Literature DB >> 26073541

Engineering of a Histone-Recognition Domain in Dnmt3a Alters the Epigenetic Landscape and Phenotypic Features of Mouse ESCs.

Kyung-Min Noh1,2, Haibo Wang3,4, Hyunjae R Kim5, Wendy Wenderski1, Fang Fang6, Charles H Li1, Scott Dewell7, Stephen H Hughes8, Ari M Melnick6, Dinshaw J Patel9, Haitao Li3,4,10, C David Allis1.   

Abstract

Histone modification and DNA methylation are associated with varying epigenetic "landscapes," but detailed mechanistic and functional links between the two remain unclear. Using the ATRX-DNMT3-DNMT3L (ADD) domain of the DNA methyltransferase Dnmt3a as a paradigm, we apply protein engineering to dissect the molecular interactions underlying the recruitment of this enzyme to specific regions of chromatin in mouse embryonic stem cells (ESCs). By rendering the ADD domain insensitive to histone modification, specifically H3K4 methylation or H3T3 phosphorylation, we demonstrate the consequence of dysregulated Dnmt3a binding and activity. Targeting of a Dnmt3a mutant to H3K4me3 promoters decreases gene expression in a subset of developmental genes and alters ESC differentiation, whereas aberrant binding of another mutant to H3T3ph during mitosis promotes chromosome instability. Our studies support the general view that histone modification "reading" and DNA methylation are closely coupled in mammalian cells, and suggest an avenue for the functional assessment of chromatin-associated proteins.
Copyright © 2015 Elsevier Inc. All rights reserved.

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Year:  2015        PMID: 26073541      PMCID: PMC4491196          DOI: 10.1016/j.molcel.2015.05.017

Source DB:  PubMed          Journal:  Mol Cell        ISSN: 1097-2765            Impact factor:   17.970


  50 in total

1.  Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b.

Authors:  Akiko Tsumura; Tomohiro Hayakawa; Yuichi Kumaki; Shin-ichiro Takebayashi; Morito Sakaue; Chisa Matsuoka; Kunitada Shimotohno; Fuyuki Ishikawa; En Li; Hiroki R Ueda; Jun-ichi Nakayama; Masaki Okano
Journal:  Genes Cells       Date:  2006-07       Impact factor: 1.891

2.  Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF.

Authors:  Haitao Li; Serge Ilin; Wooikoon Wang; Elizabeth M Duncan; Joanna Wysocka; C David Allis; Dinshaw J Patel
Journal:  Nature       Date:  2006-05-21       Impact factor: 49.962

3.  Generation of a defined and uniform population of CNS progenitors and neurons from mouse embryonic stem cells.

Authors:  Miriam Bibel; Jens Richter; Emmanuel Lacroix; Yves-Alain Barde
Journal:  Nat Protoc       Date:  2007       Impact factor: 13.491

4.  A chromatin landmark and transcription initiation at most promoters in human cells.

Authors:  Matthew G Guenther; Stuart S Levine; Laurie A Boyer; Rudolf Jaenisch; Richard A Young
Journal:  Cell       Date:  2007-07-13       Impact factor: 41.582

Review 5.  DNA methylation landscapes: provocative insights from epigenomics.

Authors:  Miho M Suzuki; Adrian Bird
Journal:  Nat Rev Genet       Date:  2008-06       Impact factor: 53.242

6.  Chromosomal transposition of PiggyBac in mouse embryonic stem cells.

Authors:  Wei Wang; Chengyi Lin; Dong Lu; Zeming Ning; Tony Cox; David Melvin; Xiaozhong Wang; Allan Bradley; Pentao Liu
Journal:  Proc Natl Acad Sci U S A       Date:  2008-06-25       Impact factor: 11.205

7.  Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation.

Authors:  Da Jia; Renata Z Jurkowska; Xing Zhang; Albert Jeltsch; Xiaodong Cheng
Journal:  Nature       Date:  2007-08-22       Impact factor: 49.962

8.  Genome-scale DNA methylation maps of pluripotent and differentiated cells.

Authors:  Alexander Meissner; Tarjei S Mikkelsen; Hongcang Gu; Marius Wernig; Jacob Hanna; Andrey Sivachenko; Xiaolan Zhang; Bradley E Bernstein; Chad Nusbaum; David B Jaffe; Andreas Gnirke; Rudolf Jaenisch; Eric S Lander
Journal:  Nature       Date:  2008-07-06       Impact factor: 49.962

9.  DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA.

Authors:  Steen K T Ooi; Chen Qiu; Emily Bernstein; Keqin Li; Da Jia; Zhe Yang; Hediye Erdjument-Bromage; Paul Tempst; Shau-Ping Lin; C David Allis; Xiaodong Cheng; Timothy H Bestor
Journal:  Nature       Date:  2007-08-09       Impact factor: 49.962

10.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.

