to make room for MCM double-hexamer formation that nucleates the 11-subunit helicase, CMG (Cdc45, Mcm2–7, Cdc45). While nucleosome remodelers could perform this function, in vitro studies indicate that nucleosome remodeling may be intrinsic to the replication machinery. Indeed, we find here that ORC contains an intrinsic nucleosome remodeling activity that is capable of ATP-stimulated removal of H2A-H2B from nucleosomes. Eukaryotic DNA replication is initiated at multiple chromosomal sites known as origins of replication that are specifically recognized by the origin recognition complex (ORC) containing multiple ATPase sites. In budding yeast, ORC binds to specific DNA sequences known as autonomously replicating sequences (ARSs) that are mostly nucleosome depleted. However, nucleosomes may still inhibit the licensing of some origins by occluding ORC binding and subsequent MCM helicase loading. Using purified proteins and single-molecule visualization, we find here that the ORC can eject histones from a nucleosome in an ATP-dependent manner. The ORC selectively evicts H2A-H2B dimers but leaves the (H3-H4)2 tetramer on DNA. It also discriminates canonical H2A from the H2A.Z variant, evicting the former while retaining the latter. Finally, the bromo-adjacent homology (BAH) domain of the Orc1 subunit is essential for ORC-mediated histone eviction. These findings suggest that the ORC is a bona fide nucleosome remodeler that functions to create a local chromatin environment optimal for origin activity.
Collapse
|
9
|
Nucleosome-directed replication origin licensing independent of a consensus DNA sequence. Nat Commun 2022; 13:4947. [PMID: 35999198 PMCID: PMC9399094 DOI: 10.1038/s41467-022-32657-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 08/09/2022] [Indexed: 02/08/2023] Open
Abstract
The numerous enzymes and cofactors involved in eukaryotic DNA replication are conserved from yeast to human, and the budding yeast Saccharomyces cerevisiae (S.c.) has been a useful model organism for these studies. However, there is a gap in our knowledge of why replication origins in higher eukaryotes do not use a consensus DNA sequence as found in S.c. Using in vitro reconstitution and single-molecule visualization, we show here that S.c. origin recognition complex (ORC) stably binds nucleosomes and that ORC-nucleosome complexes have the intrinsic ability to load the replicative helicase MCM double hexamers onto adjacent nucleosome-free DNA regardless of sequence. Furthermore, we find that Xenopus laevis nucleosomes can substitute for yeast ones in engaging with ORC. Combined with re-analyses of genome-wide ORC binding data, our results lead us to propose that the yeast origin recognition machinery contains the cryptic capacity to bind nucleosomes near a nucleosome-free region and license origins, and that this nucleosome-directed origin licensing paradigm generalizes to all eukaryotes. Most eukaryotes do not use a consensus DNA sequence as binding sites for the origin recognition complex (ORC) to initiate DNA replication, however budding yeast do. Here the authors show S. cerevisiae ORC can bind nucleosomes near nucleosome-free regions and recruit replicative helicases to form a pre-replication complex independent of the DNA sequence.
Collapse
|
10
|
Maria H, Rusche LN. The DNA replication protein Orc1 from the yeast Torulaspora delbrueckii is required for heterochromatin formation but not as a silencer-binding protein. Genetics 2022; 222:6650695. [PMID: 35894940 PMCID: PMC9434157 DOI: 10.1093/genetics/iyac110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 07/12/2022] [Indexed: 11/13/2022] Open
Abstract
To understand the process by which new protein functions emerge, we examined how the yeast heterochromatin protein Sir3 arose through gene duplication from the conserved DNA replication protein Orc1. Orc1 is a subunit of the origin recognition complex (ORC), which marks origins of DNA replication. In Saccharomyces cerevisiae, Orc1 also promotes heterochromatin assembly by recruiting the structural proteins Sir1-4 to silencer DNA. In contrast, the paralog of Orc1, Sir3, is a nucleosome-binding protein that spreads across heterochromatic loci in conjunction with other Sir proteins. We previously found that a non-duplicated Orc1 from the yeast Kluyveromyces lactis behaved like ScSir3 but did not have a silencer-binding function like ScOrc1. Moreover, K. lactis lacks Sir1, the protein that interacts directly with ScOrc1 at the silencer. Here, we examined whether the emergence of Sir1 coincided with Orc1 acting as a silencer-binding protein. In the non-duplicated species Torulaspora delbrueckii, which has an ortholog of Sir1 (TdKos3), we found that TdOrc1 spreads across heterochromatic loci independently of ORC, as ScSir3 and KlOrc1 do. This spreading is dependent on the nucleosome binding BAH domain of Orc1 and on Sir2 and Kos3. However, TdOrc1 does not have a silencer-binding function: T. delbrueckii silencers do not require ORC binding sites to function, and Orc1 and Kos3 do not appear to interact. Instead, Orc1 and Kos3 both spread across heterochromatic loci with other Sir proteins. Thus, Orc1 and Sir1/Kos3 originally had different roles in heterochromatin formation than they do now in S. cerevisiae.
