Rada-Iglesias A, Bajpai R, Swigut T et al. A unique chromatin signature uncovers early developmental enhancers in humans. Nature 2011; 470: 279-283

Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA.
Nature (Impact Factor: 41.46). 02/2011; 470(7333):279-83. DOI: 10.1038/nature09692
Source: PubMed


Cell-fate transitions involve the integration of genomic information encoded by regulatory elements, such as enhancers, with the cellular environment. However, identification of genomic sequences that control human embryonic development represents a formidable challenge. Here we show that in human embryonic stem cells (hESCs), unique chromatin signatures identify two distinct classes of genomic elements, both of which are marked by the presence of chromatin regulators p300 and BRG1, monomethylation of histone H3 at lysine 4 (H3K4me1), and low nucleosomal density. In addition, elements of the first class are distinguished by the acetylation of histone H3 at lysine 27 (H3K27ac), overlap with previously characterized hESC enhancers, and are located proximally to genes expressed in hESCs and the epiblast. In contrast, elements of the second class, which we term 'poised enhancers', are distinguished by the absence of H3K27ac, enrichment of histone H3 lysine 27 trimethylation (H3K27me3), and are linked to genes inactive in hESCs and instead are involved in orchestrating early steps in embryogenesis, such as gastrulation, mesoderm formation and neurulation. Consistent with the poised identity, during differentiation of hESCs to neuroepithelium, a neuroectoderm-specific subset of poised enhancers acquires a chromatin signature associated with active enhancers. When assayed in zebrafish embryos, poised enhancers are able to direct cell-type and stage-specific expression characteristic of their proximal developmental gene, even in the absence of sequence conservation in the fish genome. Our data demonstrate that early developmental enhancers are epigenetically pre-marked in hESCs and indicate an unappreciated role of H3K27me3 at distal regulatory elements. Moreover, the wealth of new regulatory sequences identified here provides an invaluable resource for studies and isolation of transient, rare cell populations representing early stages of human embryogenesis.

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    • "To annotate enhancers genome wide, we promiscuously identified candidate cis-regulatory regions by the presence of TF or p300 enrichment and/or increased chromatin accessibility. We then restricted our analysis primarily to enhancers by assessing the ratio of H3K4me1/H3K4me3 enrichment at these candidate sites, which distinguishes distal enhancers from promoters (Heintzman et al., 2007), and further using H3K27ac enrichment to differentiate active from inactive elements (Creyghton et al., 2010; Rada-Iglesias et al., 2011). The resulting enhancer candidates had enriched conservation signatures compared to surrounding genomic regions and were near genes annotated with craniofacial ontologies—consistent with bona fide NC enhancer status (Figures S3A–S3C). "
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    • "However, Gencode and Broad lncRNA annotations account for only a small portion of the observed chromatin-enriched transcripts; the majority represent a distinct subclass of lncRNAs that we term ''chromatin-enriched RNA'' (cheRNA). Most cheRNAs are tethered to chromatin by RNA pol II (RNAPII), and their presence correlates with neighboring gene transcriptional activity at a level similar to or better than the current state-of-the-art active enhancer annotations (ENCODE Project Consortium, 2012; Ernst et al., 2011; Rada-Iglesias et al., 2011; Zentner et al., 2011). Yet, cheRNAs appear distinct from recently described bi-directional transcripts that emanate from canonical active enhancers (Andersson et al., 2014; Kim et al., 2010; Wang et al., 2011a). "
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    ABSTRACT: A number of long noncoding RNAs (lncRNAs) have been reported to regulate transcription via recruitment of chromatin modifiers or bridging distal enhancer elements to gene promoters. However, the generality of these modes of regulation and the mechanisms of chromatin attachment for thousands of unstudied human lncRNAs remain unclear. To address these questions, we performed stringent nuclear fractionation coupled to RNA sequencing. We provide genome-wide identification of human chromatin-associated lncRNAs and demonstrate tethering of RNA to chromatin by RNAPII is a pervasive mechanism of attachment. We also uncovered thousands of chromatin-enriched RNAs (cheRNAs) that share molecular properties with known lncRNAs. Although distinct from eRNAs derived from active prototypical enhancers, the production of cheRNAs is strongly correlated with the expression of neighboring protein-coding genes. This work provides an updated framework for nuclear RNA organization that includes a large chromatin-associated transcript population correlated with active genes and may prove useful in de novo enhancer annotation. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.
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    • "The correlation of unique distal H3K27ac-accessible sites with nearest gene expression was much higher in TND1 and TND10 than in NPs, further suggesting that distal gene regulation becomes more defined as cells reach a terminally differentiated state. We further observed that the genes that have nearby open and H3K27ac-posi- tive regions exhibit significantly higher expression than genes that only have accessible regions without H3K27ac, suggesting that the presence of H3K27ac at these open sites has an enhancing effect on transcription (Fig. 2G), as previously suggested (Rada-Iglesias et al. 2011; Bonn et al. 2012 "
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