CAS Key Laboratory of Genome Sciences & Information

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. 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. During the past several years, the laboratory has also made significant breakthroughs in the inheritance and reprogramming of epigenetic information in animals. In 2019, National Genomic Science Data Center of China was established.

2. Research direction

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. The research direction: (1) New mechanisms and theories in function genomics, (2) New technologies and methods for genomics, (3) Integration and mining of big data.

3. Organization

Director: LIU Jiang
Deputy Director: FANG Xiangdong

Academic committee
Director:HE Lin, Shanghai Jiao Tong University
Deputy Director:HAN Bin, Institute of Plant Physiology and Ecology, CAS

Members (Ordered alphabetically):
CHI Xuebin, Computer Network Information Center, CAS
GONG Fuzhou, Academy of Mathematics and Systems Sciences, CAS
HANG Haiying, Institute of Biophysics, CAS
HU Songnian, Institute of Microbiology, CAS
HUANG Luqi, China Academy of Chinese Medical Sciences
LI Yixue, Shanghai Institute of Nutrition and Health, 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/China National Center for Bioinformation (CNCB)
YU Jun, Beijing Institute of Genomics, CAS/China National Center for Bioinformation (CNCB)
YE Jian, Institute of Forensic Science Ministry of Public Security

Consultative committee
Director: CHEN Runsheng, Bioinformatics Institute of Biophyscis, CAS
Members (Ordered alphabetically):
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

4. Annual research progress

We constructed an experimental framework to observe re-establishment of long-range chromatin interactions on nascent chromatin, and established an analysis pipeline to view interactions involving more than two regulatory elements. In addition, we utilized zebrafish to investigate DNA methylation reprogramming during juvenile germ cell development and adult female-to-male sex transition.

We revealed that primordial germ cells (PGCs) undergo significant DNA methylation reprogramming during germline development and Tet3 is involved in the process. Notably, we find that inhibiting DNMTs activity can prevent the female-to-male sex transition. Therefore, DNA methylation plays important roles in zebrafish germline development and sexual plasticity.

We proposed quasi-paired cohort strategy reveals the impaired detoxifying function of microbes in the gut of autistic children. (Science Advances, 2020).

Based on peripheral blood expression spectrum and machine learning framework, we established a detection model that can be applied to the detection of chronic and complex diseases including cardiovascular diseases, tumors and metabolic diseases. This model could eliminate batch effect, platform difference and ethnic difference. This method would improve the sensitivity of non-invasive screening and has been patented (Brief Bioinform, 2020).

We first reported a ST1265/K1 carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-HvKP) and revealed that the CR-HvKP evolved from HvKP through acquiring an antimicrobial-resistance plasmid (J Glob Antimicrob Resist, 2020).

The novel DNA storage technology developed by our group can reduce the cost and significantly improved the accuracy. We have applied for the patent (202010688281.X).

We present the dynamics of chromatin reprogramming during IVF, PA and AG embryogenesis. And we observed unsynchronized establishment of chromatin architecture between the uniparental embryos and IVF. (Genome Biology, 2020).

We developed a new trans-splicing detection tool (TSD), and revealed spatial clustering feature of trans-splicing (Science China -Life Sciences, 2020).

In 2020, the National Genomics Data Center developed 8 new databases (2019nCoVR, Aging Atlas, BrainBase, CGIR, GTDB, LncExpDB, scMethBank and TransCirc), and updated a series of resources, involving multiple biological contexts such as disease, aging, regulation and biodiversity (Nucleic Acids Res, 2021).

5. Annual awards and honors

XU Chenhuan, Selected into the national talent program in 2019
LIU Jiang, Second prize of overseas Chinese Contribution Award, 2020
LIU Jiang, Zhu Li Yuehua Outstanding Teacher Award of Chinese Academy of Sciences, 2020
LIU Lin and ZHANG Yuansheng, the National Graduate Scholarship, 2020
CHEN Xuepeng, Excellent Doctoral Dissertation Award of CAS, 2020
WANG Pei, Excellent Graduate of Colleges and Universities in Beijing, 2020