CHD-associated enhancers shape human cardiomyocyte lineage commitment
- The University of Texas Southwestern Medical Center, United States
Abstract
Enhancers orchestrate gene expression programs that drive multicellular development and lineage commitment. Thus, genetic variants at enhancers are thought to contribute to developmental diseases by altering cell fate commitment. However, while many variant-containing enhancers have been identified, studies to endogenously test the impact of these enhancers on lineage commitment have been lacking. We perform a single-cell CRISPRi screen to assess the endogenous roles of 25 enhancers and putative cardiac target genes implicated in genetic studies of congenital heart defects (CHD). We identify 16 enhancers whose repression leads to deficient differentiation of human cardiomyocytes (CMs). A focused CRISPRi validation screen shows that repression of TBX5 enhancers delays the transcriptional switch from mid- to late-stage CM states. Endogenous genetic deletions of two TBX5 enhancers phenocopy epigenetic perturbations. Together, these results identify critical enhancers of cardiac development and suggest that misregulation of these enhancers could contribute to cardiac defects in human patients.
Data availability
Sequencing data have been deposited in GEO under accession code: GSE190475.
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CHD-associated enhancers direct human cardiomyocyte lineage commitment.NCBI Gene Expression Omnibus, GSE190475.
Article and author information
Author details
Funding
NIH (DP2GM128203)
- Gary C Hon
Department of Defense (PR172060)
- Nikhil V Munshi
NIH (UM1HG011996)
- Nikhil V Munshi
- Gary C Hon
NIH (1R35GM145235)
- Gary C Hon
CPRIT (RP190451)
- Gary C Hon
NIH (HL136604)
- Nikhil V Munshi
NIH (HL151650)
- Nikhil V Munshi
Burroughs Wellcome Fund (1019804)
- Gary C Hon
Burroughs Wellcome Fund (1009838)
- Nikhil V Munshi
Welch Foundation (I-2103-2022033)
- Gary C Hon
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Reviewing Editor
- Benoit Bruneau, University of California, San Francisco, United States
Version history
- Preprint posted: April 10, 2022 (view preprint)
- Received: January 15, 2023
- Accepted: March 10, 2023
- Accepted Manuscript published: April 25, 2023 (version 1)
- Version of Record published: May 3, 2023 (version 2)
Copyright
© 2023, Armendariz et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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CHD-associated enhancers shape human cardiomyocyte lineage commitment
eLife 12:e86206.
https://doi.org/10.7554/eLife.86206
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