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Kujirai T, Ehara H, Sekine SI, Kurumizaka H. Structural Transition of the Nucleosome during Transcription Elongation. Cells 2023; 12:1388. [PMID: 37408222 DOI: 10.3390/cells12101388] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/10/2023] [Accepted: 05/11/2023] [Indexed: 07/07/2023] Open
Abstract
In eukaryotes, genomic DNA is tightly wrapped in chromatin. The nucleosome is a basic unit of chromatin, but acts as a barrier to transcription. To overcome this impediment, the RNA polymerase II elongation complex disassembles the nucleosome during transcription elongation. After the RNA polymerase II passage, the nucleosome is rebuilt by transcription-coupled nucleosome reassembly. Nucleosome disassembly-reassembly processes play a central role in preserving epigenetic information, thus ensuring transcriptional fidelity. The histone chaperone FACT performs key functions in nucleosome disassembly, maintenance, and reassembly during transcription in chromatin. Recent structural studies of transcribing RNA polymerase II complexed with nucleosomes have provided structural insights into transcription elongation on chromatin. Here, we review the structural transitions of the nucleosome during transcription.
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Affiliation(s)
- Tomoya Kujirai
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Haruhiko Ehara
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Shun-Ichi Sekine
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Hitoshi Kurumizaka
- Laboratory of Chromatin Structure and Function, Institute for Quantitative Biosciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-0032, Japan
- Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamics Research, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan
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2
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Zhong Z, Wang Y, Wang M, Yang F, Thomas QA, Xue Y, Zhang Y, Liu W, Jami-Alahmadi Y, Xu L, Feng S, Marquardt S, Wohlschlegel JA, Ausin I, Jacobsen SE. Histone chaperone ASF1 mediates H3.3-H4 deposition in Arabidopsis. Nat Commun 2022; 13:6970. [PMID: 36379930 PMCID: PMC9666630 DOI: 10.1038/s41467-022-34648-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 11/01/2022] [Indexed: 11/16/2022] Open
Abstract
Histone chaperones and chromatin remodelers control nucleosome dynamics, which are essential for transcription, replication, and DNA repair. The histone chaperone Anti-Silencing Factor 1 (ASF1) plays a central role in facilitating CAF-1-mediated replication-dependent H3.1 deposition and HIRA-mediated replication-independent H3.3 deposition in yeast and metazoans. Whether ASF1 function is evolutionarily conserved in plants is unknown. Here, we show that Arabidopsis ASF1 proteins display a preference for the HIRA complex. Simultaneous mutation of both Arabidopsis ASF1 genes caused a decrease in chromatin density and ectopic H3.1 occupancy at loci typically enriched with H3.3. Genetic, transcriptomic, and proteomic data indicate that ASF1 proteins strongly prefers the HIRA complex over CAF-1. asf1 mutants also displayed an increase in spurious Pol II transcriptional initiation and showed defects in the maintenance of gene body CG DNA methylation and in the distribution of histone modifications. Furthermore, ectopic targeting of ASF1 caused excessive histone deposition, less accessible chromatin, and gene silencing. These findings reveal the importance of ASF1-mediated histone deposition for proper epigenetic regulation of the genome.
