Chromatin state signatures associated with tissue-specific gene expression and enhancer activity in the embryonic limb

Department of Genetics, Yale University School of Medicine, New Haven, CT 06520, USA.
Genome Research (Impact Factor: 14.63). 03/2012; 22(6):1069-80. DOI: 10.1101/gr.129817.111
Source: PubMed


The regulatory elements that direct tissue-specific gene expression in the developing mammalian embryo remain largely unknown. Although chromatin profiling has proven to be a powerful method for mapping regulatory sequences in cultured cells, chromatin states characteristic of active developmental enhancers have not been directly identified in embryonic tissues. Here we use whole-transcriptome analysis coupled with genome-wide profiling of H3K27ac and H3K27me3 to map chromatin states and enhancers in mouse embryonic forelimb and hindlimb. We show that gene-expression differences between forelimb and hindlimb, and between limb and other embryonic cell types, are correlated with tissue-specific H3K27ac signatures at promoters and distal sites. Using H3K27ac profiles, we identified 28,377 putative enhancers, many of which are likely to be limb specific based on strong enrichment near genes highly expressed in the limb and comparisons with tissue-specific EP300 sites and known enhancers. We describe a chromatin state signature associated with active developmental enhancers, defined by high levels of H3K27ac marking, nucleosome displacement, hypersensitivity to sonication, and strong depletion of H3K27me3. We also find that some developmental enhancers exhibit components of this signature, including hypersensitivity, H3K27ac enrichment, and H3K27me3 depletion, at lower levels in tissues in which they are not active. Our results establish histone modification profiling as a tool for developmental enhancer discovery, and suggest that enhancers maintain an open chromatin state in multiple embryonic tissues independent of their activity level.

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Available from: Justin Cotney
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    • "The limb bud acquires a region-specific epigenetic profile at an early stage (Andrey et al., 2013). Numerous limb-specific enhancers are activated by H3K27 acetylation or repressed by H3K27me3, and these two modifications are mutually exclusive (Cotney et al., 2012; Visel et al., 2009). The DNA methylation status of the mammals-fishesconserved-sequence 1 (MFCS1) long-range, limb-specific shh enhancer , which is associated with shh expression in the posterior limb bud (Sagai et al., 2005), coincides with shh expression levels in limb development or regeneration (Yakushiji et al., 2007). "
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    • "For each control we compared the relative enrichment (r1) of the Sp1 motif; r1 42 means Sp1 is enriched, while r1 o1 means Sp1 is not enriched. Additional ChIP datasets were obtained from (Cotney et al., 2012; DeMare et al., 2013; Infante et al., 2013; Peterson et al., 2012; Visel et al., 2009). Each of these datasets were also intersected with previously generated GLI3 binding regions in the mouse limb (Vokes et al., 2008) and divided into two datasets: regions containing the Gli motif and regions without the Gli motif. "
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    • "Distances to the Ets1 and Ets2 TSS are indicated in kilobases. The profiles of DNaseI HS and H3K27ac marks in limb buds (E11.5) are shown in black (Cotney et al., 2012). The placental mammal conservation (Cons) plot (PhyloP ) is shown below. "
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