Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells

Abstract

Recent studies have suggested that, in ES cells, inactive genes encoding early developmental regulators possess bivalent histone modification domains and are therefore poised for activation. However, bivalent domains were not observed at typical tissuespecific genes. Here, we show that windows of unmethylated CpG dinucleotides and putative pioneer factor interactions mark enhancers for at least some tissue-specific genes in ES cells. The unmethylated windows expand in cells that express the gene and contract, disappear, or remain unchanged in nonexpressing tissues. However, in ES cells, they do not always coincide with common histone modifications. Genomic footprinting and chromatin immunoprecipitation demonstrated that transcription factor binding underlies the unmethylated windows at enhancers for the Ptcra and Alb1 genes. After stable integration of premethylated Ptcra enhancer constructs into the ES cell genome, the unmethylated windows readily appeared. In contrast, the premethylated constructs remained fully methylated and silent after introduction into Ptcra-expressing thymocytes. These findings provide initial functional support for a model in which pioneer factor interactions in ES cells promote the assembly of a chromatin structure that is permissive for subsequent activation, and in which differentiated tissues lack the machinery required for gene activation when these ES cell marks are absent. The enhancer marks may therefore represent important features of the pluripotent state.chromatin ͉ hematopoiesis

The transcriptional foundation of pluripotency

“…A Fox family member expressed in ES cells (FoxD3) can be detected by ChIP in the same region of the albumin enhancer to which FoxA1 binds in liver. This binding has been proposed to maintain unmethylated cytosines necessary to keep the site in a state compatible with normal development (Xu et al, 2007). The protein for which the evidence of a repressive function associated with lone binding looks least convincing is Oct4 (Kim et al, 2008).…”

Gene regulatory networks governing haematopoietic stem cell development and identity

“…Occupancy of CRMs by pioneer transcription factors also helps maintain their ongoing accessibility and the adoption of inactive chromatin marks can follow the loss of expression of these factors (Tagoh et al, 2002;Xu et al, 2007). Chromatin condensation and inactivation of gene expression can also be achieved by tissue specific transcription factors recruiting histone bound co-repressors to gene promoters (Xu et al, 2007).…”

Defining specificity of transcription factor regulatory activities

“…1). Chromatin marks that dictate the binding of TFs to chromatin might be deposited through regulatory events that take place before or during cellular differentiation, and might involve other Forkhead factors in the case of FOXA1 (Tagoh et al, 2004;Xu et al, 2007a).…”

“…1). Chromatin marks that dictate the binding of TFs to chromatin might be deposited through regulatory events that take place before or during cellular differentiation, and might involve other Forkhead factors in the case of FOXA1 (Tagoh et al, 2004;Xu et al, 2007a).The correlation between H3K4 methylation and TF recruitment to regulatory sites has been extended to other TFs, including signal transducer and activator of transcription 1 (STAT1) and FOXA2, suggesting that a requirement for H3K4 methylation at enhancers might be a general mechanism of regulating TF activity (Heintzman et al, 2009;Robertson et al, 2008). Importantly, epigenetic and dynamic chromatin marks occur in specific combinatorial patterns (reviewed by Cedar and Bergman, 2009;Suganuma and Workman, 2008).…”