Collapse
Affiliation(s)
- Haniam Maria
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY, 14260, USA
| | - Laura N Rusche
- Department of Biological Sciences, State University of New York at Buffalo, Buffalo NY, 14260, USA
| |
Collapse
|
11
|
Scherr MJ, Wahab SA, Remus D, Duderstadt KE. Mobile origin-licensing factors confer resistance to conflicts with RNA polymerase. Cell Rep 2022; 38:110531. [PMID: 35320708 PMCID: PMC8961423 DOI: 10.1016/j.celrep.2022.110531] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 12/10/2021] [Accepted: 02/23/2022] [Indexed: 12/30/2022] Open
Abstract
Fundamental to our understanding of chromosome duplication is the idea that replication origins function both as sites where MCM helicases are loaded during the G1 phase and where synthesis begins in S phase. However, the temporal delay between phases exposes the replisome assembly pathway to potential disruption prior to replication. Using multicolor, single-molecule imaging, we systematically study the consequences of encounters between actively transcribing RNA polymerases (RNAPs) and replication initiation intermediates in the context of chromatin. We demonstrate that RNAP can push multiple licensed MCM helicases over long distances with nucleosomes ejected or displaced. Unexpectedly, we observe that MCM helicase loading intermediates also can be repositioned by RNAP and continue origin licensing after encounters with RNAP, providing a web of alternative origin specification pathways. Taken together, our observations reveal a surprising mobility in origin-licensing factors that confers resistance to the complex challenges posed by diverse obstacles encountered on chromosomes. RNA polymerase robustly pushes MCMs without slowing down Nucleosomes are ejected or pushed by MCMs during repositioning RNA polymerase can bypass ORC or activate ORC sliding and OCCM sliding Origin licensing continues after RNA polymerase encounters and relocalization
Collapse
Affiliation(s)
- Matthias J Scherr
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Syafiq Abd Wahab
- Memorial Sloan Kettering Cancer Center, Molecular Biology Program, 1275 York Avenue, New York, NY 10065, USA
| | - Dirk Remus
- Memorial Sloan Kettering Cancer Center, Molecular Biology Program, 1275 York Avenue, New York, NY 10065, USA
| | - Karl E Duderstadt
- Structure and Dynamics of Molecular Machines, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany; Physik Department, Technische Universität München, James-Franck-Straße 1, 85748 Garching, Germany.
| |
Collapse
|
12
|
Xie J, Sun Y, Cao Y, Han L, Li Y, Ding B, Gao C, Hao P, Jin X, Chang Y, Song J, Yin D, Ding J. Transcriptomic and Metabolomic Analyses Provide Insights into the Growth and Development Advantages of Triploid Apostichopus japonicus. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:151-162. [PMID: 35122573 PMCID: PMC8940865 DOI: 10.1007/s10126-022-10093-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Polyploid breeding is widely used in aquaculture as an important area of new research. We have previously grown Apostichopus japonicus triploids with a growth advantage. The body length, body weight, and aestivation time of triploid and diploid A. japonicus were measured in this study, and the transcriptome and metabolome were used to examine the growth advantage of triploids A. japonicus. The results showed that the proportion of triploid A. japonicus with a body length of 6-12 cm and 12-18 cm was significantly higher than that of diploid A. japonicus, and triploid A. japonicus had a shorter aestivation time (39 days) than diploid (63 days). We discovered 3296 differentially expressed genes (DEGs); 13 DEGs (for example, cyclin-dependent kinase 2) related to growth advantage, immune regulation, and energy storage were screened as potential candidates. According to Gene Ontology (GO) enrichment analysis, DEGs were significantly enriched in the cytoplasm (cellular component), ATP binding process (molecular function), oxidation-reduction process (biological process), and other pathways. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment data, DEGs were significantly enriched in ribosome production and other areas. We discovered 414 significant differential metabolites (SDMs), with 11 important SDMs (for example, nocodazole) linked to a growth advantage. SDMs are significantly enriched in metabolic pathways, as well as other pathways, according to the KEGG enrichment results. According to a combined transcriptome and metabolome analysis, 6 DEGs have regulatory relationships with 11 SDMs, which act on 11 metabolic pathways together. Our results further enrich the biological data of triploid A. japonicus and provide useful resources for genetic improvement of this species.
