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
Visit my lab page here.

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. Dosage compensation in
Drosophila is a striking example of chromatin-based gene regulation, in which gene expression is increased on the single X in males (XY) to be equivalent to the ouput of both X chromosomes in females (XX). A male-specific histone acetyltransferase, the MSL complex, binds the X chromosome over active gene bodies to increase their transcription. 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 both mammals and in Drosophila demonstrate that RNAs also play an intriguing, but still poorly understood role in the regulation of chromatin structure and gene expression. The molecular mechanism by which roX RNAs target dosage compensation to active genes in Drosophila is an important question raised by our studies.

We have recently expanded our studies to analyze additional epigenetic regulators, including Heterochromatin 1 (HP1) and the Polycomb Group (PcG) proteins in
Drosophila, as well as chromatin-associated oncoproteins in human cells. The common thread is that these 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: 6/20/2014


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.

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. 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.

Wang, CI, Alekseyenko, AA, Leroy, G, Elia, AE, Gorchakov, AA, Britton, LM, Elledge, SJ, Kharchenko, PV, Garcia, BA, and
Kuroda, MI. Chromatin proteins captured by ChIP-mass spectrometry are linked to dosage compensation in Drosophila. Nat Struct Mol Biol 2013; 20: 202-209.

Alekseyenko AA, Gorchakov AA, Kharchenko PV,
Kuroda MI. Reciprocal interactions of human C10orf12 and C17orf96 with PRC2 revealed by BioTAP-XL crosslinking and affinity purification. PNAS 2014; 111: 2488-2493.

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