CAS Key Laboratory of Genome Sciences & Information
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1. Introduction


After the institute actively participated in the International Human Genome Project (HGP), the institute also led the Chinese Super-hybrid Rice Genome Project, the chicken and silkworm genome projects. Approved by CAS, the institute founded the CAS Key Laboratory of Genome Sciences and Information on November 2006 under the background of propulsion stage of CAS Knowledge Innovation Project propulsion and rapid development of genome science and bioinformatics. Since establishment in November 2006, it has always been for the national strategic needs and world scientific frontier. With the core task of genome sciences and information studies and purpose of establishing genomics and bioinformatics organic research system, the lab focuses on major basic scientific problems in order to promote research and application of genomics in China, such as human health, agricultural development, environment and other major life science and technology issues.


2. Research location


Based on the frontier fields of genomics and information technology, our library focuses on the national strategic demands of population health and biosecurity. We will develop new theories about genome structure, mutation, function and evolution, and we will also build new methods and technologies about the massive biological data acquisition, integration and mining. We aim to enhance the cross-fertilization of genomics and other disciplines and to promote integration and forward-looking research by data-driven genomic problem. Our major goal is to address key life sciences and technology issues such as public safety, biosecurity and data security.


3. Research direction


(1) New mechanism and theory about epigenetic regulation of complex traits. We aim to reveal the evolution of epigenetic information and its role in the evolution of species, to elucidate how epigenetic information including DNA modification, histone modification, RNA modification guide the reproductive development, cell differentiation and organ formation of animals, and to analyze the molecular mechanism of establishment and maintenance epigenetic information map.


(2) Research on genome structure and plasticity. Focusing on the key issues of assembling large-scale complex genomic sequences, we will develop new strategies and methods to address the high heterozygous or polyploidy problem. By developing new experimental and computational techniques, we will analyze the dynamic characteristics of genome three-dimensional high-level structures. From multidimensional omics perspective, we will reveal the genetic and epigenetic polymorphism and complexity and the decision mechanism of environmental factors on phenotypic plasticity.


(3) Genomics frontier crossover research and its application. We will develop new interdisciplinary methods which integrate genomics, mathematics, computer science, medicine and other science. We will also build standardized technical methods which analyze the correlation between omics data and clinical phenotype systematically and quickly. By these new methods, we wish to form the industry standard of the analysis and application of precise medical data. To provide the precise technical support for the public safety, biosecurity and data security, we will build the Chinese population biology characteristics knowledge database by analyze the characteristics of genotype polymorphism, age, facial phenotype, body characteristics and population origin. In addition, we also develop the new technology and software to detect the trace nucleic acid quickly and the efficient method to store and process DNA data.


4. Organization

Director: HU Songnian, Ph.D.

Deputy Director: LIU Jiang, Ph.D.

Academic committee

Director:HE Lin, Ph.D. (Academician, CAS)
Deputy Director:HAN Bin, Ph.D. (Academician, CAS)

CHI Xuebin, Computer Network Information Center, CAS

GONG Fuzhou, Academy of Mathematics and Systems Sciences, CAS

HANG Haiying, Institute of Biophysics, CAS

HU Songnian, Beijing Institute of Genomics, CAS

HUANG Luqi, China Academy of Chinese Medical Sciences (Academician, CAS)