Collapse
Affiliation(s)
- Jiahui Xie
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yi Sun
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yue Cao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Lingshu Han
- Ningbo University, Ningbo, Zhejiang, People's Republic of China, 315211
| | - Yuanxin Li
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Beichen Ding
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Chuang Gao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Pengfei Hao
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Xin Jin
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Yaqing Chang
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Jian Song
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Donghong Yin
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023
| | - Jun Ding
- Key Laboratory of Mariculture & Stock Enhancement in, Ministry of Agriculture and Rural Affairs, North China's Sea, Dalian Ocean University, Dalian, Liaoning, People's Republic of China, 116023.
| |
Collapse
|
13
|
Abstract
DNA replication in eukaryotic cells initiates from large numbers of sites called replication origins. Initiation of replication from these origins must be tightly controlled to ensure the entire genome is precisely duplicated in each cell cycle. This is accomplished through the regulation of the first two steps in replication: loading and activation of the replicative DNA helicase. Here we describe what is known about the mechanism and regulation of these two reactions from a genetic, biochemical, and structural perspective, focusing on recent progress using proteins from budding yeast. Expected final online publication date for the Annual Review of Biochemistry, Volume 91 is June 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
Collapse
Affiliation(s)
- Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, UK;
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London, UK;
| |
Collapse
|
14
|
McGinty RK, Tan S. Principles of nucleosome recognition by chromatin factors and enzymes. Curr Opin Struct Biol 2021; 71:16-26. [PMID: 34198054 DOI: 10.1016/j.sbi.2021.05.006] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 05/10/2021] [Accepted: 05/13/2021] [Indexed: 12/20/2022]
Abstract
The recent torrent of structures of chromatin complexes determined by cryoelectron microscopy provides an opportunity to discern general principles for how chromatin factors and enzymes interact with their nucleosome substrate. We find that many chromatin proteins use a strikingly similar arginine anchor and variant arginine interactions to bind to the nucleosome acidic patch. We also observe that many chromatin proteins target the H3 and H2B histone fold α1-loop1 elbows and the H2B C-terminal helix on the nucleosomal histone face. These interactions with the histones can be complemented with interactions with and distortions of nucleosomal DNA.
Collapse
Affiliation(s)
- Robert K McGinty
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
| | - Song Tan
- Department of Biochemistry and Molecular Biology, Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA.
| |
Collapse
|
15
|
Li Z, Marcel N, Devkota S, Auradkar A, Hedrick SM, Gantz VM, Bier E. CopyCatchers are versatile active genetic elements that detect and quantify inter-homolog somatic gene conversion. Nat Commun 2021; 12:2625. [PMID: 33976171 PMCID: PMC8113449 DOI: 10.1038/s41467-021-22927-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/01/2021] [Indexed: 11/08/2022] Open
Abstract
CRISPR-based active genetic elements, or gene-drives, copied via homology-directed repair (HDR) in the germline, are transmitted to progeny at super-Mendelian frequencies. Active genetic elements also can generate widespread somatic mutations, but the genetic basis for such phenotypes remains uncertain. It is generally assumed that such somatic mutations are generated by non-homologous end-joining (NHEJ), the predominant double stranded break repair pathway active in somatic cells. Here, we develop CopyCatcher systems in Drosophila to detect and quantify somatic gene conversion (SGC) events. CopyCatchers inserted into two independent genetic loci reveal unexpectedly high rates of SGC in the Drosophila eye and thoracic epidermis. Focused RNAi-based genetic screens identify several unanticipated loci altering SGC efficiency, one of which (c-MYC), when downregulated, promotes SGC mediated by both plasmid and homologous chromosome-templates in human HEK293T cells. Collectively, these studies suggest that CopyCatchers can serve as effective discovery platforms to inform potential gene therapy strategies.
