Chongyi Chen, Ph.D.

Chongyi Chen, Ph.D.
Stadtman Investigator

The Chen lab combines cutting-edge single-cell assays and genomic technologies to study chromatin structure and gene expression in human cells, from a genome-wide perspective at the single-cell level, with a focus on the roles of DNA topology. In addition, the lab develops new assays and techniques in single-cell genomics, epigenomics, and transcriptomics. The long-term goal is to apply the new knowledge in chromosome biology and the new methodologies in single-cell omics to cancer biology and medicine.

Areas of Expertise

1) single-cell omics, 2) chromatin topology, 3) gene expression, 4) genomic technology development, 5) next-generation sequencing, 6) single-molecule imaging

Contact Info

Chongyi Chen, Ph.D.
Center for Cancer Research
National Cancer Institute
Building 37, Room 6044
Bethesda, MD 20892-4260
Ph: 240-760-7493

Our research is focused on the interface between DNA sequence, chromosome organization and gene expression in both bulk samples and single cells, from a genome-wide perspective. Our approach includes traditional assays, as well as the cutting-edge technologies in single-cell omics, next-generation sequencing and single-molecule imaging. Previously we have shown that DNA supercoiling dynamics and topoisomerase activity is the primary mechanism underlying the phenomenon of transcriptional bursting in bacteria (Cell, 2014). We aim to probe DNA supercoiling dynamics in mammalian cells during multiple biological processes. A particular goal is to understand the role of DNA topology in the context of chromatin architecture, transcriptional activity, and other epigenetic features, at the single-cell level.

We have developed a single-cell whole-genome amplification method, Linear Amplification via Transposon Insertion (LIANTI), that enables the accurate detection of single-cell genomic variants, including copy-number variations (CNVs), single-nucleotide variations (SNVs), structural variations (SVs), etc. (Science, 2017). In particular, LIANTI allows the genome-wide detection of small CNVs at kilobase resolution in individual cells. Using LIANTI, we are interested in probing a variety of genomic variants in single human cells, particularly the small CNVs in cancer biology and medicine.

The Chen lab also develops new assays and techniques in single-cell genomics, transcriptomics and epigenomics, primarily based on high-throughput sequencing platforms. We aim to bring these newly invented methods to both fundamental questions in biology and clinical settings in medicine via collaborative efforts.

NIH Scientific Focus Areas:
Cell Biology, Chromosome Biology, Genetics and Genomics, Molecular Biology and Biochemistry, Systems Biology
View Dr. Chen's PubMed Summary.

Selected Key Publications

  1. Wu W, Hill SE, Nathan WJ, Paiano J, Callen E, Wang D, Shinoda K, van Wietmarschen N, Colón-Mercado JM, Zong D, De Pace R, Shih HY, Coon S, Parsadanian M, Pavani R, Hanzlikova H, Park S, Jung SK, McHugh PJ, Canela A, Chen C, Casellas R, Caldecott KW, Ward ME, Nussenzweig A.
    Nature. doi: 10.1038/s41586-021-03468-5. Online ahead of print : [ Journal Article ]
  2. Blanshard RC, Chen C, Xie XS, Hoffmann ER.
    Methods in Cell Biology. 144: 441-457, 2018. [ Journal Article ]
  3. Chen C, Xing D, Tan L, Li H, Zhou G, Huang L, Xie XS.
    Science. 356: 189-194, 2017. [ Journal Article ]
  4. Chong S, Chen C, Ge H, Xie XS.
    Cell. 158: 314-326, 2014. [ Journal Article ]
  5. Wang W, Li G, Chen C, Xie XS, Zhuang X
    Science. 333: 1445-1449, 2011. [ Journal Article ]

Dr. Chen obtained his B.S. in biology from Peking University in 2008, and a Ph.D. in biochemistry from Harvard University in 2014. Working in the lab of X. Sunney Xie, in collaboration with the lab of Xiaowei Zhuang, he applied advanced imaging tools to probe chromosome organization and gene expression at the single-molecule and super-resolution level. As a postdoctoral fellow at Harvard University, he performed single-cell whole-genome analyses by developing a new method, Linear Amplification via Transposon Insertion (LIANTI). LIANTI allows the accurate detection of genomic variants in individual cells, enabling many future studies in biology and medicine from the perspective of next-generation sequencing and single-cell genomics. He joined the Center for Cancer Research as an NIH Stadtman Investigator in 2018.

Name Position
Jun Lyu Ph.D. Postdoctoral Fellow (Visiting)
Yun Shen Ph.D. Guest Researcher
Qian Yao Ph.D. Postdoctoral Fellow (Visiting)
Linying Zhu Ph.D. Postdoctoral Fellow (Visiting)