Research Areas
Metabolic remodeling is a fundamental biological process that enables cells and tissues to adapt to environmental and physiological challenges. Dysregulation of this process contributes to major human diseases, including obesity, diabetes, and cancer. Because metabolic remodeling is orchestrated by precise gene expression programs, understanding the regulatory mechanisms that govern these programs is essential for developing effective therapeutic strategies for metabolic disorders.
Our laboratory is dedicated to understanding how gene regulation drives metabolic remodeling. We seek to uncover how genetic information and environmental cues are translated into specific gene expression programs that ultimately shape cellular metabolic states and adaptive responses. By integrating cutting-edge approaches in 3D genomics, functional genomics, single-cell omics, epigenomics, high-throughput screening, and genome engineering, we aim to systematically dissect the molecular mechanisms linking gene regulation and metabolic remodeling and explore their translational potential in metabolic diseases.
Current research areas include: (1) Three-dimensional genome organization and the genetic basis of metabolic diseases; (2) Metabolic feedback mediated by metabolites and intercellular communication.

Brief Biography
2026.09- ：Professor, Principal Investigator, Shanghai Institute of Nutrition and Health, CAS, Shanghai, China
2020.09-2026.08: Postdoctoral Fellow, Joslin Diabetes Center, Harvard Medical School, Boston, USA
2017.04-2020.08: Postdoctoral Fellow, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, USA
2011.09-2017.04: Ph.D. Shanghai Institute of Biochemistry and Cell Biology, CAS, Shanghai, China
2007.09-2011.06: B.S. Jilin University, Changchun, China

Selected Publications (#Co-first Author, *Corresponding Author)