Collapse
Affiliation(s)
- Zhiqian Li
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Nimi Marcel
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sushil Devkota
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ankush Auradkar
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Stephen M Hedrick
- Section of Molecular Biology, University of California San Diego, La Jolla, CA, USA
- Department of Cellular and Molecular Medicine, University of California San Diego, La Jolla, CA, USA
| | - Valentino M Gantz
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA
| | - Ethan Bier
- Section of Cell and Developmental Biology, University of California San Diego, La Jolla, CA, USA.
- Tata Institute for Genetics and Society-UCSD, La Jolla, CA, USA.
| |
Collapse
|
16
|
Karki M, Jangid RK, Anish R, Seervai RNH, Bertocchio JP, Hotta T, Msaouel P, Jung SY, Grimm SL, Coarfa C, Weissman BE, Ohi R, Verhey KJ, Hodges HC, Burggren W, Dere R, Park IY, Prasad BVV, Rathmell WK, Walker CL, Tripathi DN. A cytoskeletal function for PBRM1 reading methylated microtubules. SCIENCE ADVANCES 2021; 7:eabf2866. [PMID: 33811077 PMCID: PMC11059954 DOI: 10.1126/sciadv.abf2866] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 02/12/2021] [Indexed: 06/12/2023]
Abstract
Epigenetic effectors "read" marks "written" on chromatin to regulate function and fidelity of the genome. Here, we show that this coordinated read-write activity of the epigenetic machinery extends to the cytoskeleton, with PBRM1 in the PBAF chromatin remodeling complex reading microtubule methyl marks written by the SETD2 histone methyltransferase. PBRM1 binds SETD2 methyl marks via BAH domains, recruiting PBAF components to the mitotic spindle. This read-write activity was required for normal mitosis: Loss of SETD2 methylation or pathogenic BAH domain mutations disrupt PBRM1 microtubule binding and PBAF recruitment and cause genomic instability. These data reveal PBRM1 functions beyond chromatin remodeling with domains that allow it to integrate chromatin and cytoskeletal activity via its acetyl-binding BD and methyl-binding BAH domains, respectively. Conserved coordinated activity of the epigenetic machinery on the cytoskeleton opens a previously unknown window into how chromatin remodeler defects can drive disease via both epigenetic and cytoskeletal dysfunction.
Collapse
Affiliation(s)
- Menuka Karki
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rahul K Jangid
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ramakrishnan Anish
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Riyad N H Seervai
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Medical Scientist Training Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean-Philippe Bertocchio
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Genitourinary Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Takashi Hotta
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Pavlos Msaouel
- Department of Genitourinary Oncology, UT MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Yun Jung
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Sandra L Grimm
- Advanced Technology Cores, Baylor College of Medicine, Houston, TX 77030, USA
| | - Cristian Coarfa
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Bernard E Weissman
- Department of Pathology and Laboratory Medicine, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ryoma Ohi
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Kristen J Verhey
- Department of Cell and Developmental Biology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - H Courtney Hodges
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Warren Burggren
- Department of Biological Sciences, University of North Texas, Denton, TX 76201, USA
| | - Ruhee Dere
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - In Young Park
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - B V Venkataram Prasad
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - W Kimryn Rathmell
- Vanderbilt-Ingram Cancer Center, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Cheryl L Walker
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
- Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, TX 77030, USA
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA
| | - Durga N Tripathi
- Center for Precision Environmental Health, Baylor College of Medicine, Houston, TX 77030, USA.
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
17
|
Cardoso da Silva R, Vader G. Getting there: understanding the chromosomal recruitment of the AAA+ ATPase Pch2/TRIP13 during meiosis. Curr Genet 2021; 67:553-565. [PMID: 33712914 PMCID: PMC8254700 DOI: 10.1007/s00294-021-01166-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 02/16/2021] [Accepted: 02/18/2021] [Indexed: 12/21/2022]
Abstract
The generally conserved AAA+ ATPase Pch2/TRIP13 is involved in diverse aspects of meiosis, such as prophase checkpoint function, DNA break regulation, and meiotic recombination. The controlled recruitment of Pch2 to meiotic chromosomes allows it to use its ATPase activity to influence HORMA protein-dependent signaling. Because of the connection between Pch2 chromosomal recruitment and its functional roles in meiosis, it is important to reveal the molecular details that govern Pch2 localization. Here, we review the current understanding of the different factors that control the recruitment of Pch2 to meiotic chromosomes, with a focus on research performed in budding yeast. During meiosis in this organism, Pch2 is enriched within the nucleolus, where it likely associates with the specialized chromatin of the ribosomal (r)DNA. Pch2 is also found on non-rDNA euchromatin, where its recruitment is contingent on Zip1, a component of the synaptonemal complex (SC) that assembles between homologous chromosomes. We discuss recent findings connecting the recruitment of Pch2 with its association with the Origin Recognition Complex (ORC) and reliance on RNA Polymerase II-dependent transcription. In total, we provide a comprehensive overview of the pathways that control the chromosomal association of an important meiotic regulator.
