Human cardiac cis-regulatory elements, their cognate transcription factors, and regulatory DNA sequence variants.

Published

Journal Article

Cis-regulatory elements (CRE), short DNA sequences through which transcription factors (TFs) exert regulatory control on gene expression, are postulated to be the major sites of causal sequence variation underlying the genetics of complex traits and diseases. We present integrative analyses, combining high-throughput genomic and epigenomic data with sequence-based computations, to identify the causal transcriptional components in a given tissue. We use data on adult human hearts to demonstrate that (1) sequence-based predictions detect numerous, active, tissue-specific CREs missed by experimental observations, (2) learned sequence features identify the cognate TFs, (3) CRE variants are specifically associated with cardiac gene expression, and (4) a significant fraction of the heritability of exemplar cardiac traits (QT interval, blood pressure, pulse rate) is attributable to these variants. This general systems approach can thus identify candidate causal variants and the components of gene regulatory networks (GRN) to enable understanding of the mechanisms of complex disorders on a tissue- or cell-type basis.

Full Text

Duke Authors

Cited Authors

  • Lee, D; Kapoor, A; Safi, A; Song, L; Halushka, MK; Crawford, GE; Chakravarti, A

Published Date

  • October 2018

Published In

Volume / Issue

  • 28 / 10

Start / End Page

  • 1577 - 1588

PubMed ID

  • 30139769

Pubmed Central ID

  • 30139769

Electronic International Standard Serial Number (EISSN)

  • 1549-5469

International Standard Serial Number (ISSN)

  • 1088-9051

Digital Object Identifier (DOI)

  • 10.1101/gr.234633.118

Language

  • eng