Document Detail


Deciphering the heterogeneity in DNA methylation patterns during stem cell differentiation and reprogramming.
MedLine Citation:
PMID:  25404570     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
BACKGROUND: Human induced pluripotent stem cells (iPSCs) have a wide range of applications throughout the fields of basic research, disease modeling and drug screening. Epigenetic instable iPSCs with aberrant DNA methylation may divide and differentiate into cancer cells. Unfortunately, little effort has been taken to compare the epigenetic variation in iPSCs with that in differentiated cells. Here, we developed an analytical procedure to decipher the DNA methylation heterogeneity of mixed cells and further exploited it to quantitatively assess the DNA methylation variation in the methylomes of adipose-derived stem cells (ADS), mature adipocytes differentiated from ADS cells (ADS-adipose) and iPSCs reprogrammed from ADS cells (ADS-iPSCs).
RESULTS: We observed that the degree of DNA methylation variation varies across distinct genomic regions with promoter and 5'UTR regions exhibiting low methylation variation and Satellite showing high methylation variation. Compared with differentiated cells, ADS-iPSCs possess globally decreased methylation variation, in particular in repetitive elements. Interestingly, DNA methylation variation decreases in promoter regions during differentiation but increases during reprogramming. Methylation variation in promoter regions is negatively correlated with gene expression. In addition, genes showing a bipolar methylation pattern, with both completely methylated and completely unmethylated reads, are related to the carbohydrate metabolic process, cellular development, cellular growth, proliferation, etc.
CONCLUSIONS: This study delivers a way to detect cell-subset specific methylation genes in a mixed cell population and provides a better understanding of methylation dynamics during stem cell differentiation and reprogramming.
Authors:
Xiaojian Shao; Cuiyun Zhang; Ming-An Sun; Xuemei Lu; Hehuang Xie
Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2014-11-18
Journal Detail:
Title:  BMC genomics     Volume:  15     ISSN:  1471-2164     ISO Abbreviation:  BMC Genomics     Publication Date:  2014 Nov 
Date Detail:
Created Date:  2014-11-18     Completed Date:  -     Revised Date:  2014-11-19    
Medline Journal Info:
Nlm Unique ID:  100965258     Medline TA:  BMC Genomics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  978     Citation Subset:  -    
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Efficacy and safety of aclidinium bromide/formoterol fumarate fixed-dose combinations compared with ...
Next Document:  The effect of anthropogenic arsenic contamination on the earthworm microbiome.