Literature DB >> 30765112

Mechanism of Cross-talk between H2B Ubiquitination and H3 Methylation by Dot1L.

Evan J Worden1, Niklas A Hoffmann1, Chad W Hicks1, Cynthia Wolberger2.   

Abstract

Methylation of histone H3 K79 by Dot1L is a hallmark of actively transcribed genes that depends on monoubiquitination of H2B K120 (H2B-Ub) and is an example of histone modification cross-talk that is conserved from yeast to humans. We report here cryo-EM structures of Dot1L bound to ubiquitinated nucleosome that show how H2B-Ub stimulates Dot1L activity and reveal a role for the histone H4 tail in positioning Dot1L. We find that contacts mediated by Dot1L and the H4 tail induce a conformational change in the globular core of histone H3 that reorients K79 from an inaccessible position, thus enabling this side chain to insert into the active site in a position primed for catalysis. Our study provides a comprehensive mechanism of cross-talk between histone ubiquitination and methylation and reveals structural plasticity in histones that makes it possible for histone-modifying enzymes to access residues within the nucleosome core.
Copyright © 2019 Elsevier Inc. All rights reserved.

Entities:  

Keywords:  Dot1L; chromatin; cryo-EM; histones; methylation; nucleosome; structural biology; ubiquitin

Mesh:

Substances:

Year:  2019        PMID: 30765112      PMCID: PMC6498860          DOI: 10.1016/j.cell.2019.02.002

Source DB:  PubMed          Journal:  Cell        ISSN: 0092-8674            Impact factor:   41.582


  75 in total

1.  Bre1, an E3 ubiquitin ligase required for recruitment and substrate selection of Rad6 at a promoter.

Authors:  Adam Wood; Nevan J Krogan; Jim Dover; Jessica Schneider; Jonathan Heidt; Marry Ann Boateng; Kimberly Dean; Ashkan Golshani; Yi Zhang; Jack F Greenblatt; Mark Johnston; Ali Shilatifard
Journal:  Mol Cell       Date:  2003-01       Impact factor: 17.970

2.  Histone modifications defining active genes persist after transcriptional and mitotic inactivation.

Authors:  Antigone Kouskouti; Iannis Talianidis
Journal:  EMBO J       Date:  2004-12-16       Impact factor: 11.598

3.  Aberrant chromatin at genes encoding stem cell regulators in human mixed-lineage leukemia.

Authors:  Matthew G Guenther; Lee N Lawton; Tatiana Rozovskaia; Garrett M Frampton; Stuart S Levine; Thomas L Volkert; Carlo M Croce; Tatsuya Nakamura; Eli Canaani; Richard A Young
Journal:  Genes Dev       Date:  2008-12-15       Impact factor: 11.361

4.  Monoubiquitination of human histone H2B: the factors involved and their roles in HOX gene regulation.

Authors:  Bing Zhu; Yong Zheng; Anh-Dung Pham; Subhrangsu S Mandal; Hediye Erdjument-Bromage; Paul Tempst; Danny Reinberg
Journal:  Mol Cell       Date:  2005-11-23       Impact factor: 17.970

5.  Discovery of Novel Dot1L Inhibitors through a Structure-Based Fragmentation Approach.

Authors:  Chao Chen; Hugh Zhu; Frédéric Stauffer; Giorgio Caravatti; Susanne Vollmer; Rainer Machauer; Philipp Holzer; Henrik Möbitz; Clemens Scheufler; Martin Klumpp; Ralph Tiedt; Kim S Beyer; Keith Calkins; Daniel Guthy; Michael Kiffe; Jeff Zhang; Christoph Gaul
Journal:  ACS Med Chem Lett       Date:  2016-06-01       Impact factor: 4.345

6.  COMPASS: a complex of proteins associated with a trithorax-related SET domain protein.

Authors:  T Miller; N J Krogan; J Dover; H Erdjument-Bromage; P Tempst; M Johnston; J F Greenblatt; A Shilatifard
Journal:  Proc Natl Acad Sci U S A       Date:  2001-10-30       Impact factor: 11.205

7.  Ubiquitination of histone H2B regulates H3 methylation and gene silencing in yeast.

Authors:  Zu-Wen Sun; C David Allis
Journal:  Nature       Date:  2002-06-23       Impact factor: 49.962

