Research

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

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, College of Life Science and Technology, Beijing University of Chemical Technology
WANG Guoyin, Chongqing University of Posts and Telecommunications
XUE Yongbiao, Beijing Institute of Genomics, CAS (CNCB)
YU Jun, Beijing Institute of Genomics, CAS (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 find that a histone methylation reader ZCWPW1 is required for the maintenance of H3K9ac and chromatin openness at recombination hotspots, which is important for homologous recombination during meiotic double-strand break repair (Genome Biology. 2022).

We have developed a novel low-cost, ultra-high-throughput single-cell transcriptome and immune repertoire sequencing method named FIPRESCI. The application of this technique has revealed key genes involved in mechanical property of drug resistance of cancel cell (Small, 2022). We established single-cell regulatory map of human organogenesis, revealed the key factors of cell fate decision, provided an important resource for in-depth analysis of complex genetic diseases and organ reconstruction in vitro. Harnessing single-cell chromatin analysis, we deciphered driver pathways of medulloblastoma subtype which is clinically relevant.

We established an experimental method and a bioinformatic analysis tool to identify chromatin interactions composed of three different regulatory elements. A pilot study identified ~50000 such three-way interacting chromatin complexes.

In cooperation with researchers from the Broad Institute and other internationally renowned research institutions, we conducted the largest-scale research to date on human body fat distribution based on human MRI data. This work revealed the inherited genetic basis of the fat depots in visceral, abdominal subcutaneous, and gluteofemoral, and this work also uncovered the relationship between the trends of different fat distributions with the susceptibility of several common complex diseases such as coronary heart disease in humans.

We performed single-gene editing and multiplex gene editing via CRISPR/Cas9 technology to edit BCL11A erythroidspecific enhancer and BCL11A binding site on γ-globin gene promoter in adult human CD34+ cells. Multiplex gene editing led to higher γ-globin expression than single-gene editing without inhibiting erythroid differentiation (European Journal of Pharmacology, 2022); We conducted single-cell RNA sequencing to analyze the heterogeneity of its tumor microenvironments (TMEs) of Chinese patients with Acral melanoma (AM), and identified the genes (e.g., TWIST1, TNFRSF9, and CTGF) could drive the deregulation of various TME components and the molecular interaction (e.g., MIF-CD44 and TNFSF9-TNFRSF9) might be an attractive target for developing novel immunotherapeutic agents (eLife, 2022). We developed several multimodal data fusion models for the risk detection of heart failure and the scientific classcification of gout (Clinical epigenetics, 2022; Arthritis Research & Therapy, 2022).

Considering on the cell cycle, we found that cell cycle arrest plays a key role in the response of high-level chromatin structure to thermal stimulation, repairing the limitations of traditional understanding (Genome Research, 2022); The self-organization dynamics model found that chromatin self-organization can explain a considerable proportion of structural features, which poses new challenges for the study of advanced genome structures (Computational and Structural Biotechnology Journal, 2022); Comparative studies have discovered conserved genome high-level structural features (BMC Biology, 2022).

Our findings provide strong evidence that the three host plasmid ‘golden’ combinations play important and even decisive roles in the successful clonal spread/dissemination of ST11/CG258 cpKPs in China. (Genomics Proteomics Bioinformatics, 2022).

we analyzed the oral and intestinal virome from the metagenome data of children with autism, and found that the human oral and intestinal viromes rarely intersection. At the same time, the biodiversity and abundance of Streptococcus phages in the oral microbiota of children with autism were much higher than normal, and they cooperated with oral Streptococcus and Streptococcus virulence factors, leading to the domination by Streptococcus in oral microbiota, and potentials of transmitting inflammatory substances and signals into the brain through the oral cranial nerve, a novel pathogenesis of autism.

In 2022, the National Genomics Data Center developed several new databases for infectious diseases and microbiology (MPoxVR, KGCoV, ProPan), cancer-trait association (ASCancer Atlas, TWAS Atlas, Brain Catalog, CCAS) as well as tropical plants (TCOD), and updated a set of major resources, providing a family of database resources to support global academic and industrial communities. (Nucleic Acids Res, 2023).

5. Annual awards and honors

XIONG Zhuang, LIU Xiaonan, WANG Guoliang, National Graduate Scholarship, 2022
TENG Xufei, XIONG Zhuang, CAS President’s Outstanding Graduate Scholarship, 2022
ZHANG Tao, CAS-ZHU Li Yuehua Outstanding Doctoral Scholarship, 2022