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Cell DOI:10.1016/j.cell.2013.04.037

Transcriptional and epigenetic dynamics during specification of human embryonic stem cells.

Publication TypeJournal Article
Year of Publication2013
AuthorsGifford, CA, Ziller, MJ, Gu, H, Trapnell, C, Donaghey, J, Tsankov, A, Shalek, AK, Kelley, DR, Shishkin, AA, Issner, R, Zhang, X, Coyne, M, Fostel, JL, Holmes, L, Meldrim, J, Guttman, M, Epstein, C, Park, H, Kohlbacher, O, Rinn, J, Gnirke, A, Lander, ES, Bernstein, BE, Meissner, A
Date Published2013 May 23
KeywordsAcetylation, Cell Differentiation, Chromatin, DNA Methylation, Embryonic Stem Cells, Enhancer Elements, Genetic, Epigenesis, Genetic, Histones, Humans, Methylation, Transcription, Genetic

Differentiation of human embryonic stem cells (hESCs) provides a unique opportunity to study the regulatory mechanisms that facilitate cellular transitions in a human context. To that end, we performed comprehensive transcriptional and epigenetic profiling of populations derived through directed differentiation of hESCs representing each of the three embryonic germ layers. Integration of whole-genome bisulfite sequencing, chromatin immunoprecipitation sequencing, and RNA sequencing reveals unique events associated with specification toward each lineage. Lineage-specific dynamic alterations in DNA methylation and H3K4me1 are evident at putative distal regulatory elements that are frequently bound by pluripotency factors in the undifferentiated hESCs. In addition, we identified germ-layer-specific H3K27me3 enrichment at sites exhibiting high DNA methylation in the undifferentiated state. A better understanding of these initial specification events will facilitate identification of deficiencies in current approaches, leading to more faithful differentiation strategies as well as providing insights into the rewiring of human regulatory programs during cellular transitions.


Alternate JournalCell
PubMed ID23664763
PubMed Central IDPMC3709577
Grant ListF32 DK095537 / DK / NIDDK NIH HHS / United States
P01 GM099117 / GM / NIGMS NIH HHS / United States
U01ES017155 / ES / NIEHS NIH HHS / United States
P01GM099117 / GM / NIGMS NIH HHS / United States
U01 ES017155 / ES / NIEHS NIH HHS / United States