Yin Shen, PhD

Associate Professor
Department of Neurology
Institute for Human Genetics
Research Overview: 

We are a functional genomics lab interested in investigating fundamental mechanisms of transcriptional control underlying cellular function. We utilize human pluripotent stem cells to model development and diseases as well as innovative genomic and genetic tools to investigate how regulatory elements affect gene expression. Specifically, we focus on elucidating the causal relationship between genetic and epigenetic variations in regulatory sequences (e.g., enhancers) in the context of development and diseases, and how these factors interplay to control gene regulation in mammalian cells.

  1. Functional genomics (the ENCODE project): high-throughput CRISPR/Cas9 screening of functional regulatory elements.
    We are using high-throughput CRISPR/Cas9-mediated genetic screening to interrogate the biological significance of a large number of non-coding regulatory sequences in the mammalian genome in both embryonic stem cells and iPSC-derived neural cell types.
  2. Charting the regulatory landscape of human brain development and function.
    We are utilizing integrative, unbiased, and high-throughput genomic and genetic tools (ATAC-seq, RNA-seq, ChIP-seq, 4C-seq, Hi-C, and CRISPR) to identify and functionally characterize cis-regulatory elements in human brain cells.
  3. Investigating the functions of non-coding genetic variation associated with neurological diseases.
    Putative regulatory regions harbor a disproportionately large number of sequence variants associated with human traits and diseases, leading to the notion that genetic lesions in the cis-regulatory elements contribute substantially to common human diseases. We are using functional genomics tools to investigate how non-coding variants associated with complex neurological disorders (e.g., autism spectrum disorders (ASD), Alzheimer diseases (AD), and Parkinson disease (PD)) contribute to disease.
Primary Thematic Area: 
Human Genetics
Secondary Thematic Area: 
Developmental & Stem Cell Biology
Research Summary: 
Functional genomics, gene regulation, 3D chromatin architecture, and human diseases
Mentorship Development: 

5/26/20    Effective Strategies for IDPs for Partial Resumption of Lab Research    
9/11/20    Mentoring Across Differences
5/25/21  Sharpening your Mentoring Skills (SyMS) 

Websites

Publications: 

Genetically encoded chemical crosslinking of RNA in vivo.

Nature chemistry

Sun W, Wang N, Liu H, Yu B, Jin L, Ren X, Shen Y, Wang L

Coordinated transcriptional and catabolic programs support iron dependent adaptation to RAS-MAPK pathway inhibition in pancreatic cancer.

Cancer discovery

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, Perera RM

Transcriptional network orchestrating regional patterning of cortical progenitors.

Proceedings of the National Academy of Sciences of the United States of America

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, Nord AS, Rubenstein JL

An atlas of gene regulatory elements in adult mouse cerebrum.

Nature

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, Shen Y, Nunn M, Mukamel EA, Behrens MM, Ecker JR, Ren B

Parallel characterization of cis-regulatory elements for multiple genes using CRISPRpath.

Science advances

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