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Title: Structure–function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2

Abstract

Cells use specific mechanisms such as histone chaperones to abrogate the inherent barrier that the nucleosome poses to transcribing polymerases. The current model postulates that nucleosomes can be transiently disrupted to accommodate passage of RNA polymerases and that histones H3 and H4 possess their own chaperones dedicated to the recovery of nucleosomes. Here, we determined the crystal structure of the conserved C terminus of human Suppressors of Ty insertions 2 (hSpt2C) chaperone bound to an H3/H4 tetramer. The structural studies demonstrate that hSpt2C is bound to the periphery of the H3/H4 tetramer, mimicking the trajectory of nucleosomal-bound DNA. These structural studies have been complemented with in vitro binding and in vivo functional studies on mutants that disrupt key intermolecular contacts involving two acidic patches and hydrophobic residues on Spt2C. We show that contacts between both human and yeast Spt2C with the H3/H4 tetramer are required for the suppression of H3/ H4 exchange as measured by H3K56ac and new H3 deposition. Furthermore, these interactions are also crucial for the inhibition of spurious transcription from within coding regions. In conclusion, together, our data indicate that Spt2 interacts with the periphery of the H3/H4 tetramer and promotes its recycling in the wake ofmore » RNA polymerase.« less

Authors:
 [1];  [2];  [1];  [3];  [2];  [1]
  1. Memorial Sloan-Kettering Cancer Center, New York, NY (United States). Structural Biology Program
  2. Univ. of Laval, Quebec, QC (Canada)
  3. Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS) and Northeastern Collaborative Access Team (NE-CAT); cornell. Dept. of Chemistry and Chemical Biology
Publication Date:
Research Org.:
Cornell Univ., Ithaca, NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Institutes of Health (NIH)
OSTI Identifier:
1344871
Grant/Contract Number:  
AC02-06CH11357; LLS-SCOR 7132-08; I5-A554; S10 RR029205
Resource Type:
Accepted Manuscript
Journal Name:
Genes & Development
Additional Journal Information:
Journal Volume: 29; Journal Issue: 12; Journal ID: ISSN 0890-9369
Publisher:
Cold Springs Harbor Press
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; H3/H4 tetramer; epigenetics; histone chaperone; histone maintenance; Spt2; spurious transcription; transcription elongation

Citation Formats

Chen, Shoudeng, Rufiange, Anne, Huang, Hongda, Rajashankar, Kanagalaghatta R., Nourani, Amine, and Patel, Dinshaw J. Structure–function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2. United States: N. p., 2015. Web. doi:10.1101/gad.261115.115.
Chen, Shoudeng, Rufiange, Anne, Huang, Hongda, Rajashankar, Kanagalaghatta R., Nourani, Amine, & Patel, Dinshaw J. Structure–function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2. United States. https://doi.org/10.1101/gad.261115.115
Chen, Shoudeng, Rufiange, Anne, Huang, Hongda, Rajashankar, Kanagalaghatta R., Nourani, Amine, and Patel, Dinshaw J. Mon . "Structure–function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2". United States. https://doi.org/10.1101/gad.261115.115. https://www.osti.gov/servlets/purl/1344871.
@article{osti_1344871,
title = {Structure–function studies of histone H3/H4 tetramer maintenance during transcription by chaperone Spt2},
author = {Chen, Shoudeng and Rufiange, Anne and Huang, Hongda and Rajashankar, Kanagalaghatta R. and Nourani, Amine and Patel, Dinshaw J.},
abstractNote = {Cells use specific mechanisms such as histone chaperones to abrogate the inherent barrier that the nucleosome poses to transcribing polymerases. The current model postulates that nucleosomes can be transiently disrupted to accommodate passage of RNA polymerases and that histones H3 and H4 possess their own chaperones dedicated to the recovery of nucleosomes. Here, we determined the crystal structure of the conserved C terminus of human Suppressors of Ty insertions 2 (hSpt2C) chaperone bound to an H3/H4 tetramer. The structural studies demonstrate that hSpt2C is bound to the periphery of the H3/H4 tetramer, mimicking the trajectory of nucleosomal-bound DNA. These structural studies have been complemented with in vitro binding and in vivo functional studies on mutants that disrupt key intermolecular contacts involving two acidic patches and hydrophobic residues on Spt2C. We show that contacts between both human and yeast Spt2C with the H3/H4 tetramer are required for the suppression of H3/ H4 exchange as measured by H3K56ac and new H3 deposition. Furthermore, these interactions are also crucial for the inhibition of spurious transcription from within coding regions. In conclusion, together, our data indicate that Spt2 interacts with the periphery of the H3/H4 tetramer and promotes its recycling in the wake of RNA polymerase.},
doi = {10.1101/gad.261115.115},
journal = {Genes & Development},
number = 12,
volume = 29,
place = {United States},
year = {Mon Jun 15 00:00:00 EDT 2015},
month = {Mon Jun 15 00:00:00 EDT 2015}
}

