BioGPS Featured Article – Evolutionary Interrogation of Human Biology in Well-Annotated Genomic Framework of Rhesus Macaque

BioGPS has become the valuable resource that it is because of the contributions from our wonderful user community. Thank you for contributing plugins, suggestions, and ideas–all of which have improved BioGPS for everyone. In order to celebrate the contributions of BioGPS users to the scientific research community, this series will feature publications and articles generated by BioGPS users. We sincerely hope you will join us in celebrating the fascinating work that YOU do.

This week, we will feature an article from a team that not only researches the molecular mechanisms underlying multiple schlerosis and cardiovascular disease, but has also contributed greatly to the research community with their rhesus knowledge base: Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque by Shi-Jian Zhang, Chu-Jun Liu, Peng Yu, Xiaoming Zhong, Jia-Yu Chen, Xinzhuang Yang, Jiguang Peng, Shouyu Yan, Chenqu Wang, Xiaotong Zhu, Jingwei Xiong, Yong E. Zhang, Bertrand Chin-Ming Tan, and Chuan-Yun Li. (DOI 10.1093/molbev/msu084)

Dr. Chuan-Yun Li kindly answered our inquiries for this series.

1. Who is the team behind the work that was published in Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque?
   We mainly work on monkey genomics to study human biology in the context of rhesus macaque. More descriptions are available at: http://rhesusbase.org/contact.jsp.

 

2. Please provide a brief summary of the findings reported in your article, Evolutionary interrogation of human biology in well-annotated genomic framework of rhesus macaque.
   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.

 

3. How did the team learn about and/or utilize BioGPS for this research?
   We integrated the BioGPS expression data in RhesusBase.

 

4. What are some future directions for the team behind this research?
   We are working on monkey genomics and have published several papers in the field:
   • Jia-Yu Chen, Zhiyu Peng, Rongli Zhang, Xin-Zhuang Yang, Bertrand Chin-Ming Tan, Huaying Fang, Chu-Jun Liu, Yong E. Zhang, Mingming Shi, Zhi-Qiang Ye, Minghua Deng, Xiuqin Zhang and Chuan-Yun Li, RNA Editome in Rhesus Macaque Shaped by Purifying Selection, PLoS Genetics, 2014
   • Shi-Jian Zhang, Chu-Jun Liu, M Shi, Lei Kong, Jia-Yu Chen, Wei-Zhen Zhou, Xiaotong Zhu, Peng Yu, Jue Wang, Xinzhuan Yang, Ning Hou, Zhiqiang Ye, Rongli Zhang, Ruiping Xiao, Xiuqin Zhang and Chuan-Yun Li, RhesusBase: a Knowledgebase for the Monkey Research Community. Nucleic Acids Research, 2013
   • Chen Xie, Yong E. Zhang, Jia-Yu Chen, Chu-Jun Liu, Wei-Zhen Zhou, Ying Li, Mao Zhang, Rongli Zhang, Liping Wei and Chuan-Yun Li, Hominoid-specific De Novo Protein-coding Genes Originating from Long Non-coding RNAs, PLoS Genetics, 2012.

Thanks again to Dr. Chuan-Yun “CY” Li for taking the time to answer our questions. Click here to read their fascinating article. Have a look because these awesome researchers have made their compelling research open access–so you can read the whole exciting article for free! While you’re at it, check out their Rhesus knowledge base.

Used BioGPS and cited it in your publication? Let us know! We would love to feature YOUR work, no matter how long ago it was published. BioGPS Featured Article Series only started recently, but we know your contributions to science is ongoing.