LI Yixue, Shanghai Institutes for Biological Sciences, CAS

QI Yijun, National Institute of Biological Sciences, Beijing

SUN Xiaowen, Chinese Academy of Fishery Sciences

TONG Yigang, Academy of Military Medical Sciences

WANG Guoyin, Chongqing University of Posts and Telecommunications

XUE Yongbiao, Beijing Institute of Genomics, CAS

YU Jun, Beijing Institute of Genomics, CAS

Ye Jian, Institute of Forensic Science Ministry of Public Security


Consultative committee

Director:CHEN Runsheng, Bioinformatics Institute of Biophyscis, CAS

CHEN Shouyi, Institute of Genetics and Developmental Biology, CAS

CHENG Linzhao, Johns Hopkins School of Medicine

GU Xun, Iowa State University

LI Lingheng, Stowers Institute for Medical Research

MENG Anming, Institute of Zoology, CAS

ZHU Lihuang, Institute of Genetics and Developmental Biology, CAS


5. Introduction of main research progress  


(1) Cancer and disease genome research. We show that our small molecules can kill human ccRCC cells that are dependent on oncogenic cytoplasmic SPOP. Notably, these inhibitors minimally affect the viability of non-tumor kidney cells. Our findings validate the SPOP-substrate protein interaction as a truly attractive target specific to kidney cancer that may inspire novel drug discovery efforts (Cancer Cell 2016). We interrogate 0.9 million genetic variants in 939 craniofacial microsomia cases and 2,012 controls from China, and identify several novel loss-of-function mutations within the associated loci. This study provide new insights into genetic background of craniofacial macrosomia (Nature Communications 2016). The quantitative verification of the serine proteases was further extended to the clinical sera, revealing significantly higher levels of CELA1, CEL2A, CTRL/chymopasin, and TRY2 in CRC patients. Thus, the quantitative target analysis demonstrated that some serine proteases are indicative of CRC progression (Oncotarget 2016, Journal of Proteomics 2016). We found that the dysregulation of gene expression in AD and VaD is quite similar to each other at both functional and gene levels. Interestingly, the dysregulation started at the early stages of the diseases, namely mild cognitive impairment (MCI) and vascular cognitive impairment (VCI). This study may have implications to the common mechanism between AD and VaD (Curr Opin Pharmacology 2016, Mol Neurobiol 2016).

(2) Complex genome structure research. The natural rubber produced by rubber tree (Hevea brasiliensis) serves as essential industrial material and strategic supply. Genomic analysis indicated the rubber tree had undergone a recent whole genome duplication event, and the subsequent subfunctionalization of duplicated genes may play important roles during the emergence of rubber production. Briefly, we constructed a high quality genomic map and provided a solid foundation for basic biological studies on rubber tree, especially in the mechanism of rubber production (Nature Plant 2016). Taenia saginata and Taenia asiatica are parasitic flatworms of major public health and food safety importance. Here we report the draft genomes of T. saginata and T. asiatica, describe the basic biological features and identify potential targets, which provide a resource for developing new therapeutics and molecular diagnostic tools (Nature Communications 2016).

(3) Big data integration research, the lab enhanced the big data integration research and had a series of progress in the field of data integration. The lab have already developed several database such as mammalian transcriptomic database to explore gene expression and regulation (MTD, Briefings in Bioinformatics 2016), manually curated database of chromosome conformation capture data (3CDB, Database 2016). We also have developed several tools for big omics data analysis such a fast and scalable tool for phylogeny reconstruction (CloudPhylo, Bioinformatics 2016) and an online visualization and management tool for customized and annotated phylogenetic trees (EvolView, Nucleic Acids Res 2016).

6. Talents, awards and honors

LIU Jiang, Leading Scientist of Ten-Thousand Talent Program

YU Jun, CAS Distinguished Research Fellow

YU Jun, Director, committee of precision medicine and cancer rehabilitation, CARTTP

HU Songnian, Associate Director, committee of precision medicine and cancer rehabilitation, CARTTP

LEI Hongxing, First prize of scientific and technological progress award of Gansu province, 2016

FANG Xiangdong, Council member of Chinese Union of Translational Medicine (CUTM)

FANG Xiangdong, member of Clinical Genetics Specialist Committee of National Health and Family Planning Commission of the PRC

FANG Xiangdong, member of People’s Medical Publishing House Periodical Management Committee

FANG Xiangdong, member of health and medical big data government decision and standardization Specialized Committee, Chinese Health Information Association

FANG Xiangdong, member of Biological Diagnostic Technology committee, China Medicinal Biotech Association

LUO Yingfeng, CAS Youth Innovation Promotion Association, 2016