BBS Faculty Member - Mitzi Kuroda

Mitzi Kuroda

Department of Genetics

Harvard Medical School
New Research Building, Room 168E
77 Avenue Louis Pasteur
Boston, MA 02115
Tel: 617-525-4520
Fax: 617-525-4522
Lab Members: 4 postdoctoral fellows, 1 graduate student

Analysis of chromatin organization, non-coding RNAs, and epigenetic gene regulation

The organization of the genome into active and silent domains is integral to the fidelity of gene regulation in higher organisms. We study chromatin regulators in
Drosophila to discover general principles regarding genome organization, applicable to all higher organisms. A striking model is dosage compensation, in which X-linked gene expression is made equivalent in males (XY) and females (XX). In mammals, this occurs by X-inactivation in females. In contrast, in the fruitfly, dosage compensation increases transcription of X-linked genes in males. In each case, specific molecules bind the X chromosome to remodel its chromatin structure. While gene regulation is generally thought to occur through the function of regulatory proteins, the discoveries of non-coding RNAs that are required for dosage compensation and associate along the length of compensated X chromosomes in mammals and in Drosophila demonstrate that RNAs play an intriguing, but still poorly understood role in the regulation of chromatin structure and gene expression.

We have recently expanded our studies to analyze two key additional epigenetic regulators: Heterochromatin 1 (HP1) and the Polycomb Group (PcG). These conserved proteins are strongly implicated in genome organization, differentiation, and disease in higher organisms. One serious obstacle to understanding the interactions of such factors with additional proteins and RNAs on chromatin has been the trade-off between removal from the DNA, to allow purification, and the resultant loss of weak or transient interactions with key partners in function. Therefore, we have adapted a crosslinking approach that allows us to affinity-purify fragmented chromatin with protein and RNAs attached, to avoid disruption of weak interactions. After reversal of crosslinks, the DNA, protein, histone peptides, and RNA fractions can be separately analyzed using comprehensive sequencing and mass spectrometry. Our current results are providing us with a rich and comprehensive view of key epigenetic complexes bound to their chromatin templates. The ultimate goal of our work is to understand the precise molecular events that lead to proper chromatin organization and epigenetic gene regulation in higher organisms.

Last Update: 8/22/2013


For a complete listing of publications click here.



Alekseyenko AA, Peng S, Larschan E, Gorchakov AA, Lee O-K, Kharchenko P, McGrath SD, Wang CI, Mardis ER, Park PJ, Kuroda MI. A sequence motif within chromatin entry sites directs MSL establishment on the Drosophila X chromosome. Cell 2008; 134:599-609.

Gorchakov AA, Alekseyenko AA, Kharchenko P, Park PJ,
Kuroda MI. Long range spreading of dosage compensation in Drosophila captures transcribed autosomal genes inserted on X. Genes & Development 2009: 23: 2266-2271.

Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TP, Sandstrom R, Thurman RE, Macalpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC,
Kuroda MI, Pirrotta V, Karpen GH, Park PJ (2011) Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 2011; 471: 480-485.

Larschan E, Bishop EP, Kharchenko PV, Core LJ, Lis JT, Park PJ,
Kuroda MI. X chromosome dosage compensation via enhanced transcriptional elongation in Drosophila. Nature 2011; 471: 115-118.

© 2013 by the President and Fellows of Harvard College