Genome-wide compendium and functional assessment of in vivo heart enhancers
Abstract
Whole-genome sequencing is identifying growing numbers of non-coding variants in human disease studies, but the lack of accurate functional annotations prevents their interpretation. We describe the genome-wide landscape of distant-acting enhancers active in the developing and adult human heart, an organ whose impairment is a predominant cause of mortality and morbidity. Using integrative analysis of > 35 epigenomic data sets from mouse and human pre-and postnatal hearts we created a comprehensive reference of > 80,000 putative human heart enhancers. To illustrate the importance of enhancers in the regulation of genes involved in heart disease, we deleted the mouse orthologs of two human enhancers near cardiac myosin genes. In both cases, we observe in vivo expression changes and cardiac phenotypes consistent with human heart disease. Our study provides a comprehensive catalogue of human heart enhancers for use in clinical whole-genome sequencing studies and highlights the importance of enhancers for cardiac function.
- Authors:
-
[1];
[1];
[4]
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- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Ludwig Institute for Cancer Research, La Jolla, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Univ. of California, Berkeley, CA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE; National Institutes of Health (NIH)
- OSTI Identifier:
- 1377528
- Grant/Contract Number:
- AC02-05CH11231; R24HL123879; U01DE024427; R01HG003988; U54HG006997; UM1HL098166; S10RR029668; S10RR027303
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 7; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; cardiovascular diseases; epigenomics; gene regulation; transcriptional regulatory elements
Citation Formats
Dickel, Diane E., Barozzi, Iros, Zhu, Yiwen, Fukuda-Yuzawa, Yoko, Osterwalder, Marco, Mannion, Brandon J., May, Dalit, Spurrell, Cailyn H., Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth, Garvin, Tyler H., Kato, Momoe, Akiyama, Jennifer A., Afzal, Veena, Lee, Ah Young, Gorkin, David U., Ren, Bing, Rubin, Edward M., Visel, Axel, and Pennacchio, Len A. Genome-wide compendium and functional assessment of in vivo heart enhancers. United States: N. p., 2016.
Web. doi:10.1038/ncomms12923.
Dickel, Diane E., Barozzi, Iros, Zhu, Yiwen, Fukuda-Yuzawa, Yoko, Osterwalder, Marco, Mannion, Brandon J., May, Dalit, Spurrell, Cailyn H., Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth, Garvin, Tyler H., Kato, Momoe, Akiyama, Jennifer A., Afzal, Veena, Lee, Ah Young, Gorkin, David U., Ren, Bing, Rubin, Edward M., Visel, Axel, & Pennacchio, Len A. Genome-wide compendium and functional assessment of in vivo heart enhancers. United States. https://doi.org/10.1038/ncomms12923
Dickel, Diane E., Barozzi, Iros, Zhu, Yiwen, Fukuda-Yuzawa, Yoko, Osterwalder, Marco, Mannion, Brandon J., May, Dalit, Spurrell, Cailyn H., Plajzer-Frick, Ingrid, Pickle, Catherine S., Lee, Elizabeth, Garvin, Tyler H., Kato, Momoe, Akiyama, Jennifer A., Afzal, Veena, Lee, Ah Young, Gorkin, David U., Ren, Bing, Rubin, Edward M., Visel, Axel, and Pennacchio, Len A. Wed .
"Genome-wide compendium and functional assessment of in vivo heart enhancers". United States. https://doi.org/10.1038/ncomms12923. https://www.osti.gov/servlets/purl/1377528.
@article{osti_1377528,
title = {Genome-wide compendium and functional assessment of in vivo heart enhancers},
author = {Dickel, Diane E. and Barozzi, Iros and Zhu, Yiwen and Fukuda-Yuzawa, Yoko and Osterwalder, Marco and Mannion, Brandon J. and May, Dalit and Spurrell, Cailyn H. and Plajzer-Frick, Ingrid and Pickle, Catherine S. and Lee, Elizabeth and Garvin, Tyler H. and Kato, Momoe and Akiyama, Jennifer A. and Afzal, Veena and Lee, Ah Young and Gorkin, David U. and Ren, Bing and Rubin, Edward M. and Visel, Axel and Pennacchio, Len A.},
abstractNote = {Whole-genome sequencing is identifying growing numbers of non-coding variants in human disease studies, but the lack of accurate functional annotations prevents their interpretation. We describe the genome-wide landscape of distant-acting enhancers active in the developing and adult human heart, an organ whose impairment is a predominant cause of mortality and morbidity. Using integrative analysis of > 35 epigenomic data sets from mouse and human pre-and postnatal hearts we created a comprehensive reference of > 80,000 putative human heart enhancers. To illustrate the importance of enhancers in the regulation of genes involved in heart disease, we deleted the mouse orthologs of two human enhancers near cardiac myosin genes. In both cases, we observe in vivo expression changes and cardiac phenotypes consistent with human heart disease. Our study provides a comprehensive catalogue of human heart enhancers for use in clinical whole-genome sequencing studies and highlights the importance of enhancers for cardiac function.},
doi = {10.1038/ncomms12923},
journal = {Nature Communications},
number = ,
volume = 7,
place = {United States},
year = {Wed Oct 05 00:00:00 EDT 2016},
month = {Wed Oct 05 00:00:00 EDT 2016}
}
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