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

Noh, Kyung-Min; Wang, Haibo; Kim, Hyunjae R.; Wenderski, Wendy; Fang, Fang; Li, Charles H.; Dewell, Scott; Hughes, Stephen H.; Melnick, Ari M.; Patel, Dinshaw J.; Li, Haitao; Allis, C. David

doi:10.1016/j.molcel.2015.05.017

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

Journal Article · Thu Oct 15 00:00:00 EDT 2015 · Mol. Cell

DOI:https://doi.org/10.1016/j.molcel.2015.05.017· OSTI ID:1194212

Noh, Kyung-Min; Wang, Haibo; Kim, Hyunjae R.; Wenderski, Wendy; Fang, Fang; Li, Charles H.; Dewell, Scott; Hughes, Stephen H.; Melnick, Ari M.; Patel, Dinshaw J.; Li, Haitao; Allis, C. David ^[1]

MSKCC

View Accepted Manuscript (DOE)

Cite

Export

Save

Research Organization:: Argonne National Laboratory (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

Sponsoring Organization:: USDOE Office of Science (SC)

OSTI ID:: 1194212

Journal Information:: Mol. Cell, Vol. 59, Issue (1) ; 07, 2015

Country of Publication:: United States

Language:: ENGLISH

Citation Metrics:

Cited by: 61 works

Citation information provided by
Web of Science

References (51)

