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
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 Polycomb and Trithorax Groups in both flies and humans, and chromatin-associated fusion oncoproteins such as BRD4-NUT and MOZ-TIF2 in human cancers. 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.

One example is our recent work with the highly conserved Polycomb group (PcG) regulators in Drosophila. Our proteomic analyses have led my lab to propose a model in which the Polycomb Repressive Complex 1 (PRC1) and classical co-activators form ‘bivalent’ protein complexes on transcriptionally poised developmental genes. We speculate that these function as ‘master switches’ that are responsive to the amount of local acetylation or deacetylation activities recruited by cell type-specific DNA binding factors, leading to stable but reversible activation or repression, respectively. Our model is based on chromatin crosslinking, affinity purification, and mass spectrometry experiments, in which Drosophila PRC1 strongly interacts with classical co-activators, dBRD4 and dMOZ. We are currently exploring potential parallels in mammalian development.



Last Update: 4/12/2019



Publications

For a complete listing of publications click here.

 


 

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.

Zee BM, Alekseyenko AA, McElroy KA, Kuroda MI (2016). Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry. PNAS 113:1784-1789.

Alekseyenko AA, Walsh EM, Zee BM, Pakozdi T, His P, Lemieux ME, Dal Cin P, Ince TA, Kharchenko PV, Kuroda MI, French CA (2017). Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma. PNAS 114: E4184-4192.

Kang H, Jung YL, McElroy KA, Zee BM, Wallace HA, Woolnough JL, Park PJ, Kuroda MI (2017). Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila. Genes Dev. 31:1988-2002.

Shiota H, Elya JE, Alekseyenko AA, Chou PM, Gorman SA, Barbash O, Becht K, Danga K, Kuroda MI, Nardi V, French CA. (2018)
"Z4" Complex Member Fusions in NUT Carcinoma: Implications for a Novel Oncogenic Mechanism. Mol Cancer Res. Dec;16(12):1826-1833.



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