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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 evolutionarily conserved, and their target genes are expressed in a cell type–specific manner. (a) The conservation score of CEEs (black bars) compared with similarly-sized flanking regions (gray bars) from the three different Hi-C experiments (as specified). (b) The Q statistic values for CEE target (black bars) compared with non-target (gray bars) genes from the three different Hi-C experiments (as specified). Error bars indicate s.e.m. Differences are statistically significant (*P < 0.05, **P < 0.01 and ***P < 0.001, Wilcoxon rank-sum test).
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gkt188-F7: Potential enhancer elements are evolutionarily conserved, and their target genes are expressed in a cell type–specific manner. (a) The conservation score of CEEs (black bars) compared with similarly-sized flanking regions (gray bars) from the three different Hi-C experiments (as specified). (b) The Q statistic values for CEE target (black bars) compared with non-target (gray bars) genes from the three different Hi-C experiments (as specified). Error bars indicate s.e.m. Differences are statistically significant (*P < 0.05, **P < 0.01 and ***P < 0.001, Wilcoxon rank-sum test).

Mentions: Functional elements are often under evolutionary selection because of their cellular function(s) (45). To study if the CEEs are under evolutionary selection, we investigated the conservation score in these elements across the mammalian clade [cons44way conservation score (46)] compared with their upstream and downstream flanking sequences. We found that the CEEs tend to be more conserved than their flanking regions (P < 0.05 for all datasets) (Figure 7a). In total, these results revealed that the CEEs that we have identified are under purifying selection in the human genome, suggesting that they are functional enhancer elements.Figure 7.


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 evolutionarily conserved, and their target genes are expressed in a cell type–specific manner. (a) The conservation score of CEEs (black bars) compared with similarly-sized flanking regions (gray bars) from the three different Hi-C experiments (as specified). (b) The Q statistic values for CEE target (black bars) compared with non-target (gray bars) genes from the three different Hi-C experiments (as specified). Error bars indicate s.e.m. Differences are statistically significant (*P < 0.05, **P < 0.01 and ***P < 0.001, Wilcoxon rank-sum test).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

gkt188-F7: Potential enhancer elements are evolutionarily conserved, and their target genes are expressed in a cell type–specific manner. (a) The conservation score of CEEs (black bars) compared with similarly-sized flanking regions (gray bars) from the three different Hi-C experiments (as specified). (b) The Q statistic values for CEE target (black bars) compared with non-target (gray bars) genes from the three different Hi-C experiments (as specified). Error bars indicate s.e.m. Differences are statistically significant (*P < 0.05, **P < 0.01 and ***P < 0.001, Wilcoxon rank-sum test).
Mentions: Functional elements are often under evolutionary selection because of their cellular function(s) (45). To study if the CEEs are under evolutionary selection, we investigated the conservation score in these elements across the mammalian clade [cons44way conservation score (46)] compared with their upstream and downstream flanking sequences. We found that the CEEs tend to be more conserved than their flanking regions (P < 0.05 for all datasets) (Figure 7a). In total, these results revealed that the CEEs that we have identified are under purifying selection in the human genome, suggesting that they are functional enhancer elements.Figure 7.

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