Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci
- Author
- Victor Lopez Soriano, Alfredo Dueñas Rey, Rajarshi Mukherjee, Frauke Coppieters (UGent) , Miriam Bauwens (UGent) , Andy Willaert (UGent) and Elfride De Baere (UGent)
- Organization
- Project
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- Precision medicine in inherited blindness using integrated omics in human and animal models
- StarT (European Training Network to Diagnose: Understand and Treat Stargardt Disease, a Frequent Inherited Blinding Disorder - StarT)
- 3G0G3119
- 3L000709
- Abstract
- Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.
- Keywords
- CAROLINA MACULAR DYSTROPHY, NONCODING VARIANTS, ENHANCER, PAX6, MUTATION, DOMAINS, SPECIFICATION, PRIMORDIUM, ZEBRAFISH, DATABASE
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Citation
Please use this url to cite or link to this publication: http://hdl.handle.net/1854/LU-01HTYJ2YFFBJXF1N6CH89E0PE8
- MLA
- Lopez Soriano, Victor, et al. “Multi-Omics Analysis in Human Retina Uncovers Ultraconserved Cis-Regulatory Elements at Rare Eye Disease Loci.” NATURE COMMUNICATIONS, vol. 15, no. 1, 2024, doi:10.1038/s41467-024-45381-1.
- APA
- Lopez Soriano, V., Dueñas Rey, A., Mukherjee, R., Coppieters, F., Bauwens, M., Willaert, A., & De Baere, E. (2024). Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci. NATURE COMMUNICATIONS, 15(1). https://doi.org/10.1038/s41467-024-45381-1
- Chicago author-date
- Lopez Soriano, Victor, Alfredo Dueñas Rey, Rajarshi Mukherjee, Frauke Coppieters, Miriam Bauwens, Andy Willaert, and Elfride De Baere. 2024. “Multi-Omics Analysis in Human Retina Uncovers Ultraconserved Cis-Regulatory Elements at Rare Eye Disease Loci.” NATURE COMMUNICATIONS 15 (1). https://doi.org/10.1038/s41467-024-45381-1.
- Chicago author-date (all authors)
- Lopez Soriano, Victor, Alfredo Dueñas Rey, Rajarshi Mukherjee, Frauke Coppieters, Miriam Bauwens, Andy Willaert, and Elfride De Baere. 2024. “Multi-Omics Analysis in Human Retina Uncovers Ultraconserved Cis-Regulatory Elements at Rare Eye Disease Loci.” NATURE COMMUNICATIONS 15 (1). doi:10.1038/s41467-024-45381-1.
- Vancouver
- 1.Lopez Soriano V, Dueñas Rey A, Mukherjee R, Coppieters F, Bauwens M, Willaert A, et al. Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci. NATURE COMMUNICATIONS. 2024;15(1).
- IEEE
- [1]V. Lopez Soriano et al., “Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci,” NATURE COMMUNICATIONS, vol. 15, no. 1, 2024.
@article{01HTYJ2YFFBJXF1N6CH89E0PE8,
abstract = {{Cross-species genome comparisons have revealed a substantial number of ultraconserved non-coding elements (UCNEs). Several of these elements have proved to be essential tissue- and cell type-specific cis-regulators of developmental gene expression. Here, we characterize a set of UCNEs as candidate CREs (cCREs) during retinal development and evaluate the contribution of their genomic variation to rare eye diseases, for which pathogenic non-coding variants are emerging. Integration of bulk and single-cell retinal multi-omics data reveals 594 genes under potential cis-regulatory control of UCNEs, of which 45 are implicated in rare eye disease. Mining of candidate cis-regulatory UCNEs in WGS data derived from the rare eye disease cohort of Genomics England reveals 178 ultrarare variants within 84 UCNEs associated with 29 disease genes. Overall, we provide a comprehensive annotation of ultraconserved non-coding regions acting as cCREs during retinal development which can be targets of non-coding variation underlying rare eye diseases.}},
articleno = {{1600}},
author = {{Lopez Soriano, Victor and Dueñas Rey, Alfredo and Mukherjee, Rajarshi and Coppieters, Frauke and Bauwens, Miriam and Willaert, Andy and De Baere, Elfride}},
issn = {{2041-1723}},
journal = {{NATURE COMMUNICATIONS}},
keywords = {{CAROLINA MACULAR DYSTROPHY,NONCODING VARIANTS,ENHANCER,PAX6,MUTATION,DOMAINS,SPECIFICATION,PRIMORDIUM,ZEBRAFISH,DATABASE}},
language = {{eng}},
number = {{1}},
pages = {{14}},
title = {{Multi-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci}},
url = {{http://doi.org/10.1038/s41467-024-45381-1}},
volume = {{15}},
year = {{2024}},
}
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