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Affiliation(s)
- Zhenhui Zhong
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yafei Wang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Ming Wang
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Fan Yang
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Quentin Angelo Thomas
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yan Xue
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA
| | - Yaxin Zhang
- grid.256111.00000 0004 1760 2876Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Wanlu Liu
- grid.512487.dZhejiang University-University of Edinburgh Institute (ZJU-UoE Institute), Zhejiang University School of Medicine, International Campus, Zhejiang University, 718 East Haizhou Road, Haining, 314400 Zhejiang China
| | - Yasaman Jami-Alahmadi
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Linhao Xu
- grid.418934.30000 0001 0943 9907Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), OT Gatersleben, Stadt Seeland, 06466 Germany
| | - Suhua Feng
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, CA 90095 USA
| | - Sebastian Marquardt
- grid.5254.60000 0001 0674 042XCopenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - James A. Wohlschlegel
- grid.19006.3e0000 0000 9632 6718Department of Biological Chemistry, University of California, Los Angeles, CA 90095 USA
| | - Israel Ausin
- grid.144022.10000 0004 1760 4150State Key Laboratory of Crop Stress Biology for Arid Areas, College of Life Sciences and Institute of Future Agriculture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Steven E. Jacobsen
- grid.19006.3e0000 0000 9632 6718Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095 USA ,grid.19006.3e0000 0000 9632 6718Howard Hughes Medical Institute, University of California, Los Angeles, CA 90095 USA
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3
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Molenaar TM, Malik M, Silva J, Liu NQ, Haarhuis JHI, Ambrosi C, Kwesi-Maliepaard EM, van Welsem T, Baubec T, Faller WJ, van Leeuwen F. The histone methyltransferase SETD2 negatively regulates cell size. J Cell Sci 2022; 135:jcs259856. [PMID: 36052643 PMCID: PMC9659392 DOI: 10.1242/jcs.259856] [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: 01/29/2022] [Accepted: 08/23/2022] [Indexed: 11/20/2022] Open
Abstract
Cell size varies between cell types but is tightly regulated by cell intrinsic and extrinsic mechanisms. Cell size control is important for cell function, and changes in cell size are frequently observed in cancer. Here, we uncover a role for SETD2 in regulating cell size. SETD2 is a lysine methyltransferase and a tumor suppressor protein involved in transcription, RNA processing and DNA repair. At the molecular level, SETD2 is best known for associating with RNA polymerase II through its Set2-Rbp1 interacting (SRI) domain and methylating histone H3 on lysine 36 (H3K36) during transcription. Using multiple independent perturbation strategies, we identify SETD2 as a negative regulator of global protein synthesis rates and cell size. We provide evidence that overexpression of the H3K36 demethylase KDM4A or the oncohistone H3.3K36M also increase cell size. In addition, ectopic overexpression of a decoy SRI domain increased cell size, suggesting that the relevant substrate is engaged by SETD2 via its SRI domain. These data add a central role of SETD2 in regulating cellular physiology and warrant further studies on separating the different functions of SETD2 in cancer development.
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Affiliation(s)
- Thom M. Molenaar
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Muddassir Malik
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Joana Silva
- Division of Oncogenomics, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Ning Qing Liu
- Division of Gene Regulation, Oncode Institute, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Judith H. I. Haarhuis
- Division of Cell Biology, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Christina Ambrosi
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Life Science Zurich Graduate School, University of Zurich and ETH Zurich, CH-8057 Zurich, Switzerland
| | | | - Tibor van Welsem
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Tuncay Baubec
- Department of Molecular Mechanisms of Disease, University of Zurich, 8057 Zurich, Switzerland
- Genome Biology and Epigenetics, Institute of Biodynamics and Biocomplexity, Department of Biology, Utrecht University, 3584 CH Utrecht, The Netherlands
| | - William J. Faller
- Division of Oncogenomics, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
| | - Fred van Leeuwen
- Division of Gene Regulation, Netherlands Cancer Institute, 1066CX Amsterdam, The Netherlands
- Department of Medical Biology, Amsterdam UMC, University of Amsterdam, 1105AZ Amsterdam, The Netherlands
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4
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N-Terminal Tails of Histones H2A and H2B Differentially Affect Transcription by RNA Polymerase II In Vitro. Cells 2022; 11:cells11162475. [PMID: 36010552 PMCID: PMC9406932 DOI: 10.3390/cells11162475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 08/02/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022] Open
Abstract
Histone N-terminal tails and their post-translational modifications affect various biological processes, often in a context-specific manner; the underlying mechanisms are poorly studied. Here, the role of individual N-terminal tails of histones H2A/H2B during transcription through chromatin was analyzed in vitro. spFRET data suggest that the tail of histone H2B (but not of histone H2A) affects nucleosome stability. Accordingly, deletion of the H2B tail (amino acids 1–31, but not 1–26) causes a partial relief of the nucleosomal barrier to transcribing RNA polymerase II (Pol II), likely facilitating uncoiling of DNA from the histone octamer during transcription. Taken together, the data suggest that residues 27–31 of histone H2B stabilize DNA–histone interactions at the DNA region localized ~25 bp in the nucleosome and thus interfere with Pol II progression through the region localized 11–15 bp in the nucleosome. This function of histone H2B requires the presence of the histone H2A N-tail that mediates formation of nucleosome–nucleosome dimers; however, nucleosome dimerization per se plays only a minimal role during transcription. Histone chaperone FACT facilitates transcription through all analyzed nucleosome variants, suggesting that H2A/H2B tails minimally interact with FACT during transcription; therefore, an alternative FACT-interacting domain(s) is likely involved in this process.
