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Genetic effects on promoter usage are highly context-specific and contribute to complex traits
Genetic variants regulating RNA splicing and transcript usage have been implicated in both common and rare diseases. Although transcript usage quantitative trait loci (tuQTLs) have been mapped across multiple cell types and contexts, it is challenging to distinguish between the main molecular mechan...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
eLife Sciences Publications, Ltd
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349408/ https://www.ncbi.nlm.nih.gov/pubmed/30618377 http://dx.doi.org/10.7554/eLife.41673 |
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author | Alasoo, Kaur Rodrigues, Julia Danesh, John Freitag, Daniel F Paul, Dirk S Gaffney, Daniel J |
author_facet | Alasoo, Kaur Rodrigues, Julia Danesh, John Freitag, Daniel F Paul, Dirk S Gaffney, Daniel J |
author_sort | Alasoo, Kaur |
collection | PubMed |
description | Genetic variants regulating RNA splicing and transcript usage have been implicated in both common and rare diseases. Although transcript usage quantitative trait loci (tuQTLs) have been mapped across multiple cell types and contexts, it is challenging to distinguish between the main molecular mechanisms controlling transcript usage: promoter choice, splicing and 3ʹ end choice. Here, we analysed RNA-seq data from human macrophages exposed to three inflammatory and one metabolic stimulus. In addition to conventional gene-level and transcript-level analyses, we also directly quantified promoter usage, splicing and 3ʹ end usage. We found that promoters, splicing and 3ʹ ends were predominantly controlled by independent genetic variants enriched in distinct genomic features. Promoter usage QTLs were also 50% more likely to be context-specific than other tuQTLs and constituted 25% of the transcript-level colocalisations with complex traits. Thus, promoter usage might be an underappreciated molecular mechanism mediating complex trait associations in a context-specific manner. |
format | Online Article Text |
id | pubmed-6349408 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | eLife Sciences Publications, Ltd |
record_format | MEDLINE/PubMed |
spelling | pubmed-63494082019-01-30 Genetic effects on promoter usage are highly context-specific and contribute to complex traits Alasoo, Kaur Rodrigues, Julia Danesh, John Freitag, Daniel F Paul, Dirk S Gaffney, Daniel J eLife Computational and Systems Biology Genetic variants regulating RNA splicing and transcript usage have been implicated in both common and rare diseases. Although transcript usage quantitative trait loci (tuQTLs) have been mapped across multiple cell types and contexts, it is challenging to distinguish between the main molecular mechanisms controlling transcript usage: promoter choice, splicing and 3ʹ end choice. Here, we analysed RNA-seq data from human macrophages exposed to three inflammatory and one metabolic stimulus. In addition to conventional gene-level and transcript-level analyses, we also directly quantified promoter usage, splicing and 3ʹ end usage. We found that promoters, splicing and 3ʹ ends were predominantly controlled by independent genetic variants enriched in distinct genomic features. Promoter usage QTLs were also 50% more likely to be context-specific than other tuQTLs and constituted 25% of the transcript-level colocalisations with complex traits. Thus, promoter usage might be an underappreciated molecular mechanism mediating complex trait associations in a context-specific manner. eLife Sciences Publications, Ltd 2019-01-08 /pmc/articles/PMC6349408/ /pubmed/30618377 http://dx.doi.org/10.7554/eLife.41673 Text en © 2019, Alasoo et al http://creativecommons.org/licenses/by/4.0/ http://creativecommons.org/licenses/by/4.0/This article is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use and redistribution provided that the original author and source are credited. |
spellingShingle | Computational and Systems Biology Alasoo, Kaur Rodrigues, Julia Danesh, John Freitag, Daniel F Paul, Dirk S Gaffney, Daniel J Genetic effects on promoter usage are highly context-specific and contribute to complex traits |
title | Genetic effects on promoter usage are highly context-specific and contribute to complex traits |
title_full | Genetic effects on promoter usage are highly context-specific and contribute to complex traits |
title_fullStr | Genetic effects on promoter usage are highly context-specific and contribute to complex traits |
title_full_unstemmed | Genetic effects on promoter usage are highly context-specific and contribute to complex traits |
title_short | Genetic effects on promoter usage are highly context-specific and contribute to complex traits |
title_sort | genetic effects on promoter usage are highly context-specific and contribute to complex traits |
topic | Computational and Systems Biology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6349408/ https://www.ncbi.nlm.nih.gov/pubmed/30618377 http://dx.doi.org/10.7554/eLife.41673 |
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