Dynamic changes in the human methylome during differentiation.

Genome Research
Louise LaurentChia-Lin Wei

Abstract

DNA methylation is a critical epigenetic regulator in mammalian development. Here, we present a whole-genome comparative view of DNA methylation using bisulfite sequencing of three cultured cell types representing progressive stages of differentiation: human embryonic stem cells (hESCs), a fibroblastic differentiated derivative of the hESCs, and neonatal fibroblasts. As a reference, we compared our maps with a methylome map of a fully differentiated adult cell type, mature peripheral blood mononuclear cells (monocytes). We observed many notable common and cell-type-specific features among all cell types. Promoter hypomethylation (both CG and CA) and higher levels of gene body methylation were positively correlated with transcription in all cell types. Exons were more highly methylated than introns, and sharp transitions of methylation occurred at exon-intron boundaries, suggesting a role for differential methylation in transcript splicing. Developmental stage was reflected in both the level of global methylation and extent of non-CpG methylation, with hESC highest, fibroblasts intermediate, and monocytes lowest. Differentiation-associated differential methylation profiles were observed for developmentally regulated genes, inclu...Continue Reading

References

Mar 1, 1992·Proceedings of the National Academy of Sciences of the United States of America·M FrommerC L Paul
Mar 1, 1994·Nature Genetics·S H CrossA P Bird
Nov 25, 1993·Nature·E LiR Jaenisch
Jan 1, 1997·Annual Review of Genetics·E HeardP Avner
Nov 6, 1998·Science·J A ThomsonJ M Jones
May 11, 2000·Proceedings of the National Academy of Sciences of the United States of America·B H RamsahoyeR Jaenisch
Aug 11, 2001·Science·W ReikJ Walter
Jan 11, 2002·Developmental Biology·T R HainesP J Ainsworth
Apr 5, 2002·Nature·Ina RheeBert Vogelstein
Feb 25, 2005·Proceedings of the National Academy of Sciences of the United States of America·Fei SongWilliam A Held
Dec 13, 2005·Nature Structural & Molecular Biology·Eric BatschéChristian Muchardt
Dec 21, 2005·Genome Research·Robert A RollinsTimothy H Bestor
Jan 25, 2006·Proceedings of the National Academy of Sciences of the United States of America·Serge SaxonovDouglas L Brutlag
Aug 11, 2006·Genome Research·Marina BibikovaJian-Bing Fan
Dec 13, 2006·Genes & Development·Angela H TingStephen B Baylin
Jul 3, 2007·Nature·Tarjei S MikkelsenBradley E Bernstein
Oct 17, 2007·The Journal of Cell Biology·Noélia CustódioMaria Carmo-Fonseca
Jul 5, 2008·Nature·Alexander MeissnerEric S Lander
Aug 30, 2008·Nature·Franz-Josef MüllerJeanne F Loring
Sep 5, 2008·Current Protocols in Stem Cell Biology·Rodolfo GonzalezEvan Y Snyder
Nov 7, 2008·Nature·Jun WangJian Wang
Feb 3, 2009·Nature Genetics·Paulina Kolasinska-ZwierzJulie Ahringer
Mar 31, 2009·Nature Biotechnology·Madeleine P BallGeorge M Church
Jun 6, 2009·Bioinformatics·Ruiqiang LiJun Wang
Aug 18, 2009·Nature Structural & Molecular Biology·Schraga SchwartzGil Ast
Jan 1, 2008·CSH Protocols·Sohyun L McElroy, Renee A Reijo Pera