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5
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Farnung L, Ochmann M, Garg G, Vos SM, Cramer P. Structure of a backtracked hexasomal intermediate of nucleosome transcription. Mol Cell 2022; 82:3126-3134.e7. [PMID: 35858621 DOI: 10.1016/j.molcel.2022.06.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 05/17/2022] [Accepted: 06/21/2022] [Indexed: 10/17/2022]
Abstract
During gene transcription, RNA polymerase II (RNA Pol II) passes nucleosomes with the help of various elongation factors. Here, we show that RNA Pol II achieves efficient nucleosome passage when the human elongation factors DSIF, PAF1 complex (PAF), RTF1, SPT6, and TFIIS are present. The cryo-EM structure of an intermediate of the nucleosome passage shows a partially unraveled hexasome that lacks the proximal H2A-H2B dimer and interacts with the RNA Pol II jaw, DSIF, and the CTR9trestle helix. RNA Pol II adopts a backtracked state with the RNA 3' end dislodged from the active site and bound in the RNA Pol II pore. Additional structures and biochemical data show that human TFIIS enters the RNA Pol II pore and stimulates the cleavage of the backtracked RNA and nucleosome passage.
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Affiliation(s)
- Lucas Farnung
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
| | - Moritz Ochmann
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gaurika Garg
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Seychelle M Vos
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany
| | - Patrick Cramer
- Max Planck Institute for Multidisciplinary Sciences, Department of Molecular Biology, Am Fassberg 11, 37077 Göttingen, Germany.
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6
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DNA-Topology Simplification by Topoisomerases. Molecules 2021; 26:molecules26113375. [PMID: 34204901 PMCID: PMC8199745 DOI: 10.3390/molecules26113375] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 05/20/2021] [Accepted: 05/26/2021] [Indexed: 11/17/2022] Open
Abstract
The topological properties of DNA molecules, supercoiling, knotting, and catenation, are intimately connected with essential biological processes, such as gene expression, replication, recombination, and chromosome segregation. Non-trivial DNA topologies present challenges to the molecular machines that process and maintain genomic information, for example, by creating unwanted DNA entanglements. At the same time, topological distortion can facilitate DNA-sequence recognition through localized duplex unwinding and longer-range loop-mediated interactions between the DNA sequences. Topoisomerases are a special class of essential enzymes that homeostatically manage DNA topology through the passage of DNA strands. The activities of these enzymes are generally investigated using circular DNA as a model system, in which case it is possible to directly assay the formation and relaxation of DNA supercoils and the formation/resolution of knots and catenanes. Some topoisomerases use ATP as an energy cofactor, whereas others act in an ATP-independent manner. The free energy of ATP hydrolysis can be used to drive negative and positive supercoiling or to specifically relax DNA topologies to levels below those that are expected at thermodynamic equilibrium. The latter activity, which is known as topology simplification, is thus far exclusively associated with type-II topoisomerases and it can be understood through insight into the detailed non-equilibrium behavior of type-II enzymes. We use a non-equilibrium topological-network approach, which stands in contrast to the equilibrium models that are conventionally used in the DNA-topology field, to gain insights into the rates that govern individual transitions between topological states. We anticipate that our quantitative approach will stimulate experimental work and the theoretical/computational modeling of topoisomerases and similar enzyme systems.
