Dataset Information

StrepPyogenes_FFE2_LTQ

ABSTRACT: Streptococcus pyogenenes FFE LTQ exp

INSTRUMENT(S): LTQ

ORGANISM(S): Streptococcus Pyogenes

SUBMITTER: Lange V, Malmstr�m JA, Didion J, King NL, Johansson BP, Sch�fer J, Rameseder J, Wong CH, Deutsch EW, Brusniak MY, B�hlmann P, Bj�rck L, Domon B, Aebersold R

PROVIDER: PAe000285 | PeptideAtlas | 2008-12-31

REPOSITORIES: PeptideAtlas

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Dataset's files

Source:

			Action	DRS
	PAe000285_442_search.params.tar.gz	Other
	PAe000285_442_searchdatabase_sequest.fasta	Fasta
	PAe000285_442_sequest.params	Other
	PAe000285_README	Other
	PAe000285_Search_Results_442_201104200929.properties	Other

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Publications

Targeted quantitative analysis of Streptococcus pyogenes virulence factors by multiple reaction monitoring.

Lange Vinzenz V Malmström Johan A JA Didion John J King Nichole L NL Johansson Björn P BP Schäfer Juliane J Rameseder Jonathan J Wong Chee-Hong CH Deutsch Eric W EW Brusniak Mi-Youn MY Bühlmann Peter P Björck Lars L Domon Bruno B Aebersold Ruedi R

Molecular & cellular proteomics : MCP 20080413 8

In many studies, particularly in the field of systems biology, it is essential that identical protein sets are precisely quantified in multiple samples such as those representing differentially perturbed cell states. The high degree of reproducibility required for such experiments has not been achieved by classical mass spectrometry-based proteomics methods. In this study we describe the implementation of a targeted quantitative approach by which predetermined protein sets are first identified a ...[more]

PMID: 18408245

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Project description:Fast food diet consumption and sedentary life style leads to energy excess, which elevates risks for obesity, metabolic syndrome, non-alcoholic fatty liver disease (NAFLD), and cancer. Exercise training conveys many health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms globally and at select loci in an array of human tissues, however, such effects are less well documented in liver tissue. To dissect the epigenetic consequences of diet and exercise in liver, we measured DNA methylation using reduced representation bisulfite sequencing (RRBS) and transcriptome using RNA-seq in mice maintained on a fast food diet with sedentary lifestyle (FFC) or exercise (FFE) compared to control diet with (NCE) and without exercise (NCC). Our analyses demonstrate genome-wide differential DNA methylation at key regulatory regions, including different classes of promoters and enhancers, and differential regulation of gene clusters in each condition group. FFE gene expression is most differentially regulated, with enrichment of carbohydrate/lipid metabolic pathways and skeletal muscle development in altered gene sets. Through evaluation of putative protective effects of exercise on diet-induced DNA methylation and gene expression, we show that hypermethylation is effectively prevented, especially at promoters and enhancers, and hypomethylation is partially attenuated. We assessed diet-induced DNA methylation changes associated with cancer-related epigenetic modifications and identified significant increases at liver-specific enhancers in FFC and FFE, suggesting a repressive effect on the epigenomic signature specifying liver identity. Gaining methylation at a subset of gene promoters was associated with inhibition of tissue development and promotion of carcinogenic process. Taken together, our study demonstrates large-scale diet- and exercise-induced effects on the epigenetic landscape, emphasizing the functional relevance of epigenetic mechanisms as an interface between life-style modifications and phenotypic alterations.