Yin Shen, PhD
Professor
Neurology
School of Medicine

Awards

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• Weill Neurohub Investigator, 2021
• UCSF Weill Institute for Neurosciences Innovation Award, 2016-2019
• AFAR new investigator award in Alzheimer's disease, 2016-2018

Education & Training

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• Postdoc Genomics and gene regulation Ludwig Institute for Cancer Research/UCSD
• Ph.D. Human Genetics UCLA
• 2021 Diversity, Equity, and Inclusion Champion Training UCSF

Interests

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• 3D epigenome
• Neuropsychiatric Diseases
• Gene Regulation
• Genome editing
• Functional Genomics

Websites

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• Shen lab website (shenlab.ucsf.edu)

Grants and Projects

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• Study of Selective Cell and System Vulnerability in Alzheimer's Disease, NIH/NIA, 2023-2028
• Single Cell Characterization of FTLD-GRN, NIH/NINDS, 2022-2025
• Elucidate the roles of Alzheimer's disease risk genes and variants in gene expression and AD-related phenotypes, NIH/NIA, 2022-2025
• Charting the 3D epigenome in human brain development and diseases, NIH, 2020-2025
• Dissecting functional roles of MeCP2 condensates in neurons with chemogenetic tools, NIH/NIDA, 2022-2024
• Transcriptional regulation of BEST1 in retina pigment epithelium., NIH, 2017-2022
• Functional characterization of Alzheimer's disease associated genetic variants, NIH, 2017-2022
• High throughput CRISPR-mediated functional validation of regulatory elements, NIH, 2017-2022
• Development of massively parallel reporter assays that use cognate promoters, NIH/NHGRI, 2018-2020

Publications (45)

Top publication keywords:
Gene EditingEmbryonic Stem CellsOrganogenesisCRISPR-Cas SystemsMolecular Sequence AnnotationGenomeGenetic MarkersEnhancer Elements, GeneticChromatinEpigenomicsPromoter Regions, GeneticRegulatory Sequences, Nucleic AcidGenome, HumanCellsGene Expression Regulation

• High-throughput PRIME-editing screens identify functional DNA variants in the human genome.
  Molecular cell 2023 Ren X, Yang H, Nierenberg JL, Sun Y, Chen J, Beaman C, Pham T, Nobuhara M, Takagi MA, Narayan V, Li Y, Ziv E, Shen Y
• Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath.
  Science advances 2021 Ren X, Wang M, Li B, Jamieson K, Zheng L, Jones IR, Li B, Takagi MA, Lee J, Maliskova L, Tam TW, Yu M, Hu R, Lee L, Abnousi A, Li G, Li Y, Hu M, Ren B, Wang W, Shen Y
• CRISPR tiling deletion screens reveal functional enhancers of neuropsychiatric risk genes and allelic compensation effects (ACE) on transcription.
  bioRxiv : the preprint server for biology 2024 Ren X, Zheng L, Maliskova L, Tam TW, Sun Y, Liu H, Lee J, Takagi MA, Li B, Ren B, Wang W, Shen Y
• Author Correction: MYC phase separation selectively modulates the transcriptome.
  Nature structural & molecular biology 2024 Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X
• MYC phase separation selectively modulates the transcriptome.
  Nature structural & molecular biology 2024 Yang J, Chung CI, Koach J, Liu H, Navalkar A, He H, Ma Z, Zhao Q, Yang X, He L, Mittag T, Shen Y, Weiss WA, Shu X

