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High-throughput identification of long-range regulatory elements and their target promoters in the human genome.

Hwang YC, Zheng Q, Gregory BD, Wang LS - Nucleic Acids Res. (2013)

Bottom Line: We observed that these promoter-interacting hotspots significantly overlap with known enhancer-associated histone modifications and DNase I hypersensitive sites.Thus, we defined thousands of candidate enhancer elements by incorporating these features, and found that they have a significant propensity to be bound by p300, an enhancer binding transcription factor.In total, our study presents a novel high-throughput workflow for confident, genome-wide discovery of enhancer-target promoter pairs, which will significantly improve our understanding of these regulatory interactions.

View Article: PubMed Central - PubMed

Affiliation: Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.

ABSTRACT
Enhancer elements are essential for tissue-specific gene regulation during mammalian development. Although these regulatory elements are often distant from their target genes, they affect gene expression by recruiting transcription factors to specific promoter regions. Because of this long-range action, the annotation of enhancer element-target promoter pairs remains elusive. Here, we developed a novel analysis methodology that takes advantage of Hi-C data to comprehensively identify these interactions throughout the human genome. To do this, we used a geometric distribution-based model to identify DNA-DNA interaction hotspots that contact gene promoters with high confidence. We observed that these promoter-interacting hotspots significantly overlap with known enhancer-associated histone modifications and DNase I hypersensitive sites. Thus, we defined thousands of candidate enhancer elements by incorporating these features, and found that they have a significant propensity to be bound by p300, an enhancer binding transcription factor. Furthermore, we revealed that their target genes are significantly bound by RNA Polymerase II and demonstrate tissue-specific expression. Finally, we uncovered that these elements are generally found within 1 Mb of their targets, and often regulate multiple genes. In total, our study presents a novel high-throughput workflow for confident, genome-wide discovery of enhancer-target promoter pairs, which will significantly improve our understanding of these regulatory interactions.

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Related in: MedlinePlus

Potential enhancer elements are enriched for p300 binding, and their target genes are highly bound by Pol II. (a) P300 binding site enrichment in CEEs. (b) Pol II enrichment observed for the genes targeted by CEEs. Dashed line is the expected value based on a genomic control.
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gkt188-F5: Potential enhancer elements are enriched for p300 binding, and their target genes are highly bound by Pol II. (a) P300 binding site enrichment in CEEs. (b) Pol II enrichment observed for the genes targeted by CEEs. Dashed line is the expected value based on a genomic control.

Mentions: To provide further evidence that our CEEs are bona fide enhancer elements, we examined the enrichment of p300 binding within these regions. We focused on p300 because it is a known enhancer-associated co-activator that mediates the regulation of target gene expression (39,40). We found that the CEEs from all three Hi-C experiments were enriched (P < 0.001) in p300 binding compared with a background control of all extended hotspots (Figure 5a). This enrichment in p300 binding within CEEs strongly suggests we have identified bona fide enhancers, and by using the Hi-C data in this analysis we also identify the gene promoter(s) that each element can target.Figure 5.


High-throughput identification of long-range regulatory elements and their target promoters in the human genome.

Hwang YC, Zheng Q, Gregory BD, Wang LS - Nucleic Acids Res. (2013)

Potential enhancer elements are enriched for p300 binding, and their target genes are highly bound by Pol II. (a) P300 binding site enrichment in CEEs. (b) Pol II enrichment observed for the genes targeted by CEEs. Dashed line is the expected value based on a genomic control.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3643598&req=5

gkt188-F5: Potential enhancer elements are enriched for p300 binding, and their target genes are highly bound by Pol II. (a) P300 binding site enrichment in CEEs. (b) Pol II enrichment observed for the genes targeted by CEEs. Dashed line is the expected value based on a genomic control.
Mentions: To provide further evidence that our CEEs are bona fide enhancer elements, we examined the enrichment of p300 binding within these regions. We focused on p300 because it is a known enhancer-associated co-activator that mediates the regulation of target gene expression (39,40). We found that the CEEs from all three Hi-C experiments were enriched (P < 0.001) in p300 binding compared with a background control of all extended hotspots (Figure 5a). This enrichment in p300 binding within CEEs strongly suggests we have identified bona fide enhancers, and by using the Hi-C data in this analysis we also identify the gene promoter(s) that each element can target.Figure 5.

Bottom Line: We observed that these promoter-interacting hotspots significantly overlap with known enhancer-associated histone modifications and DNase I hypersensitive sites.Thus, we defined thousands of candidate enhancer elements by incorporating these features, and found that they have a significant propensity to be bound by p300, an enhancer binding transcription factor.In total, our study presents a novel high-throughput workflow for confident, genome-wide discovery of enhancer-target promoter pairs, which will significantly improve our understanding of these regulatory interactions.

View Article: PubMed Central - PubMed

Affiliation: Genomics and Computational Biology Graduate Program, University of Pennsylvania, Philadelphia, PA, USA.

ABSTRACT
Enhancer elements are essential for tissue-specific gene regulation during mammalian development. Although these regulatory elements are often distant from their target genes, they affect gene expression by recruiting transcription factors to specific promoter regions. Because of this long-range action, the annotation of enhancer element-target promoter pairs remains elusive. Here, we developed a novel analysis methodology that takes advantage of Hi-C data to comprehensively identify these interactions throughout the human genome. To do this, we used a geometric distribution-based model to identify DNA-DNA interaction hotspots that contact gene promoters with high confidence. We observed that these promoter-interacting hotspots significantly overlap with known enhancer-associated histone modifications and DNase I hypersensitive sites. Thus, we defined thousands of candidate enhancer elements by incorporating these features, and found that they have a significant propensity to be bound by p300, an enhancer binding transcription factor. Furthermore, we revealed that their target genes are significantly bound by RNA Polymerase II and demonstrate tissue-specific expression. Finally, we uncovered that these elements are generally found within 1 Mb of their targets, and often regulate multiple genes. In total, our study presents a novel high-throughput workflow for confident, genome-wide discovery of enhancer-target promoter pairs, which will significantly improve our understanding of these regulatory interactions.

Show MeSH
Related in: MedlinePlus