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Works referenced in this record:

PHENIX: a comprehensive Python-based system for macromolecular structure solution
journal, January 2010

  • Adams, Paul D.; Afonine, Pavel V.; Bunkóczi, Gábor
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 2, p. 213-221
  • DOI: 10.1107/S0907444909052925

Split Decision: What Happens to Nucleosomes during DNA Replication?
journal, January 2005


Histone Chaperones: Modulators of Chromatin Marks
journal, March 2011


Equilibrium Folding of the Core Histones:  the H3−H4 Tetramer Is Less Stable than the H2A−H2B Dimer
journal, June 2003

  • Banks, Douglas D.; Gloss, Lisa M.
  • Biochemistry, Vol. 42, Issue 22
  • DOI: 10.1021/bi026957r

FACT Facilitates Transcription-Dependent Nucleosome Alteration
journal, August 2003


Casein Kinase 2 Associates with the Yeast Chromatin Reassembly Factor Spt2/Sin1 To Regulate Its Function in the Repression of Spurious Transcription
journal, August 2013

  • Bhat, W.; Boutin, G.; Rufiange, A.
  • Molecular and Cellular Biology, Vol. 33, Issue 21
  • DOI: 10.1128/MCB.00525-13

The Histone Chaperones Nap1 and Vps75 Bind Histones H3 and H4 in a Tetrameric Conformation
journal, February 2011


Dynamics of Replication-Independent Histone Turnover in Budding Yeast
journal, March 2007


DAXX envelops a histone H3.3–H4 dimer for H3.3-specific recognition
journal, October 2012

  • Elsässer, Simon J.; Huang, Hongda; Lewis, Peter W.
  • Nature, Vol. 491, Issue 7425
  • DOI: 10.1038/nature11608

Structural Basis for the Histone Chaperone Activity of Asf1
journal, November 2006


Histone Chaperone Spt16 Promotes Redeposition of the Original H3-H4 Histones Evicted by Elongating RNA Polymerase
journal, August 2009


Transcription Elongation Factors Repress Transcription Initiation from Cryptic Sites
journal, August 2003


Splitting of H3-H4 tetramers at transcriptionally active genes undergoing dynamic histone exchange
journal, January 2011

  • Katan-Khaykovich, Y.; Struhl, K.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1018308108

Kinetics of Core Histones in Living Human Cells
journal, June 2001


Nucleosome Remodeling Induced by RNA Polymerase II
journal, March 2002


Structure of the variant histone H3.3–H4 heterodimer in complex with its chaperone DAXX
journal, November 2012

  • Liu, Chao-Pei; Xiong, Chaoyang; Wang, Mingzhu
  • Nature Structural & Molecular Biology, Vol. 19, Issue 12
  • DOI: 10.1038/nsmb.2439

Crystal structure of the nucleosome core particle at 2.8 Å resolution
journal, September 1997

  • Luger, Karolin; Mäder, Armin W.; Richmond, Robin K.
  • Nature, Vol. 389, Issue 6648
  • DOI: 10.1038/38444

Phaser crystallographic software
journal, July 2007

  • McCoy, Airlie J.; Grosse-Kunstleve, Ralf W.; Adams, Paul D.
  • Journal of Applied Crystallography, Vol. 40, Issue 4
  • DOI: 10.1107/S0021889807021206

Refinement of Macromolecular Structures by the Maximum-Likelihood Method
journal, May 1997

  • Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 53, Issue 3
  • DOI: 10.1107/S0907444996012255

Structure and function of the histone chaperone CIA/ASF1 complexed with histones H3 and H4
journal, February 2007

  • Natsume, Ryo; Eitoku, Masamitsu; Akai, Yusuke
  • Nature, Vol. 446, Issue 7133
  • DOI: 10.1038/nature05613

Evidence that Spt2/Sin1, an HMG-Like Factor, Plays Roles in Transcription Elongation, Chromatin Structure, and Genome Stability in Saccharomyces cerevisiae
journal, February 2006


The chromatin-specific transcription elongation factor FACT comprises human SPT16 and SSRP1 proteins
journal, July 1999

  • Orphanides, George; Wu, Wei-Hua; Lane, William S.
  • Nature, Vol. 400, Issue 6741
  • DOI: 10.1038/22350

Vertebrate Spt2 is a novel nucleolar histone chaperone that assists in ribosomal DNA transcription
journal, January 2013

  • Osakabe, Akihisa; Tachiwana, Hiroaki; Takaku, Motoki
  • Journal of Cell Science
  • DOI: 10.1242/jcs.112623

NMRPipe: A multidimensional spectral processing system based on UNIX pipes
journal, November 1995

