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
Email: mkuroda@genetics.med.harvard.edu
Lab Members: 4 postdoctoral fellows, 1 graduate student
Visit my lab page here.



Analysis of chromatin organization and epigenetic gene regulation in health and disease

We study epigenetic regulators using genetics, genomics and proteomics. The factors we study include the MSL dosage compensation complex in fruit flies, the Polycomb Group in both flies and humans, and a translocation oncoprotein, BRD4-NUT, that drives an aggressive form of squamous cell cancer in humans. The common thread is that each is strongly implicated in the creation of active or silent chromatin domains that are integral to the fidelity of gene regulation. 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 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 interactions that may only occur on DNA. 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.

An example is our recent work with BRD4-NUT, a translocation-encoded fusion protein that plays a defining role in NUT midline carcinoma (NMC). In collaboration with Christopher French’s lab at BWH, we discovered that nuclear foci containing BRD4-NUT protein correspond to extremely broad, cell type-specific, hyperacetylated chromatin domains in patient tissue and cell lines. These are much larger than typical activated regions or ‘super-enhancers’, ranging from 100 kb to 2 Mb. These ‘megadomains’ appear to reflect a pathologic, feed-forward regulatory loop in which hyperacetylation drives further bromodomain-dependent binding and aberrant transcriptional activity. The novelty of megadomains is that they spread from select pre-existing enhancers, surprisingly
not enriched for recently described ‘super-enhancers’, to fill individual topologically associating domains (TADs). Although the selected TADs generally differ by cell type, the c-MYC and TP63 regions are targeted in all NMC patient cells examined to date. The ability to spread to fill whole regulatory compartments surrounding genes encoding proteins like MYC and p63 is likely to explain the extremely aggressive nature of NUT midline carcinoma.



Last Update: 8/7/2015



Publications

For a complete listing of publications click here.

 


 

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

Ferrari F, Plachetka A, Alekseyenko AA, Jung YL, Ozsolak F, Kharchenko PV, Park PJ, and Kuroda MI (2013). “Jumpstart and gain” model for dosage compensation in
Drosophila based on direct sequencing of nascent transcripts. Cell Reports 5: 629-636.

Alekseyenko AA, Gorchakov AA, Zee BM, Fuchs SM, Kharchenko PV, Kuroda MI (2014). Heterochromatin-associated interactions of
Drosophila HP1a with dADD1, HIPP1, and repetitive RNAs. Genes Dev. 28: 1445-1460.

Ho JWK, Jung YL, Liu T + ModEncode Consortium (2014). Comparative analysis of metazoan chromatin organization. Nature 512: 449-452.

Kang HJ, McElroy KA, Jung YL, Alekseyenko AA, Zee BM, Park PJ, Kuroda MI (2015). Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in
Drosophila. Genes Dev. 29: 1136-1150.

Alekseyenko AA, Walsh EM, Wang X, Grayson AR, Hsi PT, Kharchenko PV, Kuroda MI, French CA (2015). The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes Dev. 29: 1507-1523



© 2015 by the President and Fellows of Harvard College