❮ Previous
Next ❯

Citations

Jul 5, 2012·Current Diabetes Reports·Robert V Intine, Michael P Sarras
Nov 8, 2012·Theory in Biosciences = Theorie in Den Biowissenschaften·Marcus LechnerVeiko Krauss
Sep 1, 2011·Journal of Ocular Biology, Diseases, and Informatics·Rajesh C RaoShiming Chen
Oct 1, 2013·Protein & Cell·Tao WangPeng Jin
Aug 21, 2013·Neuropharmacology·David P GavinRajiv P Sharma
Dec 15, 2010·The Proceedings of the Nutrition Society·Katherine E Pinnick, Fredrik Karpe
Aug 25, 2011·Expert Reviews in Molecular Medicine·Kornelia KisJames S Hagood
Oct 1, 2011·Journal of Medicinal Chemistry·Sabrina CastellanoGianluca Sbardella
Jan 10, 2013·European Journal of Human Genetics : EJHG·Galina Y ZheleznyakovaHelgi B Schiöth
Jun 1, 2010·Nature·Ramakrishna K ChodavarapuMatteo Pellegrini
Aug 9, 2013·Nature·Michael J ZillerAlexander Meissner
Oct 15, 2010·Nature Biotechnology·Alexander Meissner
Oct 15, 2010·Nature Biotechnology·Anna Portela, Manel Esteller
Nov 8, 2012·Nature Cell Biology·Trevor R LeonardoLouise C Laurent
May 10, 2012·Nature Communications·Michael T BockerAchim Breiling
Nov 9, 2010·Nature Genetics·Julie BorgelMichael Weber
May 29, 2010·Nature Methods·Joseph R Ecker
Aug 30, 2011·Nature Neuroscience·Junjie U GuoHongjun Song
Aug 16, 2012·Neuropsychopharmacology : Official Publication of the American College of Neuropsychopharmacology·Jee-Yeon HwangR Suzanne Zukin
Mar 10, 2012·Nature Protocols·Oluwatosin TaiwoLee M Butcher
Sep 5, 2012·Nature Reviews. Genetics·Holger Heyn, Manel Esteller
Sep 11, 2012·Nature Structural & Molecular Biology·Tarang KhareArturas Petronis
Mar 7, 2013·Nature Structural & Molecular Biology·Yehudit Bergman, Howard Cedar
Sep 29, 2012·Proceedings of the National Academy of Sciences of the United States of America·Trees-Juen ChuangYen-Zho Chen
Jul 18, 2012·Proceedings of the National Academy of Sciences of the United States of America·Joshua D TompkinsArthur D Riggs
Jan 11, 2013·Proceedings of the National Academy of Sciences of the United States of America·Seung-Min YangArthur I Skoultchi
Apr 2, 2011·The Journal of Biological Chemistry·Zhao-xia Chen, Arthur D Riggs
Nov 3, 2011·Antioxidants & Redox Signaling·Ji Woong Han, Young-sup Yoon
Aug 3, 2010·Briefings in Functional Genomics·Wendy N Cooper, Miguel Constância
Nov 11, 2010·Briefings in Functional Genomics·Christopher G Bell, Stephan Beck
Dec 21, 2011·Briefings in Functional Genomics·Alexandra FournierPierre-Antoine Defossez
Mar 10, 2012·Briefings in Functional Genomics·Hao WuYi Eve Sun
Sep 23, 2010·Biostatistics·Martin J AryeeRafael A Irizarry
Apr 27, 2013·Integrative and Comparative Biology·Kevin B FloresGro V Amdam
Jun 8, 2013·ILAR Journal·Ratnam S SeelanRobert M Greene
Apr 13, 2012·Nucleic Acids Research·Paraskevi SalpeaBruce H Howard
Jun 1, 2012·Nucleic Acids Research·Fumihito MiuraTakashi Ito
Aug 28, 2012·Nucleic Acids Research·Satish SatiShantanu Sengupta

❮ Previous
Next ❯

Related Concepts

Related Feeds

CZI Human Cell Atlas Seed Network

The aim of the Human Cell Atlas (HCA) is to build reference maps of all human cells in order to enhance our understanding of health and disease. The Seed Networks for the HCA project aims to bring together collaborators with different areas of expertise in order to facilitate the development of the HCA. Find the latest research from members of the HCA Seed Networks here.