ArticleeLife2019
Genetic effects on promoter usage are highly context-specific and contribute to complex traits.
Article in eLife, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers, 1 of them a synthesis that pooled it.
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Who cites it
49 citing papers in PubMed, 1 synthesis or guideline pooled it, 73 citations in OpenAlex.
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- Mitochondria-Related Genome-Wide Mendelian Randomization Identifies Putatively Genes for Chronic Fatigue.Molecular neurobiology · 2026Article
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- Genetic determinants of monocyte splicing are enriched for disease susceptibility loci.Nature communications · 2025Article
- Chromatin accessibility provides a window into the genetic etiology of human brain disease.Trends in genetics : TIG · 2025Review
- Cell-type-resolved genetic regulatory variation shapes inflammatory bowel disease risk.medRxiv : the preprint server for health sciences · 2025Article
- Genomic diversity in functionally relevant genes modifies neurodevelopmental versus neoplastic risks in individuals with germline PTEN variants.NPJ genomic medicine · 2025Article
- Quantification of single cell-type-specific alternative transcript initiation.bioRxiv : the preprint server for biology · 2025Article
- Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation.Nature genetics · 2025Article
- Long-read RNA sequencing atlas of human microglia isoforms elucidates disease-associated genetic regulation of splicing.Nature genetics · 2025Article
- Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics.Nature communications · 2024Article
- A multi-regional human brain atlas of chromatin accessibility and gene expression facilitates promoter-isoform resolution genetic fine-mapping.Nature communications · 2024Article
- Profiling genetically driven alternative splicing across the Indonesian archipelago.American journal of human genetics · 2024Article
- A compendium of genetic variations associated with promoter usage across 49 human tissues.Nature communications · 2024Article
- Global impact of unproductive splicing on human gene expression.Nature genetics · 2024Article
- Multimodal analysis of RNA sequencing data powers discovery of complex trait genetics.bioRxiv : the preprint server for biology · 2024Article
- Quantifying transcriptome diversity: a review.Briefings in functional genomics · 2024Review
- Review
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
Abstract
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 3' 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 3' end usage. We found that promoters, splicing and 3' 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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.