PXD002436

PXD002436 is an original dataset announced via ProteomeXchange.

Title	Monitoring cellular phosphorylation signaling pathways into chromatin and down to the gene level
Description	Protein phosphorylation, one of the most common and important modifications of acute and reversible regulation of protein function, plays a dominant role in almost all cellular processes. These signaling events regulate cellular responses including proliferation, differentiation, metabolism, survival and apoptosis. Several studies have been successfully used to identify phosphorylated proteins and dynamic changes in phosphorylation status after stimulation. Nevertheless, it is still rather difficult to elucidate precise complex phosphorylation signaling pathways. In particular, how signal transduction pathways directly communicate from the outer cell surface through cytoplasmic space and then directly into chromatin networks to change the transcriptional and epigenetic landscape remains poorly understood. Here we describe the optimization and comparison of methods based on thiophosphorylation affinity enrichment, which can be utilized to monitor phosphorylation signaling into chromatin by isolation of phosphoprotein containing nucleosomes, a method we term phosphorylation-specific chromatin affinity purification (PS-ChAP). We utilized this PS-ChAP approach in combination with quantitative proteomics to identify changes in the phosphorylation status of chromatin bound proteins on nucleosomes following perturbation of transcriptional processes. We also demonstrate that this method can be employed to map phosphoprotein signaling into chromatin containing nucleosomes through identifying the genes those phosphorylated proteins are found on via thiophosphate PS-ChAP-qPCR. Thus, our results showed that PS-ChAP offers a new strategy for studying cellular signaling and chromatin biology, allowing us to directly and comprehensively investigate phosphorylation signaling into chromatin to investigate if these pathways are involved in altering gene expression.
HostingRepository	PRIDE
AnnounceDate	2015-11-09
AnnouncementXML	Submission_2015-11-09_08:37:47.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD002436
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	yumiao han
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	phosphorylated residue
Instrument	LTQ Orbitrap

Revision	Datetime	Status	ChangeLog Entry
0	2015-06-29 01:41:59	ID requested
⏵ 1	2015-11-09 08:37:48	announced

Han Y, Yuan ZF, Molden RC, Garcia BA, Monitoring Cellular Phosphorylation Signaling Pathways into Chromatin and Down to the Gene Level. Mol Cell Proteomics, 15(3):834-53(2016) [pubmed]

curator keyword: Biomedical

submitter keyword: PROTEOMICS thiophosphorylation signaling

Benjamin A. Garcia
contact affiliation	Epigenetics Program Department of Biochemistry and Biophysics Smilow Center for Translational Research Perelman School of Medicine University of Pennsylvania
contact email	bgarci@mail.med.upenn.edu
lab head
yumiao han
contact affiliation	upenn
contact email	hanyumiao@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002436
     1. Label: PRIDE project
     2. Name: Monitoring cellular phosphorylation signaling pathways into chromatin and down to the gene level