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7
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Cole L, Kurscheid S, Nekrasov M, Domaschenz R, Vera DL, Dennis JH, Tremethick DJ. Multiple roles of H2A.Z in regulating promoter chromatin architecture in human cells. Nat Commun 2021; 12:2524. [PMID: 33953180 PMCID: PMC8100287 DOI: 10.1038/s41467-021-22688-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2020] [Accepted: 03/25/2021] [Indexed: 01/02/2023] Open
Abstract
Chromatin accessibility of a promoter is fundamental in regulating transcriptional activity. The histone variant H2A.Z has been shown to contribute to this regulation, but its role has remained poorly understood. Here, we prepare high-depth maps of the position and accessibility of H2A.Z-containing nucleosomes for all human Pol II promoters in epithelial, mesenchymal and isogenic cancer cell lines. We find that, in contrast to the prevailing model, many different types of active and inactive promoter structures are observed that differ in their nucleosome organization and sensitivity to MNase digestion. Key aspects of an active chromatin structure include positioned H2A.Z MNase resistant nucleosomes upstream or downstream of the TSS, and a MNase sensitive nucleosome at the TSS. Furthermore, the loss of H2A.Z leads to a dramatic increase in the accessibility of transcription factor binding sites. Collectively, these results suggest that H2A.Z has multiple and distinct roles in regulating gene expression dependent upon its location in a promoter.
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Affiliation(s)
- Lauren Cole
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
| | - Sebastian Kurscheid
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Maxim Nekrasov
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Renae Domaschenz
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia
| | - Daniel L Vera
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA
- Department of Genetics, Blavatnik Institute, Paul F. Glenn Center for Biology of Aging Research, Harvard Medical School, Boston, MA, USA
| | - Jonathan H Dennis
- College of Arts and Sciences, Department of Biological Sciences, Florida State University, Tallahassee, FL, USA.
| | - David J Tremethick
- The John Curtin School of Medical Research, The Australian National University, Canberra, Australia.
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8
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Farahani RM, Rezaei-Lotfi S, Hunter N. Genomic competition for noise reduction shaped evolutionary landscape of mir-4673. NPJ Syst Biol Appl 2020; 6:12. [PMID: 32376854 PMCID: PMC7203229 DOI: 10.1038/s41540-020-0131-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 04/09/2020] [Indexed: 12/24/2022] Open
Abstract
The genomic platform that informs evolution of microRNA cascades remains unknown. Here we capitalised on the recent evolutionary trajectory of hominin-specific miRNA-4673, encoded in intron 4 of notch-1, to uncover the identity of one such precursor genomic element and the selective forces acting upon it. The miRNA targets genes that regulate Wnt/β-catenin signalling cascade. Primary sequence of the microRNA and its target region in Wnt modulating genes evolved from homologous signatures mapped to homotypic cis-clusters recognised by TCF3/4 and TFAP2A/B/C families. Integration of homologous TFAP2A/B/C cis-clusters (short range inhibitor of β-catenin) into the transcriptional landscape of Wnt cascade genes can reduce noise in gene expression. Probabilistic adoption of miRNA secondary structure by one such cis-signature in notch-1 reflected selection for superhelical curvature symmetry of precursor DNA to localise a nucleosome that overlapped the latter cis-cluster. By replicating the cis-cluster signature, non-random interactions of the miRNA with key Wnt modulator genes expanded the transcriptional noise buffering capacity via a coherent feed-forward loop mechanism. In consequence, an autonomous transcriptional noise dampener (the cis-cluster/nucleosome) evolved into a post-transcriptional one (the miRNA). The findings suggest a latent potential for remodelling of transcriptional landscape by miRNAs that capitalise on non-random distribution of genomic cis-signatures.
