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PMID: 20526341 Published · ppublish English Journal Article

Transposable elements have rewired the core regulatory network of human embryonic stem cells.

Nature genetics ·Vol. 42 ·No. 7 ·2010-07-00 ·Pages 631-4

Kunarso G, Chia NY, Jeyakani J, Hwang C, Lu X, Chan YS, Ng HH, Bourque G

Abstract

Detection of new genomic control elements is critical in understanding transcriptional regulatory networks in their entirety. We studied the genome-wide binding locations of three key regulatory proteins (POU5F1, also known as OCT4; NANOG; and CTCF) in human and mouse embryonic stem cells. In contrast to CTCF, we found that the binding profiles of OCT4 and NANOG are markedly different, with only approximately 5% of the regions being homologously occupied. We show that transposable elements contributed up to 25% of the bound sites in humans and mice and have wired new genes into the core regulatory network of embryonic stem cells. These data indicate that species-specific transposable elements have substantially altered the transcriptional circuitry of pluripotent stem cells.

MeSH Terms
Animals Binding Sites/genetics CCCTC-Binding Factor DNA Transposable Elements/genetics Embryonic Stem Cells/metabolism Gene Expression Profiling Gene Regulatory Networks Genome-Wide Association Study Homeodomain Proteins/genetics,metabolism Humans Mice Models, Genetic Nanog Homeobox Protein Octamer Transcription Factor-3/genetics,metabolism Protein Binding RNA Interference Regulatory Sequences, Nucleic Acid/genetics Repressor Proteins/genetics,metabolism Species Specificity
Chemicals
CCCTC-Binding Factor CTCF protein, human Ctcf protein, mouse DNA Transposable Elements Homeodomain Proteins NANOG protein, human Nanog Homeobox Protein Nanog protein, mouse Octamer Transcription Factor-3 POU5F1 protein, human Pou5f1 protein, mouse Repressor Proteins
Authors & Affiliations
8 authors, click to expand affiliations / ORCID
Kunarso Galih
Computational and Mathematical Biology, Genome Institute of Singapore, Singapore, Singapore.
Chia Na-Yu
Jeyakani Justin
Hwang Catalina
Lu Xinyi
Chan Yun-Shen
Ng Huck-Hui
Bourque Guillaume
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Article Info
Journal
Nature genetics
Abbr.
Nat Genet
ISSN
1546-1718
DOI
10.1038/ng.600
Published
2010-07-00
Epub
2010-00-06
Pages
631-4
Language
English
Region
United States
NLM ID
9216904
Subset
IM
Databases
GEO
GSE21200
External Links
PubMed source DOI: 10.1038/ng.600 View journal details
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