8.  Quantifying the local resolution of cryo-EM density maps.

Authors:  Alp Kucukelbir; Fred J Sigworth; Hemant D Tagare
Journal:  Nat Methods       Date:  2013-11-10       Impact factor: 28.547

9.  Accelerated cryo-EM structure determination with parallelisation using GPUs in RELION-2.

Authors:  Dari Kimanius; Björn O Forsberg; Sjors Hw Scheres; Erik Lindahl
Journal:  Elife       Date:  2016-11-15       Impact factor: 8.140

10.  Evidence that ubiquitylated H2B corrals hDot1L on the nucleosomal surface to induce H3K79 methylation.

Authors:  Linjiao Zhou; Matthew T Holt; Nami Ohashi; Aishan Zhao; Manuel M Müller; Boyuan Wang; Tom W Muir
Journal:  Nat Commun       Date:  2016-02-02       Impact factor: 14.919

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  67 in total

1.  DOT1L-controlled cell-fate determination and transcription elongation are independent of H3K79 methylation.

Authors:  Kaixiang Cao; Michal Ugarenko; Patrick A Ozark; Juan Wang; Stacy A Marshall; Emily J Rendleman; Kaiwei Liang; Lu Wang; Lihua Zou; Edwin R Smith; Feng Yue; Ali Shilatifard
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-19       Impact factor: 11.205

Review 2.  Activation and regulation of H2B-Ubiquitin-dependent histone methyltransferases.

Authors:  Evan J Worden; Cynthia Wolberger
Journal:  Curr Opin Struct Biol       Date:  2019-06-21       Impact factor: 6.809

Review 3.  Preserving genome integrity and function: the DNA damage response and histone modifications.

Authors:  Jae Jin Kim; Seo Yun Lee; Kyle M Miller
Journal:  Crit Rev Biochem Mol Biol       Date:  2019-06-04       Impact factor: 8.250

4.  Regulation of the Dot1 histone H3K79 methyltransferase by histone H4K16 acetylation.

Authors:  Marco Igor Valencia-Sánchez; Pablo De Ioannes; Miao Wang; David M Truong; Rachel Lee; Jean-Paul Armache; Jef D Boeke; Karim-Jean Armache
Journal:  Science       Date:  2021-01-22       Impact factor: 47.728

5.  Spt5 Phosphorylation and the Rtf1 Plus3 Domain Promote Rtf1 Function through Distinct Mechanisms.

Authors:  Jennifer J Chen; Jean Mbogning; Mark A Hancock; Dorsa Majdpour; Manan Madhok; Hassan Nassour; Juliana C Dallagnol; Viviane Pagé; David Chatenet; Jason C Tanny
Journal:  Mol Cell Biol       Date:  2020-07-14       Impact factor: 4.272

6.  Structural basis for PRC2 decoding of active histone methylation marks H3K36me2/3.

Authors:  Ksenia Finogenova; Jacques Bonnet; Simon Poepsel; Ingmar B Schäfer; Katja Finkl; Katharina Schmid; Claudia Litz; Mike Strauss; Christian Benda; Jürg Müller
Journal:  Elife       Date:  2020-11-19       Impact factor: 8.140

7.  Bulky Histone Modifications May Have an Oversized Role in Nucleosome Dynamics.

Authors:  Kona Orlandi; Jeffrey McKnight
Journal:  Bioessays       Date:  2019-12-03       Impact factor: 4.345

8.  Histone H2B Ubiquitylation Regulates Histone Gene Expression by Suppressing Antisense Transcription in Fission Yeast.

Authors:  Viviane Pagé; Jennifer J Chen; Mickael Durand-Dubief; David Grabowski; Eriko Oya; Miriam Sansô; Ryan D Martin; Terence E Hébert; Robert P Fisher; Karl Ekwall; Jason C Tanny
Journal:  Genetics       Date:  2019-07-25       Impact factor: 4.562

9.  Navigating the structure of COMPASS.

Authors:  Karolin Luger; Jonathan W Markert
Journal:  Elife       Date:  2020-02-24       Impact factor: 8.140

Review 10.  Domain cross-talk in regulation of histone modifications: Molecular mechanisms and targeting opportunities.

Authors:  James E Longbotham; Meng Yao Zhang; Danica Galonić Fujimori
Journal:  Curr Opin Chem Biol       Date:  2020-08-03       Impact factor: 8.822

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