Survivin Reads Phosphorylated Histone H3 Threonine 3 to Activate the Mitotic Kinase Aurora B Kelly, Alexander E.; Ghenoiu, Cristina; Xue, John Z. Science, Vol. 330, Issue 6001 https://doi.org/10.1126/science.1189505	journal	August 2010
DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA Ooi, Steen K. T.; Qiu, Chen; Bernstein, Emily Nature, Vol. 448, Issue 7154 https://doi.org/10.1038/nature05987	journal	August 2007
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells Gifford, Casey A.; Ziller, Michael J.; Gu, Hongcang Cell, Vol. 153, Issue 5 https://doi.org/10.1016/j.cell.2013.04.037	journal	May 2013
Regulation of HP1–chromatin binding by histone H3 methylation and phosphorylation Fischle, Wolfgang; Tseng, Boo Shan; Dormann, Holger L. Nature, Vol. 438, Issue 7071 https://doi.org/10.1038/nature04219	journal	October 2005
A PHD finger of NURF couples histone H3 lysine 4 trimethylation with chromatin remodelling Wysocka, Joanna; Swigut, Tomek; Xiao, Hua Nature, Vol. 442, Issue 7098 https://doi.org/10.1038/nature04815	journal	May 2006
Exome sequencing identifies somatic mutations of DNA methyltransferase gene DNMT3A in acute monocytic leukemia Yan, Xiao-Jing; Xu, Jie; Gu, Zhao-Hui Nature Genetics, Vol. 43, Issue 4 https://doi.org/10.1038/ng.788	journal	March 2011
Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b Tsumura, Akiko; Hayakawa, Tomohiro; Kumaki, Yuichi Genes to Cells, Vol. 11, Issue 7 https://doi.org/10.1111/j.1365-2443.2006.00984.x	journal	July 2006
Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription Jones, Peter L.; Veenstra, Gert Jan C.; Wade, Paul A. Nature Genetics, Vol. 19, Issue 2 https://doi.org/10.1038/561	journal	June 1998
Substitutions of a cysteine conserved among DNA cytosine methylases result in a variety of phenotypes Wyszynski, Michael W.; Gabbara, Sam; Bhagwat, Ashok S. Nucleic Acids Research, Vol. 20, Issue 2 https://doi.org/10.1093/nar/20.2.319	journal	January 1992
The Contribution of Entropy, Enthalpy, and Hydrophobic Desolvation to Cooperativity in Repeat-Protein Folding Aksel, Tural; Majumdar, Ananya; Barrick, Doug Structure, Vol. 19, Issue 3 https://doi.org/10.1016/j.str.2010.12.018	journal	March 2011
DNA methylation landscapes: provocative insights from epigenomics Suzuki, Miho M.; Bird, Adrian Nature Reviews Genetics, Vol. 9, Issue 6 https://doi.org/10.1038/nrg2341	journal	June 2008
Linking DNA methylation and histone modification: patterns and paradigms Cedar, Howard; Bergman, Yehudit Nature Reviews Genetics, Vol. 10, Issue 5 https://doi.org/10.1038/nrg2540	journal	May 2009
DNA methylation: roles in mammalian development Smith, Zachary D.; Meissner, Alexander Nature Reviews Genetics, Vol. 14, Issue 3 https://doi.org/10.1038/nrg3354	journal	February 2013
Two Histone Marks Establish the Inner Centromere and Chromosome Bi-Orientation Yamagishi, Yuya; Honda, Takashi; Tanno, Yuji Science, Vol. 330, Issue 6001 https://doi.org/10.1126/science.1194498	journal	October 2010
Mutations in the DNA methyltransferase gene DNMT3A cause an overgrowth syndrome with intellectual disability Tatton-Brown, Katrina; Seal, Sheila; Ruark, Elise Nature Genetics, Vol. 46, Issue 4 https://doi.org/10.1038/ng.2917	journal	March 2014
Mechanism of Stimulation of Catalytic Activity of Dnmt3A and Dnmt3B DNA-(cytosine-C5)-methyltransferases by Dnmt3L Gowher, Humaira; Liebert, Kirsten; Hermann, Andrea Journal of Biological Chemistry, Vol. 280, Issue 14 https://doi.org/10.1074/jbc.M413412200	journal	April 2005
Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns Edwards, J. R.; O'Donnell, A. H.; Rollins, R. A. Genome Research, Vol. 20, Issue 7 https://doi.org/10.1101/gr.101535.109	journal	May 2010
