Journal
GENOMICS
Volume 99, Issue 1, Pages 10-17Publisher
ACADEMIC PRESS INC ELSEVIER SCIENCE
DOI: 10.1016/j.ygeno.2011.10.004
Keywords
DNA methylation; Repetitive elements; Sequence feature; Gene silencing
Funding
- National Natural Science Foundation of China [61075023, 30971645, 61075037]
- Fundamental Research Funds for the Central Universities [HIT.NSRIF.2010052]
- State Key Laboratory of Urban Water Resource and Environment [2010TS05]
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DNA methylation changes in repetitive elements (REs) are associated with the regulation of gene transcription, embryonic development, differentiation and carcinogenesis. However, genome-wide analysis of DNA methylation of human REs is lacking. Here, we performed genome-wide methylation analysis of REs in nine repeat types in human embryonic stem cells (H1) and fetal fibroblasts (IMR90), and found that the potential for changes in the DNA methylation of REs was different among the nine repeat types and within different genomic regions. DNA methylation changes in the nine repeat types were related to the GC content and CpG density of the sequence contexts. The differentially methylated REs and targeted genes of different repeat types were associated with gene silencing in the transition from H1 to IMR90 cells. Our results suggest that a quarter of REs are involved in the reprogramming of DNA methylation which may play important epigenetic roles during cellular differentiation. (C) 2011 Elsevier Inc. All rights reserved.
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