1. Zhang Y#, Zheng RB#, Tsuji T, Wang CH, Liu XY, Xing YH, Darcy J, Lynes MD, Lundh M, Arianti R, Győry F, Dong R, Emanuelli B, Johnstone SE, Rivera MN, Kristóf E, Kahn CR, Chen KF*, Tseng YH*. A conserved hormonal signalling–H2A.Z axis rapidly reorganizes 3D chromatin interactions in adipocyte thermogenesis. Nature Metabolism 2026 May, 8(5): 1086-1105.
2. Zheng RB#, Zhang Y#, Tsuji T, Gao XL, Shamsi F, Wagner A, Yosef N, Cui K, Chen H, Kiebish M, Aristizabal-Henao J, Narain N, Zhang LL, Tseng YH*, Chen KF*. MEBOCOST maps metabolite-mediated intercellular communications using single-cell RNA-seq. Nucleic Acids Research 2025 Jun 20, 53(12): gkaf569.
3. Zhang Y, Nguyen TM, Zhang XO, Wang LM, Phan T, Clohessy JG*, Pandolfi PP*. Optimized RNA-targeting CRISPR/Cas13d technology outperforms shRNA in identifying functional circRNAs. Genome Biology 2021 Jan 21, 22(1): 41.
4. Zhang Y, Yang L, Chen LL*. Characterization of circular RNAs. Methods in Molecular Biology 2021, 2372: 179-192.
5. Nguyen TM#, Zhang Y#, Pandolfi PP*. Virus against virus: a potential treatment for 2019-nCov (SARS-CoV-2) and other RNA viruses. Cell Research 2020 Mar, 30(3): 189-190.
6. Xing YH#, Yao RW#, Zhang Y#, Guo CJ, Jiang S, Xu G, Dong R, Yang L, Chen LL*. SLERT regulates DDX21-rings associated with Pol I transcription. Cell 2017 May 4, 169(4): 664-678.
   (Research highlights by Bull Chin Acad Sci, 2017, 31: 152-155)
7. Zhang Y#, Xue W#, Li X, Zhang J, Zhang JL, Yang L*, Chen LL*. The biogenesis of nascent circular RNAs. Cell Reports 2016 Apr 19, 15(3): 611-624.
8. Zhang XO#, Dong Rui#, Zhang Y#, Zhang JL, Luo Z, Zhang J, Chen LL*, Yang L*. Diverse alternative back-splicing and alternative splicing landscape of circular RNAs. Genome Research 2016 Sep, 26(9):1277-1287.
9. Zhang Y, Yang L and Chen LL*. Characterization of circular RNAs. Methods in Molecular Biology 2016, 1402: 215-227.
10. Zhang Y, Yang L and Chen LL*. Life without A tail: new formats of long noncoding RNAs. The International Journal of Biochemistry & Cell Biology 2014 Sep, 54: 338-349.
11. Zhang Y#, Zhang XO#, Chen T, Xiang JF, Yin QF, Xing YH, Zhu S, Yang L* and Chen LL*. Circular intronic long noncoding RNAs. Molecular Cell 2013 Sep 26, 51(6): 792-806.
    (Issue Highlight; Preview by Bolisetty MT and Graveley BR, Mol Cell, 2013, 51: 705-706; Research Highlights by Nature, 2013, 501:464; Research Highlights by Nature China, 2013, doi:10.1038)
12. Tsuji T, Tolstikov V, Zhang Y, Huang TL, Camara H, Halpin M, Narain NR, Yau KW, Lynes MD, Kiebish MA, Tseng YH*. Light-responsive adipose-hypothalamus axis controls metabolic regulation. Nature Communications 2024 Aug 8, 15(1): 6768.
13. Tsuji T, Zhang Y, Tseng HY*. Generation of Brown Fat-Specific Knockout Mice Using a Combined Cre-LoxP, CRISPR-Cas9, and Adeno-Associated Virus Single-Guide RNA System. Journal of Visualized Experiments 2023 Mar 24, 193: 10.3791/65083.
14. Guarnerio J, Zhang Y, Cheloni G, Panella R, Mae Katon J, Simpson M, Matsumoto A, Papa A, Loretelli C, Petri A, Kauppinen S, Garbutt C, Nielsen GP, Deshpande V, Castillo-Martin M, Cordon-Cardo C, Dimitrios S, Clohessy JG, Batish M, Pandolfi PP*. Intragenic antagonistic roles of protein and circRNA in tumorigenesis. Cell Research 2019 Aug, 29(8): 628-640.
15. Lee YR, Chen M, Lee JD, Zhang J, Lin SY, Fu TM, Chen H, Ishikawa T, Chiang SY, Katon J, Zhang Y, Shulga YV, Bester AC, Fung J, Monteleone E, Wan L, Shen C, Hsu CH, Papa A, Clohessy JG, Teruya-Feldstein J, Jain S, Wu H, Matesic L, Chen RH, Wei W, Pandolfi PP*. Reactivation of PTEN tumor suppressor for cancer treatment through inhibition of a MYC-WWP1 inhibitory pathway. Science 2019 May 17, 364(6441): eaau0159.
16. Li X, Liu CX, Xue W, Zhang Y, Jiang S, Yin QF, Wei J, Yao RW, Yang L, Chen LL*. Coordinated circRNA Biogenesis and Function with NF90/NF110 in Viral Infection. Molecular Cell 2017 Jul 20, 67(2): 214-277.
    (Featured Article; Highlighted by Editor’s Note and Meet the Authors)
17. Dong R, Zhang XO, Zhang Y, Ma XK, Chen LL*, Yang L*. CircRNA-derived pseudogenes. Cell Research 2016 Jun, 26(6):747-750.
18. Zhang XO#, Wang HB#, Zhang Y, Lu X, Chen LL* and Yang L*. Complementary sequence-mediated exon circularization. Cell 2014 Sep 25, 159(1): 134-147.
    (Featured Article; Research highlights by Nat Rev Genetics, 2014, 15:717; Research highlights by Bull Chin Acad Sci, 2014, 28: 282-284; F1000 Prime recommendataion)
19. Xiang JF, Yin QF, Chen T, Zhang Y, Zhang XO, Wang HB, Ge JH, Lu XH, Yang L and Chen LL*. Human colorectal cancer-specific CCAT1-L lncRNA regulates long-range chromatin interactions in the MYC locus. Cell Research 2014 May, 24(5): 513-531.
    (Cover Article and Issue Highlights)
20. Yin QF#, Yang L#, Zhang Y, Xiang JF, Wu YW, Carmichael GG* and Chen LL*. Long noncoding RNAs with snoRNA ends. Molecular Cell 2012 Oct 26;48(2): 219-230.
    (Cover Article; Preview by Mol Cell, 2012, 48:155-7; Research Highlights by Nat Rev Mol Cell Biol, 2012, 13:686, Best of Molecular Cell 2012)