A compendium of genetic variations associated with promoter usage across 49 human tissues

Jiapei Yuan (), Yang Tong, Le Wang, Xiaoxiao Yang, Xiaochuan Liu, Meng Shu, Zekun Li, Wen Jin, Chenchen Guan, Yuting Wang, Qiang Zhang () and Yang Yang ()
Additional contact information
Jiapei Yuan: Tianjin Medical University
Yang Tong: Tianjin Medical University
Le Wang: Tianjin Medical University
Xiaoxiao Yang: Tianjin Medical University
Xiaochuan Liu: Tianjin Medical University
Meng Shu: Tianjin Medical University
Zekun Li: Tianjin Medical University
Wen Jin: Tianjin Medical University
Chenchen Guan: Tianjin Medical University
Yuting Wang: Tianjin Medical University
Qiang Zhang: Tianjin Medical University
Yang Yang: Tianjin Medical University

Nature Communications, 2024, vol. 15, issue 1, 1-17

Abstract: Abstract Promoters play a crucial role in regulating gene transcription. However, our understanding of how genetic variants influence alternative promoter selection is still incomplete. In this study, we implement a framework to identify genetic variants that affect the relative usage of alternative promoters, known as promoter usage quantitative trait loci (puQTLs). By constructing an atlas of human puQTLs across 49 different tissues from 838 individuals, we have identified approximately 76,856 independent loci associated with promoter usage, encompassing 602,009 genetic variants. Our study demonstrates that puQTLs represent a distinct type of molecular quantitative trait loci, effectively uncovering regulatory targets and patterns. Furthermore, puQTLs are regulating in a tissue-specific manner and are enriched with binding sites of epigenetic marks and transcription factors, especially those involved in chromatin architecture formation. Notably, we have also found that puQTLs colocalize with complex traits or diseases and contribute to their heritability. Collectively, our findings underscore the significant role of puQTLs in elucidating the molecular mechanisms underlying tissue development and complex diseases.

Date: 2024
References: View references in EconPapers View complete reference list from CitEc
Citations:

Downloads: (external link)
https://www.nature.com/articles/s41467-024-53131-6 Abstract (text/html)

Related works:
This item may be available elsewhere in EconPapers: Search for items with the same title.

Export reference: BibTeX RIS (EndNote, ProCite, RefMan) HTML/Text

Persistent link: https://EconPapers.repec.org/RePEc:nat:natcom:v:15:y:2024:i:1:d:10.1038_s41467-024-53131-6

Ordering information: This journal article can be ordered from
https://www.nature.com/ncomms/

DOI: 10.1038/s41467-024-53131-6

Access Statistics for this article

Nature Communications is currently edited by Nathalie Le Bot, Enda Bergin and Fiona Gillespie

More articles in Nature Communications from Nature
Bibliographic data for series maintained by Sonal Shukla () and Springer Nature Abstracting and Indexing ().