ArticlePLoS genetics2014
Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation.
Article in PLoS genetics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed.
- The G→C rs590352 in the Protein-Coding Region of ATXN7L3B Gene Upregulates Its Expression In Vivo.Biochemical genetics · 2026Article
- The exonic SNP rs11676272-C risk allele mediates diet-induced obesity and reduces enhancer activation.EMBO reports · 2026Article
- Exonic enhancers are a widespread class of dual-function regulatory elements.Nature communications · 2026Article
- Multiplexed assays of variant effect for clinical variant interpretation.Nature reviews. Genetics · 2026Review
- Introducing the EpGEpigenomes · 2025Article
- Comparative Analysis of Deep Learning Models for Predicting Causative Regulatory Variants.Genes · 2025Article
- Functional variant rs9344 at 11q13.3 regulates CCND1 expression in multiple myeloma with t(11;14).Leukemia · 2025Article
- Article
- Computational and experimental methods for classifying variants of unknown clinical significance.Cold Spring Harbor molecular case studies · 2022Article
- Structural and functional analysis of somatic coding and UTR indels in breast and lung cancer genomes.Scientific reports · 2021Article
- Non-Coding Variants in Cancer: Mechanistic Insights and Clinical Potential for Personalized Medicine.Non-coding RNA · 2021Review
- REVA as A Well-curated Database for Human Expression-modulating Variants.Genomics, proteomics & bioinformatics · 2021Article
- Massively parallel techniques for cataloguing the regulome of the human brain.Nature neuroscience · 2020Review
- DiMSum: an error model and pipeline for analyzing deep mutational scanning data and diagnosing common experimental pathologies.Genome biology · 2020Article
- Functional genomic approaches to elucidate the role of enhancers during development.Wiley interdisciplinary reviews. Systems biology and medicine · 2020Review
- Linear models enable powerful differential activity analysis in massively parallel reporter assays.BMC genomics · 2019Article
- Exonic splice regulation imposes strong selection at synonymous sites.Genome research · 2018Article
- High-throughput screening of prostate cancer risk loci by single nucleotide polymorphisms sequencing.Nature communications · 2018Article
- Estimating the prevalence of functional exonic splice regulatory information.Human genetics · 2017Review
- Predicting gene expression in massively parallel reporter assays: A comparative study.Human mutation · 2017Article
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Authors and funding
11 authors.
Funding
Abstract
In addition to their protein coding function, exons can also serve as transcriptional enhancers. Mutations in these exonic-enhancers (eExons) could alter both protein function and transcription. However, the functional consequence of eExon mutations is not well known. Here, using massively parallel reporter assays, we dissect the enhancer activity of three liver eExons (SORL1 exon 17, TRAF3IP2 exon 2, PPARG exon 6) at single nucleotide resolution in the mouse liver. We find that both synonymous and non-synonymous mutations have similar effects on enhancer activity and many of the deleterious mutation clusters overlap known liver-associated transcription factor binding sites. Carrying a similar massively parallel reporter assay in HeLa cells with these three eExons found differences in their mutation profiles compared to the liver, suggesting that enhancers could have distinct operating profiles in different tissues. Our results demonstrate that eExon mutations could lead to multiple phenotypes by disrupting both the protein sequence and enhancer activity and that enhancers can have distinct mutation profiles in different cell types.
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