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Affiliation(s)
- Ramin M Farahani
- IDR/Westmead Institute for Medical Research and Westmead Centre for Oral Health, Sydney, NSW, Australia.
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia.
| | - Saba Rezaei-Lotfi
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia
| | - Neil Hunter
- IDR/Westmead Institute for Medical Research and Westmead Centre for Oral Health, Sydney, NSW, Australia
- Faculty of Medicine and Health Sciences, University of Sydney, Sydney, NSW, 2006, Australia
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9
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Kujirai T, Kurumizaka H. Transcription through the nucleosome. Curr Opin Struct Biol 2020; 61:42-49. [DOI: 10.1016/j.sbi.2019.10.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 10/17/2019] [Accepted: 10/22/2019] [Indexed: 11/28/2022]
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10
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Sanders TJ, Lammers M, Marshall CJ, Walker JE, Lynch ER, Santangelo TJ. TFS and Spt4/5 accelerate transcription through archaeal histone-based chromatin. Mol Microbiol 2019; 111:784-797. [PMID: 30592095 PMCID: PMC6417941 DOI: 10.1111/mmi.14191] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2018] [Indexed: 12/25/2022]
Abstract
RNA polymerase must surmount translocation barriers for continued transcription. In Eukarya and most Archaea, DNA-bound histone proteins represent the most common and troublesome barrier to transcription elongation. Eukaryotes encode a plethora of chromatin-remodeling complexes, histone-modification enzymes and transcription elongation factors to aid transcription through nucleosomes, while archaea seemingly lack machinery to remodel/modify histone-based chromatin and thus must rely on elongation factors to accelerate transcription through chromatin-barriers. TFS (TFIIS in Eukarya) and the Spt4-Spt5 complex are universally encoded in archaeal genomes, and here we demonstrate that both elongation factors, via different mechanisms, can accelerate transcription through archaeal histone-based chromatin. Histone proteins in Thermococcus kodakarensis are sufficiently abundant to completely wrap all genomic DNA, resulting in a consistent protein barrier to transcription elongation. TFS-enhanced cleavage of RNAs in backtracked transcription complexes reactivates stalled RNAPs and dramatically accelerates transcription through histone-barriers, while Spt4-Spt5 changes to clamp-domain dynamics play a lesser-role in stabilizing transcription. Repeated attempts to delete TFS, Spt4 and Spt5 from the T. kodakarensis genome were not successful, and the essentiality of both conserved transcription elongation factors suggests that both conserved elongation factors play important roles in transcription regulation in vivo, including mechanisms to accelerate transcription through downstream protein barriers.
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Affiliation(s)
- Travis J. Sanders
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Marshall Lammers
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Craig J. Marshall
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Julie E. Walker
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Current address: Renewable and Sustainable Energy Institute, University of Colorado, Boulder, Colorado, 80303, USA
| | - Erin R. Lynch
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Thomas J. Santangelo
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
- Graduate Program in Cell and Molecular Biology, Colorado State University, Fort Collins, Colorado, 80523, USA
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11
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Understanding nucleosome dynamics and their links to gene expression and DNA replication. Nat Rev Mol Cell Biol 2017; 18:548-562. [PMID: 28537572 DOI: 10.1038/nrm.2017.47] [Citation(s) in RCA: 309] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Advances in genomics technology have provided the means to probe myriad chromatin interactions at unprecedented spatial and temporal resolution. This has led to a profound understanding of nucleosome organization within the genome, revealing that nucleosomes are highly dynamic. Nucleosome dynamics are governed by a complex interplay of histone composition, histone post-translational modifications, nucleosome occupancy and positioning within chromatin, which are influenced by numerous regulatory factors, including general regulatory factors, chromatin remodellers, chaperones and polymerases. It is now known that these dynamics regulate diverse cellular processes ranging from gene transcription to DNA replication and repair.
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