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells Mikkelsen, Tarjei S.; Ku, Manching; Jaffe, David B. Nature, Vol. 448, Issue 7153 https://doi.org/10.1038/nature06008	journal	July 2007
Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex Nan, Xinsheng; Ng, Huck-Hui; Johnson, Colin A. Nature, Vol. 393, Issue 6683 https://doi.org/10.1038/30764	journal	May 1998
Histone H3 Thr-3 Phosphorylation by Haspin Positions Aurora B at Centromeres in Mitosis Wang, Fangwei; Dai, Jun; Daum, John R. Science, Vol. 330, Issue 6001 https://doi.org/10.1126/science.1189435	journal	August 2010
Generation of a defined and uniform population of CNS progenitors and neurons from mouse embryonic stem cells Bibel, Miriam; Richter, Jens; Lacroix, Emmanuel Nature Protocols, Vol. 2, Issue 5 https://doi.org/10.1038/nprot.2007.147	journal	April 2007
Phosphorylation of histone H3 at Thr3 is part of a combinatorial pattern that marks and configures mitotic chromatin Markaki, Y.; Christogianni, A.; Politou, A. S. Journal of Cell Science, Vol. 122, Issue 16 https://doi.org/10.1242/jcs.043810	journal	July 2009
Oligomerization and Binding of the Dnmt3a DNA Methyltransferase to Parallel DNA Molecules Jurkowska, Renata Z.; Rajavelu, Arumugam; Anspach, Nils Journal of Biological Chemistry, Vol. 286, Issue 27 https://doi.org/10.1074/jbc.M111.254987	journal	July 2011
Dnmt3L Antagonizes DNA Methylation at Bivalent Promoters and Favors DNA Methylation at Gene Bodies in ESCs Neri, Francesco; Krepelova, Anna; Incarnato, Danny Cell, Vol. 155, Issue 1 https://doi.org/10.1016/j.cell.2013.08.056	journal	September 2013
Reversing DNA Methylation: Mechanisms, Genomics, and Biological Functions Wu, Hao; Zhang, Yi Cell, Vol. 156, Issue 1-2 https://doi.org/10.1016/j.cell.2013.12.019	journal	January 2014
A histone H3 methyltransferase controls DNA methylation in Neurospora crassa Tamaru, Hisashi; Selker, Eric U. Nature, Vol. 414, Issue 6861 https://doi.org/10.1038/35104508	journal	November 2001
Human DNA methylomes at base resolution show widespread epigenomic differences Lister, Ryan; Pelizzola, Mattia; Dowen, Robert H. Nature, Vol. 462, Issue 7271 https://doi.org/10.1038/nature08514	journal	October 2009
Genome-scale DNA methylation maps of pluripotent and differentiated cells Meissner, Alexander; Mikkelsen, Tarjei S.; Gu, Hongcang Nature, Vol. 454, Issue 7205 https://doi.org/10.1038/nature07107	journal	July 2008
Binary switches and modification cassettes in histone biology and beyond Fischle, Wolfgang; Wang, Yanming; David Allis, C. Nature, Vol. 425, Issue 6957 https://doi.org/10.1038/nature02017	journal	October 2003
Reconstitution and Mechanism of the Stimulation of de Novo Methylation by Human DNMT3L Kareta, Michael S.; Botello, Zaida M.; Ennis, Joshua J. Journal of Biological Chemistry, Vol. 281, Issue 36 https://doi.org/10.1074/jbc.M603140200	journal	September 2006
Phosphorylation of histone H3T6 by PKCβI controls demethylation at histone H3K4 Metzger, Eric; Imhof, Axel; Patel, Dharmeshkumar Nature, Vol. 464, Issue 7289 https://doi.org/10.1038/nature08839	journal	March 2010
The kinase haspin is required for mitotic histone H3 Thr 3 phosphorylation and normal metaphase chromosome alignment Dai, J. Genes & Development, Vol. 19, Issue 4 https://doi.org/10.1101/gad.1267105	journal	January 2005
A Novel Dnmt3a Isoform Produced from an Alternative Promoter Localizes to Euchromatin and Its Expression Correlates with Activede Novo Methylation Chen, Taiping; Ueda, Yoshihide; Xie, Shaoping Journal of Biological Chemistry, Vol. 277, Issue 41 https://doi.org/10.1074/jbc.M205312200	journal	October 2002
A map of the cis-regulatory sequences in the mouse genome Shen, Yin; Yue, Feng; McCleary, David F. Nature, Vol. 488, Issue 7409 https://doi.org/10.1038/nature11243	journal	July 2012
