Transcription factors (TFs) are DNA binding proteins that link information encoded in the genome to regulation of transcription and chromatin, which is the complex of proteins and DNA that constitutes the epigenome. The mechanisms by which TFs regulate chromatin structure are not well characterized. The Max network, which includes the Myc oncoproteins, is composed of TFs that function through heterodimerization with the TF Max. This network is important in development and has been implicated in as many as 70% of human cancers. Genomic binding of the entire Max network has not been mapped and existing maps of Myc binding have led to a complicated picture of network function. Myc binds pre-established euchromatic regions and its depletion leads to collapse of active chromatin and decrease in accessibility, suggesting a role for Myc in regulating chromatin structure. However, roles for other Max network members in regulating epigenome structure are not known. Intriguingly, the Max network has been shown to interact with chromatin modifying complexes, yet the functional significance of these interactions has not been evaluated.
Three specific aims are proposed to dissect the regulation of chromatin structure by the Max network in a human B cell line model of Burkitt's lymphoma.
In Specific Aim 1, genome-wide binding of the Max network will be mapped at single- base resolution and the effects of Myc dosage on Myc binding will be determined.
In Specific Aim 2, the relationship between chromatin structure and the Max network, as well as the effect of Max network member depletion on the epigenomic landscape, will be determined. Additionally, Max network members will be mapped after depletion of Max to explore the possibility of network function independent of Max heterodimerization.
In Specific Aim 3, the functional consequences of physical interactions between the Max network and chromatin remodeling and Polycomb repressive complexes will be studied. The proposed studies will leverage a high-resolution native epigenome mapping approach to provide insights into how transcriptional regulatory networks interpret information encoded in the base-pair sequence of the genome to shape the chromatin landscape. Given the central role of the Max network in transcriptional control of growth and proliferation, the proposed studies may have implications for understanding molecular mechanisms underlying both normal development and disease.

Public Health Relevance

This proposal focuses on the Max transcription factor network, which includes the Myc proteins that regulate cell growth, proliferation, and cell death. The Max network is dysregulated in the majority of human cancers. The experiments in this proposal aim to understand the causal mechanisms by which the Max network shapes the structure of chromatin, the protein-DNA complex that makes up chromosomes. A clear understanding of the biology of Max network function will be important for diagnosis and treatment of cancers. High-resolution analysis of chromatin regulation by the Max network.

National Institute of Health (NIH)
National Cancer Institute (NCI)
Individual Predoctoral NRSA for M.D./Ph.D. Fellowships (ADAMHA) (F30)
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Special Emphasis Panel (ZRG1)
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Damico, Mark W
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Fred Hutchinson Cancer Research Center
United States
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Zentner, Gabriel E; Kasinathan, Sivakanthan; Xin, Beibei et al. (2015) ChEC-seq kinetics discriminates transcription factor binding sites by DNA sequence and shape in vivo. Nat Commun 6:8733
Orsi, Guillermo A; Kasinathan, Sivakanthan; Zentner, Gabriel E et al. (2015) Mapping regulatory factors by immunoprecipitation from native chromatin. Curr Protoc Mol Biol 110:21.31.1-25
Kasinathan, Sivakanthan; Henikoff, Steven (2014) 5-Aza-CdR delivers a gene body blow. Cancer Cell 26:449-51