RNA splicing is a primary link between genetic variation and disease
Open accessAbstract
RNA splicing links genetics to disease: Many genetic variants associated with disease have no apparent effect on any specific protein coding sequence. Li et al. systematically analyzed the effects of DNA variants on the main steps of gene regulation, from the chromatin state through protein function. One-third of expression quantitative train loci (QTLs) are mediated through transcriptional processes, not chromatin. Splice QTLs and expression QTLs are about comparable in their complex disease risk. Posttranscriptional mechanisms therefore play a large role in translating genotype to phenotype. Science , this issue p. 600
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Alternative splicing is a key contributor to transcriptome complexity and modulation of complex human traits.
“Alternative splicing is a key contributor to transcriptome complexity and modulation of complex human traits 10 .”
From How many human proteoforms are there? (2018) · cites this paper as [10]
The Abstract says splicing QTLs are major contributors to complex traits, supporting the trait-modulation part of the claim. The passage on pre-mRNA splicing discusses transcript isoforms, but our copy does not establish that alternative splicing is a key contributor to transcriptome complexity. No page number is available in the indexed copy. (LLM, conf=0.83)
Experimental — accuracy not yet measuredSplice variants are centrally involved in the modulation of complex traits.
“Li et al. (3) showed that splice variants play a central role in modulating complex traits.”
From Proteoforms as the next proteomics currency (2018) · cites this paper as [3]
Splicing alterations are related to common disease risk independently of gene expression changes.
“Notably, the differential splicing molecular signature is not driven by DGE (Extended Data Fig. 4h), consistent with the observation that splicing alterations are related to common disease risk independently of gene expression changes16.”
From Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism (2016) · cites this paper as [16]
Isoform-level alterations in disease had larger effect sizes than gene-level changes, particularly for protein-coding biotypes.
“In addition, isoform-level alterations in disease exhibited substantially larger effect sizes compared with gene-level changes (mean |log2FC| 0.25 vs 0.14, P<2×10−16, K-S test), particularly for protein coding biotypes (Fig 1A), consistent with recent work demonstrating the importance of splicing dysregulation in disease pathogenesis (25).”
From Transcriptome-wide isoform-level dysregulation in ASD, schizophrenia, and bipolar disorder (2018) · cites this paper as [25]
Genetic risk can also be mediated through mRNA splicing.
“In addition, it is becoming increasingly clear that genetic risk can also be mediated through mRNA splicing28,29.”
From Genetic analysis of the human microglial transcriptome across brain regions, aging and disease pathologies (2022) · cites this paper as [28]
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- Authors
- Li, Y. I., van de Geijn, B., Raj, A., Knowles, D. A., Petti, A. A., Golan, D., Gilad, Y., & Pritchard, J. K.
- Affiliations
- Stanford University (US)
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Stanford Medicine (US)
- Washington University in St. Louis (US)
- University of Chicago (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Gilad, Yoav
- Pritchard, Jonathan K.
- Venue
- Science
- Published
- 2016-04-29
- Volume
- 352
- Issue
- 6285
- Pages
- 600-604
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC5182069
- OpenAlex
- W2344561059
- Cited by
- 660
- References
- 29
- Citations by year
- 2026: 50 · 2025: 57 · 2024: 61 · 2023: 72 · 2022: 58 · 2021: 79 · 2020: 69 · 2019: 61 · 2018: 72 · 2017: 59 · 2016: 20 · 2012: 1
- FWCI
- 36.71
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- NIH (R01MH084703, RO1MH101825, U01HG007036, U54CA149145)
- Center for Computational, Evolutionary and Human Genomics Fellowship
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA Research and Splicing
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- RNA splicing, splicing quantitative trait loci, non-coding variants, gene expression regulation, expression quantitative trait loci, chromatin regulation, lymphoblastoid cell lines, complex traits
- MeSH terms
- Cell Line, Chromatin, Gene Expression Regulation, Humans, Immune System Diseases, Lymphocytes, Phenotype, RNA Splicing, Genetic Variation, Polymorphism, Single Nucleotide, Quantitative Trait Loci, Genome-Wide Association Study
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