Jeannie Lee, MD, PhD

Professor of Genetics (Pathology), Harvard Medical School
Molecular Biologist, Massachusetts General Hospital

Howard Hughes Medical Institute
Massachusetts General Hospital
Simches Research Building
185 Cambridge Street
Boston, MA 02114
Phone: 617-726-5943
Fax: 617-726-6893


Our laboratory uses X-chromosome inactivation (XCI) as a model to study the structure and function of long noncoding RNAs (lncRNA) in epigenetic regulation.  Nowhere in the mammalian genome are the abundance and roles of lncRNA more evident than at the X-inactivation center (Xic).  This region harbors transcripts that serve as both repressors and activators in the regulation of genes on the X-chromosome.  Interestingly, until 150 million years ago, the Xic genes were actually coding and functioned in pathways unrelated to XCI.  The replacement of the Xic with noncoding transcripts suggests that lncRNAs may be uniquely suited to some types of epigenetic processes.  Our research indicates that two such processes are allelic (cis-regulatory) and locus-specific targeting of chromatin factors (e.g., Polycomb complexes).  In addition to pursuing mechanisms of action at the Xic, we are extending analysis to lncRNA occurring on a genome-wide scale and developing novel molecular techniques to do so. Our long-term goal is to understand how lncRNAs interact with chromatin complexes to achieve locus-specific and temporally specific gene expression patterns.

Lab Members

Research fellows

Eric Aeby, Ph.D.

Rodrigo Aguilar, Ph.D.

Lieselot Carrette, Ph.D.

Hsueh-Ping (Catherine) Chu , Ph.D.

Catherine Cifuentes-Rojas, Ph.D.

Brian Del Rosario , Ph.D.

Teddy Jegu , Ph.D.

Yesu Jeon, Ph.D.

Hungoo Lee, Ph.D.

Hyun Jung Oh , Ph.D.

Michael Rosenberg, Ph.D.

Arneet Saltzman, Ph.D.

Hongjae Sunwoo, Ph.D.

Attila Szanto, M.D., Ph.D.

Chunyao Wei, Ph.D.


Roy Blum, Ph.D.

Barry Kesner, Ph.D.

Derek Lessing, Ph.D.


David Colognori

Tom Dial

John Froberg

Andrea Kriz

Nicholas Ramirez

Chen Yu Wang

Lin Yang

Montserrat Michelman, Laboratory Manager

William Press, Research Technician

Selected Publications

View all PubMed publications

Xist imprinting is promoted by the hemizygous (unpaired) state in the male germ line.

Sun S, Payer B, Namekawa S, An JY, Press W, Catalan-Dibene J, Sunwoo H, Lee JT. Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14415-22.

The Xist RNA-PRC2 complex at 20-nm resolution reveals a low Xist stoichiometry and suggests a hit-and-run mechanism in mouse cells. Sunwoo H, Wu JY, Lee JT. Proc Natl Acad Sci U S A. 2015 Aug 4;112(31):E4216-25.

Chromosomes. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Minajigi A, Froberg JE, Wei C, Sunwoo H, Kesner B, Colognori D, Lessing D, Payer B, Boukhali M, Haas W, Lee JT. Science. 2015 Jul 17;349(6245).

Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.

Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT.

Genetics. 2015 Jun;200(2):537-49.

Locus-specific targeting to the X chromosome revealed by the RNA interactome of CTCF.

Kung JT, Kesner B, An JY, Ahn JY, Cifuentes-Rojas C, Colognori D, Jeon Y, Szanto A, del Rosario BC, Pinter SF, Erwin JA, Lee JT. Mol Cell. 2015 Jan 22;57(2):361-75.


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