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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

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 (2015)
Epigenetic Priming of Enhancers Predicts Developmental Competence of hESC-Derived Endodermal Lineage Intermediates.
Cell Stem Cell;16(4):386-99
See PubMed abstract

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

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

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 (2013)
Epigenomic analysis of multilineage differentiation of human embryonic stem cells.
See PubMed abstract

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

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

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

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

Shanmugam N, Figarola JL, Li Y, Swiderski PM, Rahbar S, Natarajan R (2008)
Proinflammatory effects of advanced lipoxidation end products in monocytes.
See PubMed abstract

Jin F, Li Y, Ren B, Natarajan R (2007)
Enhancers: multi-dimensional signal integrators.
See PubMed abstract