Chromatin methylation activity of Dnmt3a and Dnmt3a/3L is guided by interaction of the ADD domain with the histone H3 tail Zhang, Yingying; Jurkowska, Renata; Soeroes, Szabolcs Nucleic Acids Research, Vol. 38, Issue 13 https://doi.org/10.1093/nar/gkq147	journal	March 2010
Dynamic Interplay between Histone H3 Modifications and Protein Interpreters: Emerging Evidence for a “Histone Language” Oliver, Samuel S.; Denu, John M. ChemBioChem, Vol. 12, Issue 2 https://doi.org/10.1002/cbic.201000474	journal	October 2010
In Vivo Activity of Murine De Novo Methyltransferases, Dnmt3a and Dnmt3b Hsieh, Chih-Lin Molecular and Cellular Biology, Vol. 19, Issue 12 https://doi.org/10.1128/MCB.19.12.8211	journal	December 1999
A Chromatin Landmark and Transcription Initiation at Most Promoters in Human Cells Guenther, Matthew G.; Levine, Stuart S.; Boyer, Laurie A. Cell, Vol. 130, Issue 1 https://doi.org/10.1016/j.cell.2007.05.042	journal	July 2007
Structure of Dnmt3a bound to Dnmt3L suggests a model for de novo DNA methylation Jia, Da; Jurkowska, Renata Z.; Zhang, Xing Nature, Vol. 449, Issue 7159 https://doi.org/10.1038/nature06146	journal	August 2007
CpG islands influence chromatin structure via the CpG-binding protein Cfp1 Thomson, John P.; Skene, Peter J.; Selfridge, Jim Nature, Vol. 464, Issue 7291 https://doi.org/10.1038/nature08924	journal	April 2010
Epigenomic Analysis of Multilineage Differentiation of Human Embryonic Stem Cells Xie, Wei; Schultz, Matthew D.; Lister, Ryan Cell, Vol. 153, Issue 5 https://doi.org/10.1016/j.cell.2013.04.022	journal	May 2013
DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development Okano, Masaki; Bell, Daphne W.; Haber, Daniel A. Cell, Vol. 99, Issue 3 https://doi.org/10.1016/S0092-8674(00)81656-6	journal	October 1999
Molecular basis for site-specific read-out of histone H3K4me3 by the BPTF PHD finger of NURF Li, Haitao; Ilin, Serge; Wang, Wooikoon Nature, Vol. 442, Issue 7098 https://doi.org/10.1038/nature04802	journal	May 2006
Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX–DNMT3–DNMT3L domain Otani, Junji; Nankumo, Toshiyuki; Arita, Kyohei EMBO reports, Vol. 10, Issue 11 https://doi.org/10.1038/embor.2009.218	journal	September 2009
Combinatorial profiling of chromatin binding modules reveals multisite discrimination Garske, Adam L.; Oliver, Samuel S.; Wagner, Elise K. Nature Chemical Biology, Vol. 6, Issue 4 https://doi.org/10.1038/nchembio.319	journal	February 2010
Control of the Embryonic Stem Cell State Young, Richard A. Cell, Vol. 144, Issue 6 https://doi.org/10.1016/j.cell.2011.01.032	journal	March 2011
Chromosomal transposition of PiggyBac in mouse embryonic stem cells Wang, W.; Lin, C.; Lu, D. Proceedings of the National Academy of Sciences, Vol. 105, Issue 27 https://doi.org/10.1073/pnas.0801017105	journal	June 2008
Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes Wu, H.; Coskun, V.; Tao, J. Science, Vol. 329, Issue 5990 https://doi.org/10.1126/science.1190485	journal	July 2010
Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase Jackson, James P.; Lindroth, Anders M.; Cao, Xiaofeng Nature, Vol. 416, Issue 6880 https://doi.org/10.1038/nature731	journal	March 2002
Promoter features related to tissue specificity as measured by Shannon entropy Schug, Jonathan; Schuller, Winfried-Paul; Kappen, Claudia Genome Biology, Vol. 6, Issue 4 https://doi.org/10.1186/gb-2005-6-4-r33	journal	March 2005
De novo DNA cytosine methyltransferase activities in mouse embryonic stem cells Lei, Hong; Oh, Suk P.; Okano, Masaki Development, Vol. 122, Issue 10 https://doi.org/10.1242/dev.122.10.3195	journal	October 1996

