Yinqing Li
Email: yinqingl@tsinghua.edu.cn
Research Interests:
Cells encode their long-term “self” in chromatin marks that are, paradoxically, erased and rewritten reversibly. Our central question is therefore not “what marks exist?” but “how do reversible reactions maintain a stable equilibrium and what pushes the system over the ridge into disease?”
To dissect these processes, we combine wet-lab innovation with computational modelling, and we focus on two complementary systems: (1) Neuronal transcription and epigenetic homeostasis: How do neurons maintain activity-dependent gene programs for years? What breaks first in Alzheimer’s disease or addiction? (2) T-cell fate decisions: How does a T cell decide a balance between proliferating, killing, or exhaustion? Can we return the set-point to boost cancer therapy or curb autoimmunity?
We develop technologies to tackle these questions, including: single-cell temporal and spatial multi-omics, genome and epigenomic editing, and integrated computational analyses.
Selected publications (#first author, *corresponding author):
Zhu M#, Yuan J#, Meng Q#, Yu J#, Xu X#, Xu M, Ren X, Hu Y, Wei G, Jia Z, Yuan G, Zang L, Liu S, Yang Y, Zheng Y, Wang J, Cong T, Xie W, Lan X, Cong L, Ma T, Ding S, Guo W, Zhang X*, Li Y*. Minimizing far-extending chromatin perturbation in genome editing preserves stem cell identity. CELL STEM CELL. 2026 Feb 24:S1934-5909(26)00038-X. doi: 10.1016/j.stem.2026.01.015. Epub ahead of print. PMID: 41742419.
Jia Z, Yu J, Li Y. Protocol to perform assay for chromatin-bound condensates by exploratory sequencing in mouse embryonic stem cells. STAR PROTOCOLS. 2025 Sep 19;6(3):104067. doi: 10.1016/j.xpro.2025.104067. Epub 2025 Sep 10. PMID: 40934074; PMCID: PMC12491159.
Huang M#, Fu J#, Wang P#, Chen B#, Yuan Q#, Yu J, Wang H, Liu Y, Li Z, Wu Y, Ying T, Wu Q, Zhu M*, Qin W*, Li Y*. Nearly complete redirection of insertion-type indel into recombination enhances knock-in and facilitates endogenous biomolecular condensate analysis. CELL RESEARCH. 2025 Oct 29. doi: 10.1038/s41422-025-01190-9. Epub ahead of print. PMID: 41152564.
Xu J#, Jia Z#, Zhao X#, Wang L, Jin G, Li Z, Yin N, Li Y*, Peng M*. BCOR and ZC3H12A suppress a core stemness program in exhausted CD8+ T cells. JOURNAL OF EXPERIMENTAL MEDICINE. 2025 Aug 4;222(8):e20241133.
Zhu M#, Xu R#, Yuan J#, Wang J#, Ren X, Cong T, You Y, Ju A, Xu L, Wang H, Zheng P, Tao H, Lin C, Yu H, Du J, Lin X, Xie W, Li Y*, Lan X*. Tracking-seq reveals the heterogeneity of off-target effects in CRISPR-Cas9-mediated genome editing. NATURE BIOTECHNOLOGY. 2025 May;43(5):799-810.
He J#, Huo X#, Pei G#, Jia Z#, Yan Y, Yu J, Qu H, Xie Y, Yuan J, Zheng Y, Hu Y, Shi M, You K, Li T, Ma T, Zhang MQ, Ding S, Li P*, Li Y*. Dual-role transcription factors stabilize intermediate expression levels. CELL. 2024 May 23;187(11):2746-2766.e25.
Li Y#, Lopez-Huerta VG#, Adiconis X#, Levandowski K, Choi S, Simmons SK, Arias-Garcia MA, Guo B, Yao AY, Blosser TR, Wimmer RD, Aida T, Atamian A, Naik T, Sun X, Bi D, Malhotra D, Hession CC, Shema R, Gomes M, Li T, Hwang E, Krol A, Kowalczyk M, Peça J, Pan G, Halassa MM, Levin JZ, Fu Z, Feng G. Distinct subnetworks of the thalamic reticular nucleus. NATURE. 2020, 583(7818):819-824.
Habib N#, Li Y#, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta JJ, Hession C, Zhang F, Regev A. Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. SCIENCE. 2016, 353(6302):925-8.
