Integrating intact protein proteomics with ChIP-Seq for identification and functional characterization of epigenetic histone modifications
EMSL Project ID
44727
Abstract
Biological systems are exceedingly more complex than defined by the genome due to differential protein expression and degradation, altered mRNA splicing, and the presence of multiple post-translational modifications (PTMs) that occur in different cellular contexts. Histone proteins in particular are subject to multiple PTMs that influence chromatin structure and transcription factor recruitment to regulate transcription in the short or long (e.g. epigenetic) terms. We hypothesize that histones and their complex array of modifications may serve as a link between environmental perturbations that activate cell signaling pathways and alterations in gene and protein expression. In response to a perturbation in the environment, activated cell signaling pathways alter PTMs, localization, and histone binding affinities of proteins that write and read the specific histone modifications that regulate gene expression patterns. A key component of our research plan is to utilize intact protein mass spectrometry to comprehensively map changes in histone PTMs caused by stress, in this case, exposure to low doses of ionizing radiation. Functional consequences of these altered histone PTMs will be assessed using chromatin immunoprecipitation coupled to EMSL's next generation sequencing capabilities (ChIP-Seq). Merging of the ChIP-Seq capability with complimentary proteomic approaches will provide EMSL with a very unique capability to comprehensively study transcriptional and epigenetic regulation at the protein and DNA level. This proposal will directly benefit ongoing work funded by the DOE low dose radiation research program and the Defense Threat Reduction Agency as well as provide necessary data to obtain additional funding from NIH and other agencies.
Project Details
Project type
Large-Scale EMSL Research
Start Date
2011-10-01
End Date
2014-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Liu X, SM Hengel, S Wu, N Tolic, L Pasa-Tolic, and PA Pevzner. 2013. "Identification of Ultramodified Proteins Using Top-Down Mass Spectra." PNNL-SA-94025, Pacific Northwest National Laboratory, Richland, WA. doi:10.1007/978-3-642-37195-0_11 [Unpublished]
Tian Z, N Tolic, R Zhao, RJ Moore, SM Hengel, EW Robinson, DL Stenoien, S Wu, RD Smith, and L Pasa-Tolic. 2012. "Enhanced liquid chromatography mass spectrometry platform for top-down characterization of histone post-translational modifications ." PNNL-SA-90867, Pacific Northwest National Laboratory, Richland, WA.
Tian Z, N Tolic, R Zhao, RJ Moore, SM Hengel, EW Robinson, DL Stenoien, S Wu, RD Smith, and L Pasa-Tolic. 2012. "Enhanced top-down characterization of histone post-translational modifications ." Genome Biology 13(10):R86. doi:10.1186/gb-2012-13-10-r86.