ArticleMolecular biology and evolution2017
Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events.
Article in Molecular biology and evolution, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed, 48 citations in OpenAlex.
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- Targeted DNA-seq and RNA-seq of Reference Samples with Short-read and Long-read Sequencing.Scientific data · 2024Article
- Comparative single-cell transcriptomic analysis of primate brains highlights human-specific regulatory evolution.Nature ecology & evolution · 2023Article
- Transcript Isoform Diversity of Ampliconic Genes on the Y Chromosome of Great Apes.Genome biology and evolution · 2023Article
- Succinate dehydrogenase is essential for epigenetic and metabolic homeostasis in hearts.Basic research in cardiology · 2023Article
- annotate_my_genomes: an easy-to-use pipeline to improve genome annotation and uncover neglected genes by hybrid RNA sequencing.GigaScience · 2022Article
- Evolution of isoform-level gene expression patterns across tissues during lotus species divergence.The Plant journal : for cell and molecular biology · 2022Article
- Full-Length Transcriptome Maps of Reef-Building Coral Illuminate the Molecular Basis of Calcification, Symbiosis, and Circadian Genes.International journal of molecular sciences · 2022Article
- Identification and Characterization of Alternative Splicing Variants and Positive Selection Genes Related to Distinct Growth Rates of Antlers Using Comparative Transcriptome Sequencing.Animals : an open access journal from MDPI · 2022Article
- Transcriptome innovations in primates revealed by single-molecule long-read sequencing.Genome research · 2022Article
- Dominant transcript expression profiles of human protein-coding genes interrogated with GTEx dataset.Scientific reports · 2022Article
- Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure.Briefings in bioinformatics · 2021Article
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- Anti-Inflammatory and Pro-Autophagy Effects of the Cannabinoid Receptor CB2R: Possibility of Modulation in Type 1 Diabetes.Frontiers in pharmacology · 2021Review
- Dynamic transcriptional and chromatin accessibility landscape of medaka embryogenesis.Genome research · 2020Article
Corrections and comments
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Recent RNA-seq technology revealed thousands of splicing events that are under rapid evolution in primates, whereas the reliability of these events, as well as their combination on the isoform level, have not been adequately addressed due to its limited sequencing length. Here, we performed comparative transcriptome analyses in human and rhesus macaque cerebellum using single molecule long-read sequencing (Iso-seq) and matched RNA-seq. Besides 359 million RNA-seq reads, 4,165,527 Iso-seq reads were generated with a mean length of 14,875 bp, covering 11,466 human genes, and 10,159 macaque genes. With Iso-seq data, we substantially expanded the repertoire of alternative RNA processing events in primates, and found that intron retention and alternative polyadenylation are surprisingly more prevalent in primates than previously estimated. We then investigated the combinatorial mode of these alternative events at the whole-transcript level, and found that the combination of these events is largely independent along the transcript, leading to thousands of novel isoforms missed by current annotations. Notably, these novel isoforms are selectively constrained in general, and 1,119 isoforms have even higher expression than the previously annotated major isoforms in human, indicating that the complexity of the human transcriptome is still significantly underestimated. Comparative transcriptome analysis further revealed 502 genes encoding selectively constrained, lineage-specific isoforms in human but not in rhesus macaque, linking them to some lineage-specific functions. Overall, we propose that the independent combination of alternative RNA processing events has contributed to complex isoform evolution in primates, which provides a new foundation for the study of phenotypic difference among primates.
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