The primary research interest of the Chen lab is to understand the emerging roles of the “unannotated genome,” which encodes a whole new class of uncharacterized microproteins. In particular, the lab focuses on the relevance and function of this “dark proteome” in regulating development and disease. More broadly, the major goal is to study how gene regulation is controlled at the translational level, and how translational control is misregulated in cancer and other disease contexts. The lab is exploring these mechanisms using a repertoire of interdisciplinary approaches, including CRISPR-based functional genomics, next generation deep-sequencing techniques, biophysical characterization, and bioinformatics.
Jin Chen, Ph.D.
Assistant Professor
Endowed Title Michael L. Rosenberg Scholar in Medical Research
Department Green Ctr for Reprod Bio Scncs | Pharmacology
Graduate Programs Genetics, Development and Disease
Biography
Jin Chen received his B.S. from Yale University in 2010, and his Ph.D. from Stanford University in 2015 with Jody Puglisi as a Stanford Interdisciplinary Graduate Fellow. He did his postdoctoral work with Jonathan Weissman at UCSF/HHMI as a Jane Coffin Childs postdoctoral fellow, and was awarded the NIH K99/R00 Pathway to Independence Award. In 2020, he joined the faculty at UT Southwestern in 2020 as an Endowed Scholar and CPRIT Scholar in the Cecil H. and Ida Green Center for Reproductive Biology Sciences (a center focused on gene regulation) and the Department of Pharmacology. In 2022, he was awarded the Searle Scholar Award (declined).
Research Interest
- CRISPR-based and single-cell functional genomics
- Gene regulation in development and disease
- Proteomic "dark matter" and novel proteins
- RNA biology
- Translational control
Publications
Featured Publications
- Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing.
- Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS, Cell 2021 Apr
- Pervasive functional translation of noncanonical human open reading frames.
- Chen J, Brunner AD, Cogan JZ, Nuñez JK, Fields AP, Adamson B, Itzhak DN, Li JY, Mann M, Leonetti MD, Weissman JS, Science (New York, N.Y.) 2020 03 367 6482 1140-1146
- Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions.
- Chen J, Coakley A, O'Connor M, Petrov A, O'Leary SE, Atkins JF, Puglisi JD, Cell 2015 Nov 163 5 1267-1280
- Dynamic pathways of -1 translational frameshifting.
- Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD, Nature 2014 Aug 512 7514 328-32
- High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence.
- Chen J, Dalal RV, Petrov AN, Tsai A, O'Leary SE, Chapin K, Cheng J, Ewan M, Hsiung PL, Lundquist P, Turner SW, Hsu DR, Puglisi JD, Proceedings of the National Academy of Sciences of the United States of America 2014 Jan 111 2 664-9
- Coordinated conformational and compositional dynamics drive ribosome translocation.
- Chen J, Petrov A, Tsai A, O'Leary SE, Puglisi JD, Nature structural & molecular biology 2013 Jun 20 6 718-27
- Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing.
- Replogle JM, Norman TM, Xu A, Hussmann JA, Chen J, Cogan JZ, Meer EJ, Terry JM, Riordan DP, Srinivas N, Fiddes IT, Arthur JG, Alvarado LJ, Pfeiffer KA, Mikkelsen TS, Weissman JS, Adamson B, Nature biotechnology 2020 Aug 38 8 954-961
- Maf and Mafb control mouse pallial interneuron fate and maturation through neuropsychiatric disease gene regulation.
- Pai EL, Chen J, Fazel Darbandi S, Cho FS, Chen J, Lindtner S, Chu JS, Paz JT, Vogt D, Paredes MF, Rubenstein JL, eLife 2020 May 9
- Amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences.
- Navon SP, Kornberg G, Chen J, Schwartzman T, Tsai A, Puglisi EV, Puglisi JD, Adir N, Proceedings of the National Academy of Sciences of the United States of America 2016 06 113 26 7166-70
- Multiple Parallel Pathways of Translation Initiation on the CrPV IRES.
- Petrov A, Grosely R, Chen J, O'Leary SE, Puglisi JD, Molecular cell 2016 Apr 62 1 92-103
Honors & Awards
- Searle Scholar Award (declined)
(2022) - Cancer Prevention Research Institute of Texas First Time Faculty Recruitment Award
(2020-2025) - UT Southwestern Endowed Scholar
(2020) - NIH Pathway to Independence Award (K99/R00)
(2019-2023) - Jane Coffin Childs Memorial Fund Postdoctoral Fellowship
(2016-2019)