Abstract
Previous studies have generated controversial findings regarding the correlation between DNA methylation in the human genome and gene expression. Some reports have indicated that promoter methylation is negatively correlated with gene expression levels; however, in some cases, a poor or positive correlation was reported. Most previous findings were based on general trends observed with whole-genome data analysis. Here, we present a novel chromosome-specific statistical analysis design of empirical Bayes differential tests for five phases of erythroid development. To better understand the common methylation patterns of differentially methylated regions (DMRs) during specific stages, we defined differential phases for each CpG locus, based on a maximum log2 fold change. Analyzing hypermethylated and hypomethylated CpG loci separately showed variations in methylation patterns during erythropoiesis in the gene body, promoter and enhancer regions. Hypomethylated DMRs showed stronger associations with erythroid-specific enhancers at the differentiation start phase and with exons in the intermediate phase. To investigate the hypomethylated DMRs further, transcription factor binding site-enrichment analysis was conducted. This analysis...Continue Reading
References
Jan 10, 2002·Genes & Development·Adrian Bird
Jan 22, 2005·Experimental Hematology·Sadaki AsariTakeshi Tokuhisa
Apr 25, 2006·Cell·Bradley E BernsteinEric S Lander
Jun 3, 2006·Developmental Cell·Thomas SandmannEileen E M Furlong
Mar 29, 2008·Cell Stem Cell·Shaun D FouseGuoping Fan
Jan 20, 2009·Nature Genetics·Rafael A IrizarryAndrew P Feinberg
Jan 20, 2009·Nature Reviews. Immunology·I-Cheng HoSung-Yun Pai
May 31, 2011·Blood·Louis C Doré, John D Crispino
Nov 15, 2011·Science·Jeffrey R ShearstoneMerav Socolovsky
Jun 12, 2012·Genome Research·Amber HogartDavid M Bodine
Oct 9, 2012·Developmental Cell·Jian XuStuart H Orkin
Jan 12, 2013·The Journal of Biological Chemistry·Yiting YuAmit Verma
Jun 28, 2013·Genome Research·Bo ZhangTing Wang
Jan 1, 2014·Cell Reports·Jozef MadzoLucy A Godley
Jul 31, 2014·Genome Biology·Shaoke LouKevin Y Yip
Oct 21, 2014·PLoS Genetics·Douglas Vernimmen
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
Jan 22, 2015·Genome Medicine·Samuel LessardGuillaume Lettre
Nov 11, 2015·Nucleic Acids Research·Nuala A O'LearyKim D Pruitt
Jul 15, 2016·Journal of Biomedical Science·Jayu Jen, Yi-Ching Wang