The genomes of higher organisms are highly annotated by specific chromosomal proteins and histone modifications along active genes, regulatory elements, or silent regions. An ongoing challenge is to decipher the rules that establish and maintain chromatin organization. In the upcoming funding period, we propose to focus on analysis of the Polycomb group (PcG) proteins, based on their central importance in development and disease, the intriguing hypotheses raised by our current results, and our ability to use new approaches to probe chromatin protein interactions with precision. Our studies will focus on the versatile Drosophila model, but due to the high conservation of this key regulatory system we can move between fly and human systems with ease. Our experiments will address two central problems in chromatin biology: understanding the targeting and spreading of chromatin domains, and probing the ability of chromatin factors to mark genes as future regulators of cell type specificity.
In Aim 1, we will define the series of molecular interactions that coordinate canonical and variant PcG complexes.
In Aim 2, we will analyze how H3K27me3 is propagated in cis, to create heritable repressive domains.
In Aim 3, we will determine whether a bivalent state primes developmental genes in Drosophila. Success in our studies will be highly relevant to understanding normal and aberrant genome organization and function in development and disease.

Public Health Relevance

The packaging of the genome into active and silent domains plays a key role in the fidelity of gene expression in higher organisms. Our project will focus on studies of the Polycomb Group (PcG) proteins, which form regulatory complexes that play crucial roles in development and disease. Our studies are aimed at understanding how chromatin domains are created and maintained for the precise control of gene expression, using the fruitfly model system to explore novel insights into epigenetic regulation.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Molecular Genetics B Study Section (MGB)
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Carter, Anthony D
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Brigham and Women's Hospital
United States
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Shiota, Hitoshi; Elya, Janine E; Alekseyenko, Artyom A et al. (2018) ""Z4"" Complex Member Fusions in NUT Carcinoma: Implications for a Novel Oncogenic Mechanism. Mol Cancer Res 16:1826-1833
Kang, Hyuckjoon; Jung, Youngsook L; McElroy, Kyle A et al. (2017) Bivalent complexes of PRC1 with orthologs of BRD4 and MOZ/MORF target developmental genes in Drosophila. Genes Dev 31:1988-2002
Alekseyenko, Artyom A; Walsh, Erica M; Zee, Barry M et al. (2017) Ectopic protein interactions within BRD4-chromatin complexes drive oncogenic megadomain formation in NUT midline carcinoma. Proc Natl Acad Sci U S A 114:E4184-E4192
McElroy, Kyle A; Jung, Youngsook L; Zee, Barry M et al. (2017) upSET, the Drosophila homologue of SET3, Is Required for Viability and the Proper Balance of Active and Repressive Chromatin Marks. G3 (Bethesda) 7:625-635
Zee, Barry M; Alekseyenko, Artyom A; McElroy, Kyle A et al. (2016) Streamlined discovery of cross-linked chromatin complexes and associated histone modifications by mass spectrometry. Proc Natl Acad Sci U S A 113:1784-9
Zee, Barry M; Dibona, Amy B; Alekseyenko, Artyom A et al. (2016) The Oncoprotein BRD4-NUT Generates Aberrant Histone Modification Patterns. PLoS One 11:e0163820
Alekseyenko, Artyom A; Walsh, Erica M; Wang, Xin et al. (2015) The oncogenic BRD4-NUT chromatin regulator drives aberrant transcription within large topological domains. Genes Dev 29:1507-23
Kang, Hyuckjoon; McElroy, Kyle A; Jung, Youngsook Lucy et al. (2015) Sex comb on midleg (Scm) is a functional link between PcG-repressive complexes in Drosophila. Genes Dev 29:1136-50
Alekseyenko, Artyom A; McElroy, Kyle A; Kang, Hyuckjoon et al. (2015) BioTAP-XL: Cross-linking/Tandem Affinity Purification to Study DNA Targets, RNA, and Protein Components of Chromatin-Associated Complexes. Curr Protoc Mol Biol 109:21.30.1-32
Jung, Youngsook L; Kang, Hyuckjoon; Park, Peter J et al. (2015) Correspondence of Drosophila polycomb group proteins with broad H3K27me3 silent domains. Fly (Austin) 9:178-82

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