title: Transcriptional competence and the active marking of tissue-specific enhancers by defined transcription factors in embryonic and induced pluripotent stem cells.
abstract: We reported previously that well-characterized enhancers but not promoters for typical tissue-specific genes, including the classic Alb1 gene, contain unmethylated CpG dinucleotides and evidence of pioneer factor interactions in embryonic stem (ES) cells. These properties, which are distinct from the bivalent histone modification domains that characterize the promoters of genes involved in developmental decisions, raise the possibility that genes expressed only in differentiated cells may need to be marked at the pluripotent stage. Here, we demonstrate that the forkhead family member FoxD3 is essential for the unmethylated mark observed at the Alb1 enhancer in ES cells, with FoxA1 replacing FoxD3 following differentiation into endoderm. Up-regulation of FoxD3 and loss of CpG methylation at the Alb1 enhancer accompanied the reprogramming of mouse embryonic fibroblasts (MEFs) into induced pluripotent stem (iPS) cells. Studies of two genes expressed in specific hematopoietic lineages revealed that the establishment of enhancer marks in ES cells and iPS cells can be regulated both positively and negatively. Furthermore, the absence of a pre-established mark consistently resulted in resistance to transcriptional activation in the repressive chromatin environment that characterizes differentiated cells. These results support the hypothesis that pluripotency and successful reprogramming may be critically dependent on the marking of enhancers for many or all tissue-specific genes.
authors.affiliation: Molecular Biology Institute, Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research, University of California at Los Angeles, Los Angeles, California 90095, USA.
authors.forename: Jian
authors.initials: J
authors.lastname: Xu
authors.forename: Jason A
authors.initials: JA
authors.lastname: Watts
authors.forename: Scott D
authors.initials: SD
authors.lastname: Pope
authors.forename: Paul
authors.initials: P
authors.lastname: Gadue
authors.forename: Mark
authors.initials: M
authors.lastname: Kamps
authors.forename: Kathrin
authors.initials: K
authors.lastname: Plath
authors.forename: Kenneth S
authors.initials: KS
authors.lastname: Zaret
authors.forename: Stephen T
authors.initials: ST
authors.lastname: Smale
mesh_terms: D000818:Animals; D002460:Cell Line; D065150:Cellular Reprogramming; D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000378:metabolism*; D004742:Enhancer Elements, Genetic / Q000235:genetics*; D005347:Fibroblasts / Q000166:cytology; D051858:Forkhead Transcription Factors / Q000378:metabolism*; D018507:Gene Expression Regulation, Developmental; D057026:Induced Pluripotent Stem Cells / Q000378:metabolism*; D008264:Macrophages / Q000378:metabolism; D051379:Mice; D008810:Mice, Inbred C57BL; D014158:Transcription, Genetic / Q000235:genetics*; D015854:Up-Regulation
chemical_list: D051858:Forkhead Transcription Factors