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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    ABSTRACT: cis-regulatory changes play a central role in mor- phological divergence, yet the regulatory principles underlying emergence of human traits remain poorly understood. Here, we use epigenomic profiling from human and chimpanzee cranial neural crest cells to systematically and quantitatively annotate diver- gence of craniofacial cis-regulatory landscapes. Epi- genomic divergence is often attributable to genetic variation within TF motifs at orthologous enhancers, with a novel motif being most predictive of activity biases. We explore properties of this cis-regulatory change, revealing the role of particular retroele- ments, uncovering broad clusters of species-biased enhancers near genes associated with human facial variation, and demonstrating that cis-regulatory divergence is linked to quantitative expression differ- ences of crucial neural crest regulators. Our work provides a wealth of candidates for future evolu- tionary studies and demonstrates the value of ‘‘cellular anthropology,’’ a strategy of using in-vitro- derived embryonic cell types to elucidate both fundamental and evolving mechanisms underlying morphological variation in higher primates
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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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    ABSTRACT: Gene regulation in mammals involves a complex interplay between promoters and distal regulatory elements that function in concert to drive precise spatio-temporal gene expression programs. However, the dynamics of distal gene regulatory landscape and its function in the transcriptional reprogramming that underlies neurogenesis and neuronal activity remain largely unknown. Here, we performed a combinatorial analysis of genome-wide datasets for chromatin accessibility (FAIRE-seq) and the enhancer mark H3K27ac that reveal the highly dynamic nature of distal gene regulation during neurogenesis, which gets progressively restricted to distinct genomic regions as neurons acquire a post-mitotic, terminally differentiated state. We further find that the distal accessible and active regions serve as target sites for distinct transcription factors that function in a stage-specific manner to contribute to the transcriptional program underlying neuronal commitment and maturation. Mature neurons respond to a sustained activity of NMDA receptors by epigenetic reprogramming at a large number of distal regulatory regions as well as dramatic reorganization of super-enhancers. Such massive remodeling of distal regulatory landscape in turn results in a transcriptome that confers a transient loss of neuronal identity and gain of cellular plasticity. Furthermore, NMDA receptor activity also induces many novel pro-survival genes that function in neuroprotective pathways. Taken together, these findings reveal the dynamics of the distal regulatory landscape during neurogenesis and uncover novel regulatory elements that function in concert with epigenetic mechanisms and transcription factors to generate the transcriptome underlying neuronal development and activity. Published by Cold Spring Harbor Laboratory Press.
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