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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Published in:bioRxiv
Main Authors: Montefiori, Lindsey E, Sobreira, Debora R, Sakabe, Noboru J, Aneas, Ivy, Joslin, Amelia C, Hansen, Grace T, Bozek, Grazyna, Moskowitz, Ivan P, Mcnally, Elizabeth M, Nobrega, Marcelo A
Format: Paper
Language:English
Published: Cold Spring Harbor Cold Spring Harbor Laboratory Press 08.06.2018
Cold Spring Harbor Laboratory
Edition:1.1
Subjects:
Cardiomyocytes
Cardiovascular diseases
Chromatin
Gene expression
Gene mapping
Genetics
Pluripotency
Single-nucleotide polymorphism
Stem cells
ISSN:2692-8205, 2692-8205
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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.
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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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...
SourceID biorxiv
proquest
SourceType Open Access Repository
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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
URI https://www.proquest.com/docview/2068570151
https://www.biorxiv.org/content/10.1101/340869
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