Mitzi Kuroda headshot
Mitzi I. Kuroda, Ph.D.
Professor of Genetics

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.

Cell state-dependent chromatin targeting in NUT carcinoma.
Authors: Authors: Alekseyenko AA, Zee BM, Dhoondia Z, Kang H, Makofske JL, Kuroda MI.
Genetics
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Cell state-dependent chromatin targeting in NUT carcinoma.
Authors: Authors: Alekseyenko AA, Zee BM, Dhoondia Z, Kang H, Makofske JL, Kuroda MI.
bioRxiv
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Integrated loss- and gain-of-function screens define a core network governing human embryonic stem cell behavior.
Authors: Authors: Naxerova K, Di Stefano B, Makofske JL, Watson EV, de Kort MA, Martin TD, Dezfulian M, Ricken D, Wooten EC, Kuroda MI, Hochedlinger K, Elledge SJ.
Genes Dev
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Chemical screen identifies diverse and novel HDAC inhibitors as repressors of NUT function: implications for NUT carcinoma pathogenesis and treatment.
Authors: Authors: Shiota H, Alekseyenko AA, Wang ZA, Filic I, Knox TM, Luong NM, Huang Y, Scott DA, Jones KL, Gokhale PC, Lemieux ME, Cole PA, Kuroda MI, French CA.
Mol Cancer Res
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Dynamic Competition of Polycomb and Trithorax in Transcriptional Programming.
Authors: Authors: Kuroda MI, Kang H, De S, Kassis JA.
Annu Rev Biochem
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Combination Targeting of the Bromodomain and Acetyltransferase Active Site of p300/CBP.
Authors: Authors: Zucconi BE, Makofske JL, Meyers DJ, Hwang Y, Wu M, Kuroda MI, Cole PA.
Biochemistry
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Sex-specific phenotypes of histone H4 point mutants establish dosage compensation as the critical function of H4K16 acetylation in Drosophila.
Authors: Authors: Copur Ö, Gorchakov A, Finkl K, Kuroda MI, Müller J.
Proc Natl Acad Sci U S A
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"Z4" Complex Member Fusions in NUT Carcinoma: Implications for a Novel Oncogenic Mechanism.
Authors: Authors: Shiota H, Elya JE, Alekseyenko AA, Chou PM, Gorman SA, Barbash O, Becht K, Danga K, Kuroda MI, Nardi V, French CA.
Mol Cancer Res
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Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila.
Authors: Authors: Kang H, Jung YL, McElroy KA, Zee BM, Wallace HA, Woolnough JL, Park PJ, Kuroda MI.
Genes Dev
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Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma.
Authors: Authors: Alekseyenko AA, Walsh EM, Zee BM, Pakozdi T, Hsi P, Lemieux ME, Dal Cin P, Ince TA, Kharchenko PV, Kuroda MI, French CA.
Proc Natl Acad Sci U S A
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