A promoter interaction map for cardiovascular disease genetics
Over 500 genetic loci have been associated with risk of cardiovascular diseases (CVDs), however most loci are located in gene-distal non-coding regions and their target genes are not known. Here, we generated high-resolution promoter capture Hi-C (PCHi-C) maps in human induced pluripotent stem cells...
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Cold Spring Harbor Laboratory Press
08.06.2018
Cold Spring Harbor Laboratory |
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| Abstract | Over 500 genetic loci have been associated with risk of cardiovascular diseases (CVDs), however most loci are located in gene-distal non-coding regions and their target genes are not known. Here, we generated high-resolution promoter capture Hi-C (PCHi-C) maps in human induced pluripotent stem cells (iPSCs) and iPSC-derived cardiomyocytes (CMs) to provide a resource for identifying and prioritizing the functional targets of CVD associations. We validate these maps by demonstrating that promoters preferentially contact distal sequences enriched for tissue-specific transcription factor motifs and are enriched for chromatin marks that correlate with dynamic changes in gene expression. Using the CM PCHi-C map, we linked 1,999 CVD-associated SNPs to 347 target genes. Remarkably, more than 90% of SNP-target gene interactions did not involve the nearest gene, while 40% of SNPs interacted with at least two genes, demonstrating the importance of considering long-range chromatin interactions when interpreting functional targets of disease loci. |
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| AbstractList | Over 500 genetic loci have been associated with risk of cardiovascular diseases (CVDs), however most loci are located in gene-distal non-coding regions and their target genes are not known. Here, we generated high-resolution promoter capture Hi-C (PCHi-C) maps in human induced pluripotent stem cells (iPSCs) and iPSC-derived cardiomyocytes (CMs) to provide a resource for identifying and prioritizing the functional targets of CVD associations. We validate these maps by demonstrating that promoters preferentially contact distal sequences enriched for tissue-specific transcription factor motifs and are enriched for chromatin marks that correlate with dynamic changes in gene expression. Using the CM PCHi-C map, we linked 1,999 CVD-associated SNPs to 347 target genes. Remarkably, more than 90% of SNP-target gene interactions did not involve the nearest gene, while 40% of SNPs interacted with at least two genes, demonstrating the importance of considering long-range chromatin interactions when interpreting functional targets of disease loci. |
| Author | Montefiori, Lindsey E Joslin, Amelia C Sobreira, Debora R Hansen, Grace T Moskowitz, Ivan P Aneas, Ivy Nobrega, Marcelo A Sakabe, Noboru J Mcnally, Elizabeth M Bozek, Grazyna |
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| Copyright | 2018. This article is published under http://creativecommons.org/licenses/by/4.0/ ( the License ). Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License. 2018, Posted by Cold Spring Harbor Laboratory |
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| DOI | 10.1101/340869 |
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| Snippet | Over 500 genetic loci have been associated with risk of cardiovascular diseases (CVDs), however most loci are located in gene-distal non-coding regions and... |
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| SubjectTerms | Cardiomyocytes Cardiovascular diseases Chromatin Gene expression Gene mapping Genetics Pluripotency Single-nucleotide polymorphism Stem cells |
| Title | A promoter interaction map for cardiovascular disease genetics |
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