One of the most compositionally diverse structures in a eukaryotic cell is a chromosome. A multitude of macromolecular protein interactions must properly occur on chromatin to drive functional aspects of chromosome biology like gene transcription, DNA replication, recombination, repair, and sister chromatid segregation. Importantly, unwanted alterations in PTM states and defects in the enzymatic machineries that regulate chromatin metabolism are linked to a wide variety of illnesses and diseases that are epigenetic in scope, including cancer. However, analyzing how protein assemblies interact in vivo with chromatin to direct these activities remains a significant challenge due to the temporal and dynamic nature of their associations. The in vivo analysis of macromolecular protein interactions in the context of chromatin has been a primary collaborative focus of the Taverna and Tackett laboratories for the last 6 years. Together, using the complementary skill sets of our groups, we have developed novel tools to unambiguously identify protein- protein interactions of macromolecular complexes on chromatin. Most importantly, our combined efforts recently culminated in the development of a technique termed Chromatin Affinity Purification with Mass Spectrometry or ChAP-MS. ChAP-MS provides for the enrichment of a unique 1 kb section of a chromosome for site-specific identification of macromolecular protein interactions and associated histone posttranslational modifications. The establishment of ChAP-MS in human cells will permit unprecedented insight into mammalian transcription regulation as well as epigenetic disregulation in human disease, and potentially mechanisms of action for therapeutics. In this proposal, we hypothesize that ChAP-MS can be adapted to human cell culture and tissues to provide a novel tool for the analysis of in vivo macromolecular protein interactions. Our short-term goal is to apply ChAP-MS to human cell lines and tissues, while our long-term goal is to move development into animal models like mice and to use ChAP-MS to profile across an entire chromosome. To test our hypothesis and work towards our short term goal, we will pursue the following three Aims: (1) Develop and Apply ChAP-MS for the analysis of macromolecular chromatin composition at actively transcribing genes in mammalian cell lines, (2) Develop an antisense enrichment procedure for ChAP-MS and (3) Application of Multiplex ChAP-MS in mammalian cells and tissues.

Public Health Relevance

Since mis-regulation of chromatin structure and post-translational modification of histones is linked to cancer and other epigenetic diseases, it is imperative to establish new methodologies that will allow comprehensive studies and unbiased screens for protein participants in epigenetic mechanisms. We have developed a new technology termed ChAP-MS that provides for the analysis of macromolecular protein interactions on chromatin at a single defined genomic position in vivo. Our planned extension of ChAP-MS to human cells and tissues will undoubtedly provide a major tool for epigeneticists to explore mammalian transcription regulation as well as the epigenetic disregulation associated with human diseases, including cancer.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
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Special Emphasis Panel (ZGM1-CBB-0 (MI))
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Sledjeski, Darren D
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Johns Hopkins University
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Cheema, Amrita K; Byrum, Stephanie D; Sharma, Neel Kamal et al. (2018) Proteomic Changes in Mouse Spleen after Radiation-Induced Injury and its Modulation by Gamma-Tocotrienol. Radiat Res 190:449-463
Hartman, Jessica H; Miller, Grover P; Caro, Andres A et al. (2017) 1,3-Butadiene-induced mitochondrial dysfunction is correlated with mitochondrial CYP2E1 activity in Collaborative Cross mice. Toxicology 378:114-124
Shields, Bradley D; Mahmoud, Fade; Taylor, Erin M et al. (2017) Indicators of responsiveness to immune checkpoint inhibitors. Sci Rep 7:807
Atanassov, Boyko S; Mohan, Ryan D; Lan, Xianjiang et al. (2016) ATXN7L3 and ENY2 Coordinate Activity of Multiple H2B Deubiquitinases Important for Cellular Proliferation and Tumor Growth. Mol Cell 62:558-71
Byrum, Stephanie D; Burdine, Marie S; Orr, Lisa et al. (2016) A Quantitative Proteomic Analysis of Urine from Gamma-Irradiated Non-Human Primates. J Proteomics Bioinform 9:
Ayyadevara, Srinivas; Mercanti, Federico; Wang, Xianwei et al. (2016) Age- and Hypertension-Associated Protein Aggregates in Mouse Heart Have Similar Proteomic Profiles. Hypertension 67:1006-13
Harr, Jennifer C; Reddy, Karen L (2016) Tagged Chromosomal Insertion Site System: A Method to Study Lamina-Associated Chromatin. Methods Enzymol 569:433-53
Heard, Melissa E; Besio, Roberta; Weis, MaryAnn et al. (2016) Sc65-Null Mice Provide Evidence for a Novel Endoplasmic Reticulum Complex Regulating Collagen Lysyl Hydroxylation. PLoS Genet 12:e1006002
Wu, Tao P; Wang, Tao; Seetin, Matthew G et al. (2016) DNA methylation on N(6)-adenine in mammalian embryonic stem cells. Nature 532:329-33
Salinas, Eduardo; Byrum, Stephanie D; Moreland, Linley E et al. (2016) Identification of Viral and Host Proteins That Interact with Murine Gammaherpesvirus 68 Latency-Associated Nuclear Antigen during Lytic Replication: a Role for Hsc70 in Viral Replication. J Virol 90:1397-413

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