  • Delaglio, Frank; Grzesiek, Stephan; Vuister, GeertenW.
  • Journal of Biomolecular NMR, Vol. 6, Issue 3
  • DOI: 10.1007/BF00197809

Genome-Wide Replication-Independent Histone H3 Exchange Occurs Predominantly at Promoters and Implicates H3 K56 Acetylation and Asf1
journal, August 2007


Ty-mediated gene expression of the LYS2 and HIS4 genes of Saccharomyces cerevisiae is controlled by the same SPT genes.
journal, April 1984

  • Simchen, G.; Winston, F.; Styles, C. A.
  • Proceedings of the National Academy of Sciences, Vol. 81, Issue 8
  • DOI: 10.1073/pnas.81.8.2431

Transcription-associated histone modifications and cryptic transcription
journal, January 2013

  • Smolle, Michaela; Workman, Jerry L.
  • Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms, Vol. 1829, Issue 1
  • DOI: 10.1016/j.bbagrm.2012.08.008

Activation of the yeast HO gene by release from multiple negative controls
journal, February 1987


Transcription Regulation by the Noncoding RNA SRG1 Requires Spt2-Dependent Chromatin Deposition in the Wake of RNA Polymerase II
journal, January 2011

  • Thebault, P.; Boutin, G.; Bhat, W.
  • Molecular and Cellular Biology, Vol. 31, Issue 6
  • DOI: 10.1128/MCB.01083-10

Replication-independent core histone dynamics at transcriptionally active loci in vivo
journal, March 2005

  • Thiriet, Christophe; Hayes, Jeffrey J.
  • Genes & Development, Vol. 19, Issue 6
  • DOI: 10.1101/gad.1265205

Molecular replacement with MOLREP
journal, December 2009

  • Vagin, Alexei; Teplyakov, Alexei
  • Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 1
  • DOI: 10.1107/S0907444909042589

MUTATIONS AFFECTING TY-MEDIATED EXPRESSION OF THE HIS4 GENE OF SACCHAROMYCES CEREVISIAE
journal, June 1984


Construction of a set of convenientsaccharomyces cerevisiae strains that are isogenic to S288C
journal, January 1995

  • Winston, Fred; Dollard, Catherine; Ricupero-Hovasse, Stephanie L.
  • Yeast, Vol. 11, Issue 1
  • DOI: 10.1002/yea.320110107

Partitioning of Histone H3-H4 Tetramers During DNA Replication-Dependent Chromatin Assembly
journal, April 2010


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A novel histone H4 variant H4G regulates rDNA transcription in breast cancer
journal, June 2019

  • Long, Mengping; Sun, Xulun; Shi, Wenjin
  • Nucleic Acids Research, Vol. 47, Issue 16
  • DOI: 10.1093/nar/gkz547

Histone chaperone networks shaping chromatin function
journal, January 2017

  • Hammond, Colin M.; Strømme, Caroline B.; Huang, Hongda
  • Nature Reviews Molecular Cell Biology, Vol. 18, Issue 3
  • DOI: 10.1038/nrm.2016.159

The Oligomerization Landscape of Histones
journal, May 2019


Structural insights into the ability of nucleoplasmin to assemble and chaperone histone octamers for DNA deposition
journal, July 2019


MCM2 binding to histones H3–H4 and ASF1 supports a tetramer-to-dimer model for histone inheritance at the replication fork
journal, August 2015

  • Clément, Camille; Almouzni, Geneviève
  • Nature Structural & Molecular Biology, Vol. 22, Issue 8
  • DOI: 10.1038/nsmb.3067

Structural insights into the ability of nucleoplasmin to assemble and chaperone histone octamers for DNA deposition
journal, July 2019


A Quantitative Characterization of Nucleoplasmin/Histone Complexes Reveals Chaperone Versatility
journal, August 2016

  • Fernández-Rivero, Noelia; Franco, Aitor; Velázquez-Campoy, Adrian
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep32114

Casein kinase 2 mediated phosphorylation of Spt6 modulates histone dynamics and regulates spurious transcription
journal, June 2018

  • Gouot, Emmanuelle; Bhat, Wajid; Rufiange, Anne
  • Nucleic Acids Research, Vol. 46, Issue 15
  • DOI: 10.1093/nar/gky515

A novel histone H4 variant H4G regulates rDNA transcription in breast cancer
journal, June 2019

  • Long, Mengping; Sun, Xulun; Shi, Wenjin
  • Nucleic Acids Research, Vol. 47, Issue 16
  • DOI: 10.1093/nar/gkz547

Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes
journal, March 2020

  • Poramba-Liyanage, Deepani W.; Korthout, Tessy; Cucinotta, Christine E.
  • Genome Research, Vol. 30, Issue 4
  • DOI: 10.1101/gr.256255.119