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• The PRC2.1 Subcomplex Opposes G1 Progression through Regulation of CCND1 and CCND2.
  bioRxiv : the preprint server for biology 2024 Longhurst AD, Wang K, Suresh HG, Ketavarapu M, Ward HN, Jones IR, Narayan V, Hundley FV, Hassan AZ, Boone C, Myers CL, Shen Y, Ramani V, Andrews BJ, Toczyski DP
• Phase separation of YAP-MAML2 differentially regulates the transcriptome.
  Proceedings of the National Academy of Sciences of the United States of America 2024 Chung CI, Yang J, Yang X, Liu H, Ma Z, Szulzewsky F, Holland EC, Shen Y, Shu X
• Functional characterization of Alzheimer's disease genetic variants in microglia.
  Nature genetics 2023 Yang X, Wen J, Yang H, Jones IR, Zhu X, Liu W, Li B, Clelland CD, Luo W, Wong MY, Ren X, Cui X, Song M, Liu H, Chen C, Eng N, Ravichandran M, Sun Y, Lee D, Van Buren E, Jiang MZ, Chan CSY, Ye CJ, …
• Efficient bi-allelic tagging in human induced pluripotent stem cells using CRISPR.
  STAR protocols 2023 Ren X, Takagi MA, Shen Y
• High-throughput CRISPRi and CRISPRa technologies in 3D genome regulation for neuropsychiatric diseases.
  Human molecular genetics 2022 Jones IR, Ren X, Shen Y
• Genetically encoded chemical crosslinking of RNA in vivo.
  Nature chemistry 2022 Sun W, Wang N, Liu H, Yu B, Jin L, Ren X, Shen Y, Wang L
• Dual genome-wide coding and lncRNA screens in neural induction of induced pluripotent stem cells.
  Cell genomics 2022 Wu D, Poddar A, Ninou E, Hwang E, Cole MA, Liu SJ, Horlbeck MA, Chen J, Replogle JM, Carosso GA, Eng NWL, Chang J, Shen Y, Weissman JS, Lim DA
• Coordinated Transcriptional and Catabolic Programs Support Iron-Dependent Adaptation to RAS-MAPK Pathway Inhibition in Pancreatic Cancer.
  Cancer discovery 2022 Ravichandran M, Hu J, Cai C, Ward NP, Venida A, Foakes C, Kuljanin M, Yang A, Hennessey CJ, Yang Y, Desousa BR, Rademaker G, Staes AAL, Cakir Z, Jain IH, Aguirre AJ, Mancias JD, Shen Y, DeNicola GM, …
• Transcriptional network orchestrating regional patterning of cortical progenitors.
  Proceedings of the National Academy of Sciences of the United States of America 2021 Ypsilanti AR, Pattabiraman K, Catta-Preta R, Golonzhka O, Lindtner S, Tang K, Jones IR, Abnousi A, Juric I, Hu M, Shen Y, Dickel DE, Visel A, Pennachio LA, Hawrylycz M, Thompson CL, Zeng H, Barozzi I,…
• An atlas of gene regulatory elements in adult mouse cerebrum.
  Nature 2021 Li YE, Preissl S, Hou X, Zhang Z, Zhang K, Qiu Y, Poirion OB, Li B, Chiou J, Liu H, Pinto-Duarte A, Kubo N, Yang X, Fang R, Wang X, Han JY, Lucero J, Yan Y, Miller M, Kuan S, Gorkin D, Gaulton KJ, …
• Deletion of CTCF sites in the SHH locus alters enhancer-promoter interactions and leads to acheiropodia.
  Nature communications 2021 Ushiki A, Zhang Y, Xiong C, Zhao J, Georgakopoulos-Soares I, Kane L, Jamieson K, Bamshad MJ, Nickerson DA, University of Washington Center for Mendelian Genomics, Shen Y, Lettice LA, Silveira-Lucas EL…
• The C. elegans homolog of human panic-disorder risk gene TMEM132D orchestrates neuronal morphogenesis through the WAVE-regulatory complex.
  Molecular brain 2021 Wang X, Jiang W, Luo S, Yang X, Wang C, Wang B, Dang Y, Shen Y, Ma DK
• Cell-type-specific 3D epigenomes in the developing human cortex.
  Nature 2020 Song M, Pebworth MP, Yang X, Abnousi A, Fan C, Wen J, Rosen JD, Choudhary MNK, Cui X, Jones IR, Bergenholtz S, Eze UC, Juric I, Li B, Maliskova L, Lee J, Liu W, Pollen AA, Li Y, Wang T, Hu M, …
• An atlas of dynamic chromatin landscapes in mouse fetal development.
  Nature 2020 Gorkin DU, Barozzi I, Zhao Y, Zhang Y, Huang H, Lee AY, Li B, Chiou J, Wildberg A, Ding B, Zhang B, Wang M, Strattan JS, Davidson JM, Qiu Y, Afzal V, Akiyama JA, Plajzer-Frick I, Novak CS, Kato M, …
• Expanded encyclopaedias of DNA elements in the human and mouse genomes.
  Nature 2020 ENCODE Project Consortium, Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz …
• SMART-Q:  An Integrative Pipeline Quantifying Cell Type-Specific RNA Transcription.
  PloS one 2020 Yang X, Bergenholtz S, Maliskova L, Pebworth MP, Kriegstein AR, Li Y, Shen Y
• SAME-clustering: Single-cell Aggregated Clustering via Mixture Model Ensemble.
  Nucleic acids research 2020 Huh R, Yang Y, Jiang Y, Shen Y, Li Y
• Mapping cis-regulatory chromatin contacts in neural cells links neuropsychiatric disorder risk variants to target genes.
  Nature genetics 2019 Song M, Yang X, Ren X, Maliskova L, Li B, Jones IR, Wang C, Jacob F, Wu K, Traglia M, Tam TW, Jamieson K, Lu SY, Ming GL, Li Y, Yao J, Weiss LA, Dixon JR, Judge LM, Conklin BR, Song H, Gan L, Shen Y