Collapse
Affiliation(s)
- Richard Cardoso da Silva
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Department of Molecular Mechanisms of Disease, University of Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland.
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Otto-Hahn-Strasse 11, 44227, Dortmund, Germany. .,Department of Clinical Genetics, Section of Oncogenetics, Cancer Center Amsterdam, De Boelelaan 1118, 1081 HV, Amsterdam, The Netherlands.
| |
Collapse
|
18
|
Valencia-Sánchez MI, De Ioannes P, Wang M, Truong DM, Lee R, Armache JP, Boeke JD, Armache KJ. Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation. Science 2021; 371:371/6527/eabc6663. [PMID: 33479126 DOI: 10.1126/science.abc6663] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 10/27/2020] [Indexed: 12/30/2022]
Abstract
Dot1 (disruptor of telomeric silencing-1), the histone H3 lysine 79 (H3K79) methyltransferase, is conserved throughout evolution, and its deregulation is found in human leukemias. Here, we provide evidence that acetylation of histone H4 allosterically stimulates yeast Dot1 in a manner distinct from but coordinating with histone H2B ubiquitination (H2BUb). We further demonstrate that this stimulatory effect is specific to acetylation of lysine 16 (H4K16ac), a modification central to chromatin structure. We provide a mechanism of this histone cross-talk and show that H4K16ac and H2BUb play crucial roles in H3K79 di- and trimethylation in vitro and in vivo. These data reveal mechanisms that control H3K79 methylation and demonstrate how H4K16ac, H3K79me, and H2BUb function together to regulate gene transcription and gene silencing to ensure optimal maintenance and propagation of an epigenetic state.
Collapse
Affiliation(s)
- Marco Igor Valencia-Sánchez
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Pablo De Ioannes
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Miao Wang
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - David M Truong
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA
| | - Rachel Lee
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Jean-Paul Armache
- Department of Biochemistry and Molecular Biology, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Jef D Boeke
- Institute for Systems Genetics, Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA
| | - Karim-Jean Armache
- Skirball Institute of Biomolecular Medicine, Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY 10016, USA.
| |
Collapse
|
19
|
Millard CJ, Fairall L, Ragan TJ, Savva CG, Schwabe JWR. The topology of chromatin-binding domains in the NuRD deacetylase complex. Nucleic Acids Res 2020; 48:12972-12982. [PMID: 33264408 PMCID: PMC7736783 DOI: 10.1093/nar/gkaa1121] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 10/22/2020] [Accepted: 11/03/2020] [Indexed: 01/22/2023] Open
Abstract
Class I histone deacetylase complexes play essential roles in many nuclear processes. Whilst they contain a common catalytic subunit, they have diverse modes of action determined by associated factors in the distinct complexes. The deacetylase module from the NuRD complex contains three protein domains that control the recruitment of chromatin to the deacetylase enzyme, HDAC1/2. Using biochemical approaches and cryo-electron microscopy, we have determined how three chromatin-binding domains (MTA1-BAH, MBD2/3 and RBBP4/7) are assembled in relation to the core complex so as to facilitate interaction of the complex with the genome. We observe a striking arrangement of the BAH domains suggesting a potential mechanism for binding to di-nucleosomes. We also find that the WD40 domains from RBBP4 are linked to the core with surprising flexibility that is likely important for chromatin engagement. A single MBD2 protein binds asymmetrically to the dimerisation interface of the complex. This symmetry mismatch explains the stoichiometry of the complex. Finally, our structures suggest how the holo-NuRD might assemble on a di-nucleosome substrate.
