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Genetics Faculty

Yan Li
Assistant Professor
Department of Genetics
School of Medicine
Case Western Reserve University
Biomedical Research Building 622
2109 Adelbert Road
Cleveland, Ohio 44106-4955
Tel: (216) 368-0305
Fax: (216) 368-3432

About Yan Li

Dr. Yan Li received her Ph.D in epigenetics and diabetes research from Beckman Research Institute, City of Hope. In graduate school, Dr. Li was trained as a molecular biologist studying the epigenetic regulation of inflammatory response in atherosclerosis, a common complication in diabetes. After graduation, Dr. Li joined Dr. Bing Ren's lab in Ludwig Institute for Cancer Research, UCSD for postdoc training. During her postdoc, she continued her research interests in the transcription regulation of inflammation and diabetes genes, but mainly using genomic and epigenomic approaches. Dr. Li's previously works characterized the dynamics of transcription enhancers using several model systems including inflammation and embryonic stem cell (ESC) differentiation. Dr. Li joined the Department of Genetics and Genomics Sciences as an assistant professor in 2015.


One major focus of our lab is to study the functions of non-coding cis-regulatory elements (such as enhancers) in development and complex diseases, especially related to diabetic conditions. For example, amount thousands of disease associated SNPs identified from genome-wide association studies (GWAS), ~20% are related to complex diabetic conditions including high BMI, hypertension, hyperglycemia, high LDL, atherosclerosis etc. Several difficulties are preventing us from understanding these genetic variants. First, over 90% of those SNPs do not change protein sequences. One prevalent theory is that some of these common variants are affecting enhancers, leading to misregulation of important target genes, but this theory remains to be tested in detail. The other difficulty is that many different tissues or organs may contribute to complex metabolic traits, we need to test the function of a SNP in the right tissue or cell types. We will tackle these important questions using several cutting edge genetic and genomic technologies, such as CRISPR, ChIP-seq, RNA-seq and Hi-C. My lab is also interested in studying the 3D genome architecture. We are trying to use 3D genome data to explain the functions of non-coding genetic variants relevant to disease states.

Selected Publications

Single-Cell Heterogeneity Analysis and CRISPR Screen Identify Key β-Cell-Specific Disease Genes.
Fang Z, Weng C, Li H, Tao R, Mai W, Liu X, Lu L, Lai S, Duan Q, Alvarez C, Arvan P, Wynshaw-Boris A, Li Y, Pei Y, Jin F*, Li Y*
Cell Rep (2019);26(11):3132-3144.e7
See PubMed abstract

Chemical Screening Identifies Enhancers of Mutant Oligodendrocyte Survival and Unmasks a Distinct Pathological Phase in Pelizaeus-Merzbacher Disease.
Elitt MS, Shick HE, Madhavan M, Allan KC, Clayton BLL, Weng C, Miller TE, Factor DC, Barbar L, Nawash BS, Nevin ZS, Lager AM, Li Y, Jin F, Adams DJ, Tesar PJ
Stem Cell Reports (2018);11(3):711-726
See PubMed abstract

Easy Hi-C: A simple efficient protocol for 3D genome mapping in small cell populations.
Lu L, Liu X, Peng J, Li Y*, Jin F*
bioRxiv (2018);doi:

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling.
Mack SC, Pajtler KW, Chavez L, ..., Li Y, ..., Kool M, Taylor MD, Rich JN
Nature (2018);553(7686):101-105
See PubMed abstract

Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates.
Wang A*, Yue F*, Li Y*, Xie R, Harper T, Patel NA, Muth K, Palmer J, Qiu Y, Wang J, Lam DK, Raum JC, Stoffers DA, Ren B, Sander M
Cell Stem Cell (2015);16(4):386-99
See PubMed abstract

CRISPR reveals a distal super-enhancer required for Sox2 expression in mouse embryonic stem cells.
Li Y*, Rivera CM*, Ishii H*, Jin F, Selvaraj S, Lee AY, Dixon JR, Ren B
PLoS One (2014);9(12):e114485
See PubMed abstract

A high-resolution map of the three-dimensional chromatin interactome in human cells.
Jin F*, Li Y*, Dixon JR, Selvaraj S, Ye Z, Lee AY, Yen CA, Schmitt AD, Espinoza CA, Ren B
Nature (2013);503(7475):290-4
See PubMed abstract

Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B
Cell (2013);153(5):1134-48
See PubMed abstract

RFECS: a random-forest based algorithm for enhancer identification from chromatin state.
Rajagopal N, Xie W, Li Y, Wagner U, Wang W, Stamatoyannopoulos J, Ernst J, Kellis M, Ren B
PLoS Comput Biol (2013);9(3):e1002968
See PubMed abstract

Topological domains in mammalian genomes identified by analysis of chromatin interactions.
Dixon JR, Selvaraj S, Yue F, Kim A, Li Y, Shen Y, Hu M, Liu JS, Ren B
Nature (2012);485(7398):376-80
See PubMed abstract

Enhancers: multi-dimensional signal integrators.
Jin F, Li Y, Ren B, Natarajan R
Transcription (2011);2(5):226-30
See PubMed abstract

PU.1 and C/EBP(alpha) synergistically program distinct response to NF-kappaB activation through establishing monocyte specific enhancers.
Jin F*, Li Y*, Ren B, Natarajan R
Proc Natl Acad Sci U S A (2011);108(13):5290-5
See PubMed abstract

Role of the histone H3 lysine 4 methyltransferase, SET7/9, in the regulation of NF-kappaB-dependent inflammatory genes. Relevance to diabetes and inflammation.
Li Y, Reddy MA, Miao F, Shanmugam N, Yee JK, Hawkins D, Ren B, Natarajan R
J Biol Chem (2008);283(39):26771-81
See PubMed abstract

Proinflammatory effects of advanced lipoxidation end products in monocytes.
Shanmugam N, Figarola JL, Li Y, Swiderski PM, Rahbar S, Natarajan R
Diabetes (2008);57(4):879-88
See PubMed abstract