The RhesusBase team identified a catalog of 9,295 human-biased regulatory events
2014-02-27
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, for evolutionary interrogation of human genes and the associated regulations. 1,667 next-generation sequencing (NGS) datasets were processed, integrated and evaluated, generating 51.2 million new functional annotation records. With extensive NGS annotations, we 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.
Cover Story: RhesusBase is a resource for comparative analyses of the gene structure and associated regulations in humans and monkeys (Volume 31, pp. 1309-1324). Artwork provided by the RhesusBase Team and Shaomei Hu.
For more details, please refer to the paper:
Evolutionary Interrogation of Human Biology in Well-annotated Genomic Framework of Rhesus Macaque. Molecular Biology and Evolution, 27 February 2014 doi: 10.1093/molbev/msu084.Shi-Jian Zhang et al.