Collapse
Affiliation(s)
- Christopher J Millard
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Louise Fairall
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Timothy J Ragan
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Christos G Savva
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| | - John W R Schwabe
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester LE1 7RH, UK
| |
Collapse
|
20
|
Skrajna A, Goldfarb D, Kedziora KM, Cousins E, Grant GD, Spangler CJ, Barbour EH, Yan X, Hathaway NA, Brown NG, Cook JG, Major MB, McGinty RK. Comprehensive nucleosome interactome screen establishes fundamental principles of nucleosome binding. Nucleic Acids Res 2020; 48:9415-9432. [PMID: 32658293 PMCID: PMC7515726 DOI: 10.1093/nar/gkaa544] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 06/03/2020] [Accepted: 06/17/2020] [Indexed: 02/03/2023] Open
Abstract
Nuclear proteins bind chromatin to execute and regulate genome-templated processes. While studies of individual nucleosome interactions have suggested that an acidic patch on the nucleosome disk may be a common site for recruitment to chromatin, the pervasiveness of acidic patch binding and whether other nucleosome binding hot-spots exist remain unclear. Here, we use nucleosome affinity proteomics with a library of nucleosomes that disrupts all exposed histone surfaces to comprehensively assess how proteins recognize nucleosomes. We find that the acidic patch and two adjacent surfaces are the primary hot-spots for nucleosome disk interactions, whereas nearly half of the nucleosome disk participates only minimally in protein binding. Our screen defines nucleosome surface requirements of nearly 300 nucleosome interacting proteins implicated in diverse nuclear processes including transcription, DNA damage repair, cell cycle regulation and nuclear architecture. Building from our screen, we demonstrate that the Anaphase-Promoting Complex/Cyclosome directly engages the acidic patch, and we elucidate a redundant mechanism of acidic patch binding by nuclear pore protein ELYS. Overall, our interactome screen illuminates a highly competitive nucleosome binding hub and establishes universal principles of nucleosome recognition.
Collapse
Affiliation(s)
- Aleksandra Skrajna
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Dennis Goldfarb
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
| | - Katarzyna M Kedziora
- Computational Medicine Program, University of North Carolina, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina, Chapel Hill, NC, USA
| | - Emily M Cousins
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Gavin D Grant
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Cathy J Spangler
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Emily H Barbour
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Xiaokang Yan
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
| | - Nathaniel A Hathaway
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
| | - Nicholas G Brown
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Jeanette G Cook
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| | - Michael B Major
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Pharmacology, University of North Carolina, Chapel Hill, NC, USA
| | - Robert K McGinty
- Division of Chemical Biology and Medicinal Chemistry, Center for Integrative Chemical Biology and Drug Discovery, UNC Eshelman School of Pharmacy, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC, USA
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, NC, USA
| |
Collapse
|
21
|
Villar-Fernández MA, Cardoso da Silva R, Firlej M, Pan D, Weir E, Sarembe A, Raina VB, Bange T, Weir JR, Vader G. Biochemical and functional characterization of a meiosis-specific Pch2/ORC AAA+ assembly. Life Sci Alliance 2020; 3:3/11/e201900630. [PMID: 32826290 PMCID: PMC7442955 DOI: 10.26508/lsa.201900630] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 08/13/2020] [Accepted: 08/13/2020] [Indexed: 12/14/2022] Open
Abstract
The AAA+ protein Pch2 forms a biochemical complex with Orc1/ORC to suppress DNA break formation in the meiotic G2/prophase. Pch2 is a meiosis-specific AAA+ protein that controls several important chromosomal processes. We previously demonstrated that Orc1, a subunit of the ORC, functionally interacts with budding yeast Pch2. The ORC (Orc1-6) AAA+ complex loads the AAA+ MCM helicase to origins of replication, but whether and how ORC collaborates with Pch2 remains unclear. Here, we show that a Pch2 hexamer directly associates with ORC during the meiotic G2/prophase. Biochemical analysis suggests that Pch2 uses its non-enzymatic NH2-terminal domain and AAA+ core and likely engages the interface of ORC that also binds to Cdc6, a factor crucial for ORC-MCM binding. Canonical ORC function requires association with origins, but we show here that despite causing efficient removal of Orc1 from origins, nuclear depletion of Orc2 and Orc5 does not trigger Pch2/Orc1-like meiotic phenotypes. This suggests that the function for Orc1/Pch2 in meiosis can be executed without efficient association of ORC with origins of replication. In conclusion, we uncover distinct functionalities for Orc1/ORC that drive the establishment of a non-canonical, meiosis-specific AAA+ assembly with Pch2.
