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Genetics Faculty


Fulai Jin
Assistant Professor
Department of Genetics
School of Medicine
Case Western Reserve University
Biomedical Research Building 621
2109 Adelbert Road
Cleveland, Ohio 44106-4955
Tel: (216) 368-1811
Fax: (216) 368-3432
E-mail: fulai.jin@case.edu


About Fulai Jin

Dr. Fulai Jin has an interdisciplinary background. He got a B.S. degree of biology and a B.E. degree of computer sciences from University of Science and Technology of China (USTC). He then obtained a PhD degree in Molecular and Medical Pharmacology from University of California, Los Angeles (UCLA). In graduate school, Dr. Jin worked in the field of chemical biology performing screens for small molecules or drug target genes using various functional genomic approaches. He developed a smart-pooling method to improve the efficiency of such screening experiments. In the meantime, Dr. Jin also obtained formal training in biostatistics. After graduation, Dr. Jin did his postdoc training at Ludwig Institute for Cancer Research and switched to the field of genomics, epigenetics and transcription regulation. During his postdoc, Dr. Jin used Hi-C to generate the first high-resolution genome-wide map of DNA looping interactions in mammalian cell, which can reveal contacts between any two 5-10kb DNA segments. Such information of 3D genome architecture is critical for our understanding of gene regulation in human diseases. Dr. Jin joined the Genetics Department in 2015 as an assistant professor.


Research

Organization of mammalian genome is very complex. Recent advances of sequencing technologies have already allowed us to characterize genome and epigenome in one-dimensional space. For example, using antibodies against histone marks or protein factors, we can use ChIP-seq to map euchromatin, heterochromatin, as well as many types of cis-regulatory elements including promoters, enhancers, and insulators (see Figure). In the 3D space, mammalian genome is also folded and packed in a highly organized fashion. Besides the well know chromatin relaxation and compaction associated with "open" and "closed" chromatin, DNA also form long-range loops which allow contacts between various cis-regulatory elements. Understanding genome organization is very important for genetics study. For example, mutations at enhancers may alter the expression levels of target genes from hundreds of kilobases away, leading to human diseases.

The Jin lab is interested in the genome-wide study of 3D genome architecture. The lab has both "wet" components and "dry" components. Research projects focus on several key challenges in this emerging field. (1) Developing experimental and computational tools for genome-wide identification of DNA looping interactions at high-resolution. (2) Understanding the genetic and epigenetic mechanisms that may governs genome architecture. (3) Understanding the impacts of genome architecture on cellular functions and human diseases.

Single cell genomics is another major focus of my lab. We are using single cell RNA-seq and epigenomic tools to study the transcriptional regulation at single cell level in the context of human diseases, including diabetes, cancer, and neuronal diseases.



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 Reports (2019);(In Press)

Integrative functional genomic analysis of human brain development and neuropsychiatric risks.
Li M, Santpere G, Imamura Kawasawa Y, ..., Jin F, ..., Sullivan PF, Gerstein MB, Lein ES, Knowles JA, Sestan N
Science (2018);362(6420):
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

Genome-wide association analyses identify 44 risk variants and refine the genetic architecture of major depression.
Wray NR, Ripke S, Mattheisen M, ..., Jin F, ..., Breen G, Børglum AD, Sullivan PF
Nat Genet (2018);50(5):668-681
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: https://doi.org/10.1

HiView: an integrative genome browser to leverage Hi-C results for the interpretation of GWAS variants.
Xu Z, Zhang G, Duan Q, Chai S, Zhang B, Wu C, Jin F, Yue F, Li Y, Hu M
BMC Res Notes (2016);9(1):159
See PubMed abstract

A hidden Markov random field-based Bayesian method for the detection of long-range chromosomal interactions in Hi-C data.
Xu Z, Zhang G, Jin F, Chen M, Furey TS, Sullivan PF, Qin Z, Hu M, Li Y
Bioinformatics (2015);:
See PubMed abstract

5mC oxidation by Tet2 modulates enhancer activity and timing of transcriptome reprogramming during differentiation.
Hon GC, Song CX, Du T, Jin F, Selvaraj S, Lee AY, Yen CA, Ye Z, Mao SQ, Wang BA, Kuan S, Edsall LE, Zhao BS, Xu GL, He C, Ren B
Mol Cell (2014);56(2):286-97
See PubMed abstract

Lysine 2-hydroxyisobutyrylation is a widely distributed active histone mark.
Dai L, Peng C, Montellier E, Lu Z, Chen Y, Ishii H, Debernardi A, Buchou T, Rousseaux S, Jin F, Sabari BR, Deng Z, Allis CD, Ren B, Khochbin S, Zhao Y
Nat Chem Biol (2014);10(5):365-70
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

Combined gene expression and DNA occupancy profiling identifies potential therapeutic targets of t(8;21) AML.
Lo MC, Peterson LF, Yan M, Cong X, Jin F, Shia WJ, Matsuura S, Ahn EY, Komeno Y, Ly M, Ommen HB, Chen IM, Hokland P, Willman CL, Ren B, Zhang DE
Blood (2012);120(7):1473-84
See PubMed abstract

CBX3 regulates efficient RNA processing genome-wide.
Smallwood A, Hon GC, Jin F, Henry RE, Espinosa JM, Ren B
Genome Res (2012);22(8):1426-36
See PubMed abstract

Identification of 67 histone marks and histone lysine crotonylation as a new type of histone modification.
Tan M, Luo H, Lee S, Jin F, Yang JS, Montellier E, Buchou T, Cheng Z, Rousseaux S, Rajagopal N, Lu Z, Ye Z, Zhu Q, Wysocka J, Ye Y, Khochbin S, Ren B, Zhao Y
Cell (2011);146(6):1016-28
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

A yeast two-hybrid smart-pool-array system for protein-interaction mapping.
Jin F, Avramova L, Huang J, Hazbun T
Nat Methods (2007);4(5):405-7
See PubMed abstract

A pooling-deconvolution strategy for biological network elucidation.
Jin F, Hazbun T, Michaud GA, Salcius M, Predki PF, Fields S, Huang J
Nat Methods (2006);3(3):183-9
See PubMed abstract

Insights into TOR function and rapamycin response: chemical genomic profiling by using a high-density cell array method.
Xie MW, Jin F, Hwang H, Hwang S, Anand V, Duncan MC, Huang J
Proc Natl Acad Sci U S A (2005);102(20):7215-20
See PubMed abstract

Finding new components of the target of rapamycin (TOR) signaling network through chemical genetics and proteome chips.
Huang J, Zhu H, Haggarty SJ, Spring DR, Hwang H, Jin F, Snyder M, Schreiber SL
Proc Natl Acad Sci U S A (2004);101(47):16594-9
See PubMed abstract