• Live-cell imaging reveals enhancer-dependent Sox2 transcription in the absence of enhancer proximity.
  eLife 2019 Alexander JM, Guan J, Li B, Maliskova L, Song M, Shen Y, Huang B, Lomvardas S, Weiner OD
• Proximal recolonization by self-renewing microglia re-establishes microglial homeostasis in the adult mouse brain.
  PLoS biology 2019 Zhan L, Krabbe G, Du F, Jones I, Reichert MC, Telpoukhovskaia M, Kodama L, Wang C, Cho SH, Sayed F, Li Y, Le D, Zhou Y, Shen Y, West B, Gan L
• Gene regulation in the 3D genome.
  Human molecular genetics 2018 Li Y, Hu M, Shen Y
• SOX2 regulates acinar cell development in the salivary gland.
  eLife 2017 Emmerson E, May AJ, Nathan S, Cruz-Pacheco N, Lizama CO, Maliskova L, Zovein AC, Shen Y, Muench MO, Knox SM
• A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells.
  Nature methods 2017 Diao Y, Fang R, Li B, Meng Z, Yu J, Qiu Y, Lin KC, Huang H, Liu T, Marina RJ, Jung I, Shen Y, Guan KL, Ren B
• Improved regulatory element prediction based on tissue-specific local epigenomic signatures.
  Proceedings of the National Academy of Sciences of the United States of America 2017 He Y, Gorkin DU, Dickel DE, Nery JR, Castanon RG, Lee AY, Shen Y, Visel A, Pennacchio LA, Ren B, Ecker JR
• A new class of temporarily phenotypic enhancers identified by CRISPR/Cas9-mediated genetic screening.
  Genome research 2016 Diao Y, Li B, Meng Z, Jung I, Lee AY, Dixon J, Maliskova L, Guan KL, Shen Y, Ren B
• Chromatin architecture reorganization during stem cell differentiation.
  Nature 2015 Dixon JR, Jung I, Selvaraj S, Shen Y, Antosiewicz-Bourget JE, Lee AY, Ye Z, Kim A, Rajagopal N, Xie W, Diao Y, Liang J, Zhao H, Lobanenkov VV, Ecker JR, Thomson JA, Ren B
• A comparative encyclopedia of DNA elements in the mouse genome.
  Nature 2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, Rynes E, Kirilusha A, Marinov GK, Williams BA, Trout D,…
• A panel of CpG methylation sites distinguishes human embryonic stem cells and induced pluripotent stem cells.
  Stem cell reports 2013 Huang K, Shen Y, Xue Z, Bibikova M, April C, Liu Z, Cheng L, Nagy A, Pellegrini M, Fan JB, Fan G
• Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues.
  Nature genetics 2013 Hon GC, Rajagopal N, Shen Y, McCleary DF, Yue F, Dang MD, Ren B
• An encyclopedia of mouse DNA elements (Mouse ENCODE).
  Genome biology 2012 Mouse ENCODE Consortium, Stamatoyannopoulos JA, Snyder M, Hardison R, Ren B, Gingeras T, Gilbert DM, Groudine M, Bender M, Kaul R, Canfield T, Giste E, Johnson A, Zhang M, Balasundaram G, Byron R, …
• A map of the cis-regulatory sequences in the mouse genome.
  Nature 2012 Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, Kuan S, Wagner U, Dixon J, Lee L, Lobanenkov VV, Ren B
• Base-resolution analysis of 5-hydroxymethylcytosine in the mammalian genome.
  Cell 2012 Yu M, Hon GC, Szulwach KE, Song CX, Zhang L, Kim A, Li X, Dai Q, Shen Y, Park B, Min JH, Jin P, Ren B, He C
• Topological domains in mammalian genomes identified by analysis of chromatin interactions.
  Nature 2012 Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B
• Polycomb-like 3 promotes polycomb repressive complex 2 binding to CpG islands and embryonic stem cell self-renewal.
  PLoS genetics 2012 Hunkapiller J, Shen Y, Diaz A, Cagney G, McCleary D, Ramalho-Santos M, Krogan N, Ren B, Song JS, Reiter JF
• Functional modules distinguish human induced pluripotent stem cells from embryonic stem cells.
  Stem cells and development 2011 Wang A, Huang K, Shen Y, Xue Z, Cai C, Horvath S, Fan G
• Genome-wide DNA methylation profiling: the mDIP-chip technology.
  Methods in molecular biology (Clifton, N.J.) 2009 Shen Y, Fouse SD, Fan G
• X-inactivation in female human embryonic stem cells is in a nonrandom pattern and prone to epigenetic alterations.
  Proceedings of the National Academy of Sciences of the United States of America 2008 Shen Y, Matsuno Y, Fouse SD, Rao N, Root S, Xu R, Pellegrini M, Riggs AD, Fan G
• Promoter CpG methylation contributes to ES cell gene regulation in parallel with Oct4/Nanog, PcG complex, and histone H3 K4/K27 trimethylation.
  Cell stem cell 2008 Fouse SD, Shen Y, Pellegrini M, Cole S, Meissner A, Van Neste L, Jaenisch R, Fan G
• Abnormal CpG island methylation occurs during in vitro differentiation of human embryonic stem cells.
  Human molecular genetics 2006 Shen Y, Chow J, Wang Z, Fan G
• DNA methylation controls the timing of astrogliogenesis through regulation of JAK-STAT signaling.
  Development (Cambridge, England) 2005 Fan G, Martinowich K, Chin MH, He F, Fouse SD, Hutnick L, Hattori D, Ge W, Shen Y, Wu H, ten Hoeve J, Shuai K, Sun YE