Cited By (19)

The role and mechanisms of DNA methylation in the oocyte. Sendžikaitė, Gintarė; Kelsey, Gavin Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.48370	text	January 2019
Allosteric control of mammalian DNA methyltransferases – a new regulatory paradigm Jeltsch, Albert; Jurkowska, Renata Z. Nucleic Acids Research, Vol. 44, Issue 18 https://doi.org/10.1093/nar/gkw723	journal	August 2016
Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes Jeltsch, Albert; Broche, Julian; Bashtrykov, Pavel Genes, Vol. 9, Issue 11 https://doi.org/10.3390/genes9110566	journal	November 2018
Bivalent promoter hypermethylation in cancer is linked to the H327me3/H3K4me3 ratio in embryonic stem cells Dunican, Donnchadh S.; Mjoseng, Heidi K.; Duthie, Leanne BMC Biology, Vol. 18, Issue 1 https://doi.org/10.1186/s12915-020-0752-3	journal	March 2020
Establishment and functions of DNA methylation in the germline Stewart, Kathleen R.; Veselovska, Lenka; Kelsey, Gavin Epigenomics, Vol. 8, Issue 10 https://doi.org/10.2217/epi-2016-0056	journal	October 2016
Mechanisms of DNA Methyltransferase Recruitment in Mammals Laisné, Marthe; Gupta, Nikhil; Kirsh, Olivier Genes, Vol. 9, Issue 12 https://doi.org/10.3390/genes9120617	journal	December 2018
Mammalian DNA methyltransferases: new discoveries and open questions Gowher, Humaira; Jeltsch, Albert Biochemical Society Transactions, Vol. 46, Issue 5 https://doi.org/10.1042/bst20170574	journal	August 2018
Establishment and functions of DNA methylation in the germline. Stewart, Kathleen R.; Veselovska, Lenka; Kelsey, Gavin Apollo - University of Cambridge Repository https://doi.org/10.17863/cam.42515	text	January 2016
Methylation-Demethylation Dynamics: Implications of Changes in Acute Kidney Injury Chakraborty, Anubhav; Viswanathan, Pragasam Analytical Cellular Pathology, Vol. 2018 https://doi.org/10.1155/2018/8764384	journal	July 2018
TETs Regulate Proepicardial Cell Migration through Extracellular Matrix Organization during Zebrafish Cardiogenesis Lan, Yahui; Pan, Heng; Li, Cheng Cell Reports, Vol. 26, Issue 3 https://doi.org/10.1016/j.celrep.2018.12.076	journal	January 2019
Molecular Processes Connecting DNA Methylation Patterns with DNA Methyltransferases and Histone Modifications in Mammalian Genomes Jeltsch, Albert; Broche, Julian; Bashtrykov, Pavel Genes, Vol. 10, Issue 5 https://doi.org/10.3390/genes10050388	journal	May 2019
Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2 Rajavelu, Arumugam; Lungu, Cristiana; Emperle, Max Universität Stuttgart https://doi.org/10.18419/opus-10057	collection	January 2018
Chromatin-dependent allosteric regulation of DNMT3A activity by MeCP2 Rajavelu, Arumugam; Lungu, Cristiana; Emperle, Max Nucleic Acids Research, Vol. 46, Issue 17 https://doi.org/10.1093/nar/gky715	journal	August 2018
The role and mechanisms of DNA methylation in the oocyte Sendžikaitė, Gintarė; Kelsey, Gavin Essays in Biochemistry, Vol. 63, Issue 6 https://doi.org/10.1042/ebc20190043	journal	November 2019
reChIP-seq reveals widespread bivalency of H3K4me3 and H3K27me3 in CD4+ memory T cells Kinkley, Sarah; Helmuth, Johannes; Polansky, Julia K. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms12514	journal	August 2016
InterPep2: global peptide–protein docking using interaction surface templates Johansson-Åkhe, Isak; Mirabello, Claudio; Wallner, Björn Bioinformatics, Vol. 36, Issue 8 https://doi.org/10.1093/bioinformatics/btaa005	journal	January 2020
Genetic Studies on Mammalian DNA Methyltransferases Dan, Jiameng; Chen, Taiping Advances in Experimental Medicine and Biology https://doi.org/10.1007/978-3-319-43624-1_6	book	January 2016
Role of TET enzymes in DNA methylation, development, and cancer Rasmussen, Kasper Dindler; Helin, Kristian Genes & Development, Vol. 30, Issue 7 https://doi.org/10.1101/gad.276568.115	journal	April 2016
An epigenetic switch regulates de novo DNA methylation at a subset of pluripotency gene enhancers during embryonic stem cell differentiation Petell, Christopher J.; Alabdi, Lama; He, Ming Nucleic Acids Research, Vol. 44, Issue 16 https://doi.org/10.1093/nar/gkw426	journal	May 2016

Similar Records

Developmental exposure to 50 parts-per-billion arsenic influences histone modifications and associated epigenetic machinery in a region- and sex-specific manner in the adult mouse brain

Journal Article · Thu Oct 01 00:00:00 EDT 2015 · Toxicology and Applied Pharmacology · OSTI ID:1194212

Tyler, Christina R.; Hafez, Alexander K.; Solomon, Elizabeth R.

MERS-CoV and H5N1 influenza virus antagonize antigen presentation by altering the epigenetic landscape

Journal Article · Tue Jan 16 00:00:00 EST 2018 · Proceedings of the National Academy of Sciences of the United States of America · OSTI ID:1194212

Menachery, Vineet D.; Schafer, Alexandra; Burnum-Johnson, Kristin E.; +17 more

Genomic Features of the Human Dopamine Transporter Gene and Its Potential Epigenetic States: Implications for Phenotypic Diversity

Journal Article · Tue Jun 01 00:00:00 EDT 2010 · PLoS One · OSTI ID:1194212

Shumay, E; Shumay, E; Fowler, J S; +1 more

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

Citation Formats

References (51)

Cited By (19)

Similar Records

Related Subjects