Collapse
Affiliation(s)
- María Ascensión Villar-Fernández
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,International Max Planck Research School in Chemical and Molecular Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Richard Cardoso da Silva
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | | | - Dongqing Pan
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Elisabeth Weir
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Annika Sarembe
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Vivek B Raina
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,International Max Planck Research School in Chemical and Molecular Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Tanja Bange
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - John R Weir
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany.,Friedrich Miescher Laboratory, Tübingen, Germany
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| |
Collapse
|
22
|
Cardoso da Silva R, Villar-Fernández MA, Vader G. Active transcription and Orc1 drive chromatin association of the AAA+ ATPase Pch2 during meiotic G2/prophase. PLoS Genet 2020; 16:e1008905. [PMID: 32569318 PMCID: PMC7332104 DOI: 10.1371/journal.pgen.1008905] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 07/02/2020] [Accepted: 06/03/2020] [Indexed: 01/26/2023] Open
Abstract
Pch2 is an AAA+ protein that controls DNA break formation, recombination and checkpoint signaling during meiotic G2/prophase. Chromosomal association of Pch2 is linked to these processes, and several factors influence the association of Pch2 to euchromatin and the specialized chromatin of the ribosomal (r)DNA array of budding yeast. Here, we describe a comprehensive mapping of Pch2 localization across the budding yeast genome during meiotic G2/prophase. Within non-rDNA chromatin, Pch2 associates with a subset of actively RNA Polymerase II (RNAPII)-dependent transcribed genes. Chromatin immunoprecipitation (ChIP)- and microscopy-based analysis reveals that active transcription is required for chromosomal recruitment of Pch2. Similar to what was previously established for association of Pch2 with rDNA chromatin, we find that Orc1, a component of the Origin Recognition Complex (ORC), is required for the association of Pch2 to these euchromatic, transcribed regions, revealing a broad connection between chromosomal association of Pch2 and Orc1/ORC function. Ectopic mitotic expression is insufficient to drive recruitment of Pch2, despite the presence of active transcription and Orc1/ORC in mitotic cells. This suggests meiosis-specific ‘licensing’ of Pch2 recruitment to sites of transcription, and accordingly, we find that the synaptonemal complex (SC) component Zip1 is required for the recruitment of Pch2 to transcription-associated binding regions. Interestingly, Pch2 binding patterns are distinct from meiotic axis enrichment sites (as defined by Red1, Hop1, and Rec8). Inactivating RNAPII-dependent transcription/Orc1 does not lead to effects on the chromosomal abundance of Hop1, a known chromosomal client of Pch2, suggesting a complex relationship between SC formation, Pch2 recruitment and Hop1 chromosomal association. We thus report characteristics and dependencies for Pch2 recruitment to meiotic chromosomes, and reveal an unexpected link between Pch2, SC formation, chromatin and active transcription. Meiosis is a specialized cellular division program that is required to produce haploid reproductive cells, also known as gametes. To allow meiosis to occur faithfully, several processes centred around DNA breakage and recombination are needed. Pch2, an AAA+ ATPase enzyme is important to coordinate several of these processes. Here, we analyze the genome-wide association of Pch2 to budding yeast meiotic chromosomes. Our results show that Pch2 is recruited to a subset of actively transcribed genes, and we find that active RNAPII transcription contributes to Pch2 chromosomal association. In addition, we reveal a general contribution of Orc1, a subunit of the ORC assembly, to Pch2 chromosomal recruitment. These findings thus reveal a connection between Pch2, Orc1 and RNAPII activity during meiosis.
Collapse
Affiliation(s)
- Richard Cardoso da Silva
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - María Ascensión Villar-Fernández
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- International Max Planck Research School (IMPRS) in Chemical and Molecular Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
| | - Gerben Vader
- Department of Mechanistic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany
- * E-mail:
| |
Collapse
|
23
|
Sundaram R, Vasudevan D. Structural Basis of Nucleosome Recognition and Modulation. Bioessays 2020; 42:e1900234. [DOI: 10.1002/bies.201900234] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 05/05/2020] [Indexed: 12/14/2022]
Affiliation(s)
- Rajivgandhi Sundaram
- Laboratory of Macromolecular Crystallography Institute of Life Sciences Bhubaneswar 751023 India
- Manipal Academy of Higher Education Manipal 576104 India
| | - Dileep Vasudevan
- Laboratory of Macromolecular Crystallography Institute of Life Sciences Bhubaneswar 751023 India
| |
Collapse
|