Post-translational modifications (PTMs) to histone proteins constitute a major type of epigenetic mechanism that regulates chromatin structure and gene expression patterns in eukaryotes. In addition to their important roles in standard physiology, disruptions in histone PTM signaling patterns have been suggested to be significant, potentially causative factors in various human diseases such as cancer. As most histone PTM work in the chromatin biology field is accomplished using site-specific antibodies, the quantitative measurement of combinational histone PTMs co-occurring on the same molecule has been unmet. Our objectives include the continued development of mass spectrometry-based proteomics and bioinformatic methods for quantitatively interrogating combinatorial histone PTM patterns, and applying these approaches to investigate histone mediated epigenetics mechanisms behind key areas of health related biological research. Here we will specifically apply our approaches to investigate epigenetic histone PTM signaling during human embryonic stem cell differentiation.
Our specific aims are three in number and include identifying changing histone PTMs during stem cell differentiation, characterizing combinatorial histone PTM binding protein complexes that translate these PTM patterns, and determining the role of these combinatorial PTMs in maintaining the pluripotent state or facilitating to a specific lineage We expect that these comprehensive proteomic strategies will continue to generate new tools to study epigenetic histone PTMs and generate novel insights into the mechanism of combinatorial histone PTMs in gene regulation during diverse biological events such as cellular differentiation.

Public Health Relevance

Histone post-translational modifications (PTMs) are an intensely investigated research field and alterations in these PTM patterns have been suggested to play roles in the pathology of some diseases, or in developmental biology. This research will help establish the role of these PTMs in human biology, and will impact areas such as regenerative medicine and cancer biology, thus laying down the foundation for potential development of epigenetic therapy.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
1R01GM110174-01
Application #
8672940
Study Section
Enabling Bioanalytical and Imaging Technologies Study Section (EBIT)
Program Officer
Edmonds, Charles G
Project Start
2014-08-15
Project End
2018-07-31
Budget Start
2014-08-15
Budget End
2015-07-31
Support Year
1
Fiscal Year
2014
Total Cost
$304,000
Indirect Cost
$114,000
Name
University of Pennsylvania
Department
Biochemistry
Type
Schools of Medicine
DUNS #
042250712
City
Philadelphia
State
PA
Country
United States
Zip Code
19104
Guo, Qi; Sidoli, Simone; Garcia, Benjamin A et al. (2018) Assessment of Quantification Precision of Histone Post-Translational Modifications by Using an Ion Trap and down To 50?000 Cells as Starting Material. J Proteome Res 17:234-242
Weiner, Amber K; Sidoli, Simone; Diskin, Sharon J et al. (2018) Graphical Interpretation and Analysis of Proteins and their Ontologies (GiaPronto): A One-Click Graph Visualization Software for Proteomics Data Sets. Mol Cell Proteomics 17:1426-1431
Shastrula, Prashanth Krishna; Lund, Peder J; Garcia, Benjamin A et al. (2018) Rpp29 regulates histone H3.3 chromatin assembly through transcriptional mechanisms. J Biol Chem 293:12360-12377
Greer, Sylvester M; Sidoli, Simone; Coradin, Mariel et al. (2018) Extensive Characterization of Heavily Modified Histone Tails by 193 nm Ultraviolet Photodissociation Mass Spectrometry via a Middle-Down Strategy. Anal Chem 90:10425-10433
Bharathy, Narendra; Berlow, Noah E; Wang, Eric et al. (2018) The HDAC3-SMARCA4-miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma. Sci Signal 11:
Woll, Kellie A; Guzik-Lendrum, Stephanie; Bensel, Brandon M et al. (2018) An allosteric propofol-binding site in kinesin disrupts kinesin-mediated processive movement on microtubules. J Biol Chem 293:11283-11295
Liu, Xiaojing; Cooper, Daniel E; Cluntun, Ahmad A et al. (2018) Acetate Production from Glucose and Coupling to Mitochondrial Metabolism in Mammals. Cell 175:502-513.e13
Lin-Shiao, Enrique; Lan, Yemin; Coradin, Mariel et al. (2018) KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis. Genes Dev 32:181-193
Aebersold, Ruedi; Agar, Jeffrey N; Amster, I Jonathan et al. (2018) How many human proteoforms are there? Nat Chem Biol 14:206-214
Shields, Emily J; Sheng, Lihong; Weiner, Amber K et al. (2018) High-Quality Genome Assemblies Reveal Long Non-coding RNAs Expressed in Ant Brains. Cell Rep 23:3078-3090

Showing the most recent 10 out of 101 publications