Authors:  Tarjei S Mikkelsen; Manching Ku; David B Jaffe; Biju Issac; Erez Lieberman; Georgia Giannoukos; Pablo Alvarez; William Brockman; Tae-Kyung Kim; Richard P Koche; William Lee; Eric Mendenhall; Aisling O'Donovan; Aviva Presser; Carsten Russ; Xiaohui Xie; Alexander Meissner; Marius Wernig; Rudolf Jaenisch; Chad Nusbaum; Eric S Lander; Bradley E Bernstein
Journal:  Nature       Date:  2007-07-01       Impact factor: 49.962

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  37 in total

1.  Role of transcription complexes in the formation of the basal methylation pattern in early development.

Authors:  Razi Greenfield; Amalia Tabib; Ilana Keshet; Joshua Moss; Ofra Sabag; Alon Goren; Howard Cedar
Journal:  Proc Natl Acad Sci U S A       Date:  2018-09-26       Impact factor: 11.205

2.  Lysine 4 of histone H3.3 is required for embryonic stem cell differentiation, histone enrichment at regulatory regions and transcription accuracy.

Authors:  Maja Gehre; Daria Bunina; Simone Sidoli; Marlena J Lübke; Nichole Diaz; Matteo Trovato; Benjamin A Garcia; Judith B Zaugg; Kyung-Min Noh
Journal:  Nat Genet       Date:  2020-03-05       Impact factor: 38.330

3.  Characteristics of a PHD Finger Subtype.

Authors:  Daniel Boamah; Tao Lin; Franchesca A Poppinga; Shraddha Basu; Shahariar Rahman; Francisca Essel; Suvobrata Chakravarty
Journal:  Biochemistry       Date:  2018-01-05       Impact factor: 3.162

Review 4.  Mammalian DNA methyltransferases: new discoveries and open questions.

Authors:  Humaira Gowher; Albert Jeltsch
Journal:  Biochem Soc Trans       Date:  2018-08-28       Impact factor: 5.407

5.  reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4(+) memory T cells.

Authors:  Sarah Kinkley; Johannes Helmuth; Julia K Polansky; Ilona Dunkel; Gilles Gasparoni; Sebastian Fröhler; Wei Chen; Jörn Walter; Alf Hamann; Ho-Ryun Chung
Journal:  Nat Commun       Date:  2016-08-17       Impact factor: 14.919

6.  Epigenetic Perturbations by Arg882-Mutated DNMT3A Potentiate Aberrant Stem Cell Gene-Expression Program and Acute Leukemia Development.

Authors:  Rui Lu; Ping Wang; Trevor Parton; Yang Zhou; Kaliopi Chrysovergis; Shira Rockowitz; Wei-Yi Chen; Omar Abdel-Wahab; Paul A Wade; Deyou Zheng; Gang Greg Wang
Journal:  Cancer Cell       Date:  2016-06-23       Impact factor: 31.743

7.  Multifaceted Histone H3 Methylation and Phosphorylation Readout by the Plant Homeodomain Finger of Human Nuclear Antigen Sp100C.

Authors:  Xiaojie Zhang; Dan Zhao; Xiaozhe Xiong; Zhimin He; Haitao Li
Journal:  J Biol Chem       Date:  2016-04-22       Impact factor: 5.157

8.  Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells.

Authors:  Andrew D King; Kevin Huang; Liudmilla Rubbi; Shuo Liu; Cun-Yu Wang; Yinsheng Wang; Matteo Pellegrini; Guoping Fan
Journal:  Cell Rep       Date:  2016-09-27       Impact factor: 9.423

Review 9.  Epigenetic dynamics in cancer stem cell dormancy.

Authors:  Alejandra I Ferrer; Jonathan R Trinidad; Oleta Sandiford; Jean-Pierre Etchegaray; Pranela Rameshwar
Journal:  Cancer Metastasis Rev       Date:  2020-09       Impact factor: 9.264

Review 10.  Greater Than the Sum of Parts: Complexity of the Dynamic Epigenome.

Authors:  Alexey A Soshnev; Steven Z Josefowicz; C David Allis
Journal:  Mol Cell       Date:  2016-06-02       Impact factor: 17.970

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