The human blood DNA methylome displays a highly distinctive profile compared with other somatic tissues

被引：47
作者：
Lowe, Robert [1 ]
Slodkowicz, Greg [2 ]
Goldman, Nick [2 ]
Rakyan, Vardhman K. [1 ]
机构：
[1] Queen Mary Univ London, Barts & London Sch Med & Dent, Blizard Inst, London, England
[2] European Bioinformat Inst, European Mol Biol Lab, Cambridge, England
来源：
EPIGENETICS | 2015年 / 10卷 / 04期
基金：
欧盟第七框架计划; 英国生物技术与生命科学研究理事会;
关键词：
blood; Illumina 450K Array; methylation; tissue specific; METHYLATION; BIOCONDUCTOR;
D O I：
10.1080/15592294.2014.1003744
中图分类号：
Q5 [生物化学]; Q7 [分子生物学];
学科分类号：
071010 ; 081704 ;
摘要：
In mammals, DNA methylation profiles vary substantially between tissues. Recent genome-scale studies report that blood displays a highly distinctive methylomic profile from other somatic tissues. In this study, we sought to understand why blood DNA methylation state is so different to the one found in other tissues. We found that whole blood contains approximately twice as many tissue-specific differentially methylated positions (tDMPs) than any other somatic tissue examined. Furthermore, a large subset of blood tDMPs showed much lower levels of methylation than tDMPs for other tissues. Surprisingly, these regions of low methylation in blood show no difference regarding genomic location, genomic content, evolutionary rates, or histone marks when compared to other tDMPs. Our results reveal why blood displays a distinctive methylation profile relative to other somatic tissues. In the future, it will be important to study how these blood specific tDMPs are mechanistically involved in blood-specific functions.
引用
收藏
页码：274 / 281
页数：8
相关论文
共 24 条
[1]  
[Anonymous], NUCL ACIDS RES
[2]   Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays [J].
Aryee, Martin J. ;
Jaffe, Andrew E. ;
Corrada-Bravo, Hector ;
Ladd-Acosta, Christine ;
Feinberg, Andrew P. ;
Hansen, Kasper D. ;
Irizarry, Rafael A. .
BIOINFORMATICS, 2014, 30 (10) :1363-1369
[3]   The NIH Roadmap Epigenomics Mapping Consortium [J].
Bernstein, Bradley E. ;
Stamatoyannopoulos, John A. ;
Costello, Joseph F. ;
Ren, Bing ;
Milosavljevic, Aleksandar ;
Meissner, Alexander ;
Kellis, Manolis ;
Marra, Marco A. ;
Beaudet, Arthur L. ;
Ecker, Joseph R. ;
Farnham, Peggy J. ;
Hirst, Martin ;
Lander, Eric S. ;
Mikkelsen, Tarjei S. ;
Thomson, James A. .
NATURE BIOTECHNOLOGY, 2010, 28 (10) :1045-1048
[4]   CPG-RICH ISLANDS AND THE FUNCTION OF DNA METHYLATION [J].
BIRD, AP .
NATURE, 1986, 321 (6067) :209-213
[5]   BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis [J].
Durinck, S ;
Moreau, Y ;
Kasprzyk, A ;
Davis, S ;
De Moor, B ;
Brazma, A ;
Huber, W .
BIOINFORMATICS, 2005, 21 (16) :3439-3440
[6]   ChromHMM: automating chromatin-state discovery and characterization [J].
Ernst, Jason ;
Kellis, Manolis .
NATURE METHODS, 2012, 9 (03) :215-216
[7]   Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates [J].
Hannum, Gregory ;
Guinney, Justin ;
Zhao, Ling ;
Zhang, Li ;
Hughes, Guy ;
Sadda, SriniVas ;
Klotzle, Brandy ;
Bibikova, Marina ;
Fan, Jian-Bing ;
Gao, Yuan ;
Deconde, Rob ;
Chen, Menzies ;
Rajapakse, Indika ;
Friend, Stephen ;
Ideker, Trey ;
Zhang, Kang .
MOLECULAR CELL, 2013, 49 (02) :359-367
[8]   Distinct roles of the methylcytosine oxidases Tet1 and Tet2 in mouse embryonic stem cells [J].
Huang, Yun ;
Chavez, Lukas ;
Chang, Xing ;
Wang, Xue ;
Pastor, William A. ;
Kang, Jinsuk ;
Zepeda-Martinez, Jorge A. ;
Pape, Utz J. ;
Jacobsen, Steven E. ;
Peters, Bjoern ;
Rao, Anjana .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2014, 111 (04) :1361-1366
[9]   Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications [J].
Krueger, Felix ;
Andrews, Simon R. .
BIOINFORMATICS, 2011, 27 (11) :1571-1572
[10]   The power and the promise of DNA methylation markers [J].
Laird, PW .
NATURE REVIEWS CANCER, 2003, 3 (04) :253-266
123