title: Understanding impediments to cellular conversion to pluripotency by assessing the earliest events in ectopic transcription factor binding to the genome.
abstract: In all known cases of transcription factor (TF)-based reprogramming, the process is relatively slow and inefficient. For example, it takes about a month for the ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) to fully reprogram human somatic cells to pluripotency. Furthermore, recent studies indicate that there is an initial stochastic phase, whereby random cells in the converting population begin to express a few genes of the new fate, followed by a so-called deterministic phase, whereby activation of a network for the new fate leads to homogeneous changes in gene expression patterns within a subset of the cell population. We recently mapped the initial interactions between OSKM factors and the human genome during the first 48 h of human fibroblast conversion to pluripotency. Unlike that reported in ES and iPS cells, distal enhancer sites in closed chromatin dominate the initial O, S, K and M binding distribution, showing that promoter occupancy is a later event in reprogramming. O, S and K act as pioneer factors for c-Myc, and c-Myc enhances the engagement of O, S and K. Despite the ability of OSKM to access closed chromatin, megabase-scale chromatin regions in somatic cells, referred to as "differentially bound regions" (DBRs), are remarkably refractory to OSKM binding at 48 h, though they become bound in pluripotent cells. These DBRs are highly enriched for the repressive H3K9me3 mark and span genes at the top of the deterministic hierarchy. Transient knockdown of the relevant chromatin modifiers allows access of OSKM to DBRs and a more rapid and efficient conversion to pluripotency. Thus, overcoming DBR barriers helps explain the conversion from a stochastic to a deterministic phase of transcription factor-mediated cell type conversion.
authors.affiliation: Institute for Regenerative Medicine, Epigenetics Program and Department of Cell and Developmental Biology, Smilow Center for Translational Research, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
authors.forename: Abdenour
authors.initials: A
authors.lastname: Soufi
authors.forename: Kenneth S
authors.initials: KS
authors.lastname: Zaret
mesh_terms: D019070:Cell Lineage; D065150:Cellular Reprogramming; D053595:Embryonic Stem Cells / Q000166:cytology*; D016678:Genome; D006570:Heterochromatin / Q000378:metabolism; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors / Q000235:genetics / Q000378:metabolism; D050814:Octamer Transcription Factor-3 / Q000235:genetics / Q000378:metabolism; D011485:Protein Binding; D016271:Proto-Oncogene Proteins c-myc / Q000235:genetics / Q000378:metabolism; D055748:SOXB1 Transcription Factors / Q000235:genetics / Q000378:metabolism; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D006570:Heterochromatin; C000715467:KLF4 protein, human; D000090062:Kruppel-Like Factor 4; D051741:Kruppel-Like Transcription Factors; D050814:Octamer Transcription Factor-3; D016271:Proto-Oncogene Proteins c-myc; D055748:SOXB1 Transcription Factors; D014157:Transcription Factors
keywords: H3K9me3; Klf4; Oct4; Sox2; c-Myc; chromatin; heterochromatin; pioneer factors; pluripotency; reprogramming