ArticleMolecular biology and evolution2014
Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.
Article in Molecular biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed, 38 citations in OpenAlex.
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- Genomic Evidence for the Complex Evolutionary History of Macaques (Genus Macaca).Journal of molecular evolution · 2024Article
- Resequencing of a Pekin duck breeding population provides insights into the genomic response to short-term artificial selection.GigaScience · 2023Article
- Polyadenylation-related isoform switching in human evolution revealed by full-length transcript structure.Briefings in bioinformatics · 2021Article
- Adaptive Proteome Diversification by Nonsynonymous A-to-I RNA Editing in Coleoid Cephalopods.Molecular biology and evolution · 2021Article
- Functional and Adaptive Significance of Promoter Mutations That Affect Divergent Myocardial Expressions of TRIM72 in Primates.Molecular biology and evolution · 2021Article
- Histone deacetylase HDA-1 modulates mitochondrial stress response and longevity.Nature communications · 2020Article
- Animal-ImputeDB: a comprehensive database with multiple animal reference panels for genotype imputation.Nucleic acids research · 2020Article
- Genetic Diversity, Inbreeding Level, and Genetic Load in Endangered Snub-Nosed Monkeys (Frontiers in genetics · 2020Article
- Central role of IPCell death & disease · 2019Article
- Evolutionarily significant A-to-I RNA editing events originated through G-to-A mutations in primates.Genome biology · 2019Article
- Human exonization through differential nucleosome occupancy.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Deficiency of PRKD2 triggers hyperinsulinemia and metabolic disorders.Nature communications · 2018Article
- Characterization of spontaneously-developed non-alcoholic fatty liver disease in aged rhesus monkeys.Diabetology & metabolic syndrome · 2018Article
- Isoform Evolution in Primates through Independent Combination of Alternative RNA Processing Events.Molecular biology and evolution · 2017Article
- Spliceosomal protein eftud2 mutation leads to p53-dependent apoptosis in zebrafish neural progenitors.Nucleic acids research · 2017Article
- RhesusBase PopGateway: Genome-Wide Population Genetics Atlas in Rhesus Macaque.Molecular biology and evolution · 2016Article
- Small activating RNA binds to the genomic target site in a seed-region-dependent manner.Nucleic acids research · 2016Article
- Selectively Constrained RNA Editing Regulation Crosstalks with piRNA Biogenesis in Primates.Molecular biology and evolution · 2015Article
- Emergence, Retention and Selection: A Trilogy of Origination for Functional De Novo Proteins from Ancestral LncRNAs in Primates.PLoS genetics · 2015Article
Corrections and comments
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Authors and funding
14 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
With genome sequence and composition highly analogous to human, rhesus macaque represents a unique reference for evolutionary studies of human biology. Here, we developed a comprehensive genomic framework of rhesus macaque, the RhesusBase2, for evolutionary interrogation of human genes and the associated regulations. A total of 1,667 next-generation sequencing (NGS) data sets were processed, integrated, and evaluated, generating 51.2 million new functional annotation records. With extensive NGS annotations, RhesusBase2 refined the fine-scale structures in 30% of the macaque Ensembl transcripts, reporting an accurate, up-to-date set of macaque gene models. On the basis of these annotations and accurate macaque gene models, we further developed an NGS-oriented Molecular Evolution Gateway to access and visualize macaque annotations in reference to human orthologous genes and associated regulations (www.rhesusbase.org/molEvo). We highlighted the application of this well-annotated genomic framework in generating hypothetical link of human-biased regulations to human-specific traits, by using mechanistic characterization of the DIEXF gene as an example that provides novel clues to the understanding of digestive system reduction in human evolution. On a global scale, we also identified a catalog of 9,295 human-biased regulatory events, which may represent novel elements that have a substantial impact on shaping human transcriptome and possibly underpin recent human phenotypic evolution. Taken together, we provide an NGS data-driven, information-rich framework that will broadly benefit genomics research in general and serves as an important resource for in-depth evolutionary studies of human biology.
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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.