ArticleProceedings of the National Academy of Sciences of the United States of America2013
Drift and conservation of differential exon usage across tissues in primate species.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 81 papers, 1 of them a synthesis that pooled it.
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Who cites it
81 citing papers in PubMed, 1 synthesis or guideline pooled it, 143 citations in OpenAlex.
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- Transcriptional reprogramming of the stress response and translational-secretory machinery enhances recombinant secreted protein production in Yarrowia lipolytica.Microbial cell factories · 2026Article
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- TREX2 component PCID2 scaffolds alternative SAC3-based subcomplexes with distinct RNA processing and export function.bioRxiv : the preprint server for biology · 2026Article
- FOXM1 influences DNA methylation to augment TACC3 alternative splicing directed by KAT2A in hepatocellular carcinoma.Clinical and molecular hepatology · 2026Article
- Inverted Alu repeats in loop-out exon skipping across hominoid evolution.Nucleic acids research · 2026Article
- Nuclear import of malaria RNA rewires splicing in host immune cells.Cell reports · 2026Article
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- Differentiation in the human urothelia is defined by distinct alternative polyadenylation.Cell reports · 2026Article
- Aip mutation leads to significant alterations in gene expression, altered sensitivity to Ahr ligands, and early lethality in zebrafish.Frontiers in toxicology · 2026Article
- Primate-specific adaptation of Ku protects transcriptomic integrity by suppressing Alu-mediated alternative splicing.bioRxiv : the preprint server for biology · 2025Article
- Integrative gene and isoform co-expression networks reveal regulatory rewiring in stress-related psychiatric disorders.iScience · 2025Article
- Antisense-mediated regulation of exon usage in the elastic spring region of Titin modulates sarcomere function.Cardiovascular research · 2025Article
- The tau isoform 1N4R confers vulnerability of MAPT knockout human iPSC-derived neurons to amyloid beta and phosphorylated tau-induced neuronal dysfunction.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2025Article
- The Hao-Fountain syndrome protein USP7 regulates neuronal connectivity in the brain via a novel p53-independent ubiquitin signaling pathway.Cell reports · 2025Article
21 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Alternative usage of exons provides genomes with plasticity to produce different transcripts from the same gene, modulating the function, localization, and life cycle of gene products. It affects most human genes. For a limited number of cases, alternative functions and tissue-specific roles are known. However, recent high-throughput sequencing studies have suggested that much alternative isoform usage across tissues is nonconserved, raising the question of the extent of its functional importance. We address this question in a genome-wide manner by analyzing the transcriptomes of five tissues for six primate species, focusing on exons that are 1:1 orthologous in all six species. Our results support a model in which differential usage of exons has two major modes: First, most of the exons show only weak differences, which are dominated by interspecies variability and may reflect neutral drift and noisy splicing. These cases dominate the genome-wide view and explain why conservation appears to be so limited. Second, however, a sizeable minority of exons show strong differences between tissues, which are mostly conserved. We identified a core set of 3,800 exons from 1,643 genes that show conservation of strongly tissue-dependent usage patterns from human at least to macaque. This set is enriched for exons encoding protein-disordered regions and untranslated regions. Our findings support the theory that isoform regulation is an important target of evolution in primates, and our method provides a powerful tool for discovering potentially functional tissue-dependent isoforms.
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