Dataset Information

LSD1 complexes - Assembly of methylated KDM1A and CHD1 drives androgen receptor-dependent transcription and translocation

ABSTRACT: PCP-SILAC analysis of LSD1 protein complexes isolated from LNCaP cells

OTHER RELATED OMICS DATASETS IN: PRJNA271254PRJNA271256PRJNA271255

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell, Cell Culture

DISEASE(S): Prostate Adenocarcinoma

SUBMITTER: Joern Dengjel

LAB HEAD: Joern Dengjel

PROVIDER: PXD003262 | Pride | 2016-01-11

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	20140814_KP_Schuele_4_01.raw	Raw
	20140814_KP_Schuele_4_02.raw	Raw
	20140814_KP_Schuele_4_03.raw	Raw
	20140814_KP_Schuele_4_04.raw	Raw
	20140814_KP_Schuele_4_05.raw	Raw

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Publications

Assembly of methylated KDM1A and CHD1 drives androgen receptor-dependent transcription and translocation.

Metzger Eric E Willmann Dominica D McMillan Joel J Forne Ignasi I Metzger Philipp P Gerhardt Stefan S Petroll Kerstin K von Maessenhausen Anne A Urban Sylvia S Schott Anne-Kathrin AK Espejo Alexsandra A Eberlin Adrien A Wohlwend Daniel D Schüle Katrin M KM Schleicher Michael M Perner Sven S Bedford Mark T MT Jung Manfred M Dengjel Jörn J Flaig Ralf R Imhof Axel A Einsle Oliver O Schüle Roland R

Nature structural & molecular biology 20160111 2

Prostate cancer evolution is driven by a combination of epigenetic and genetic alterations such as coordinated chromosomal rearrangements, termed chromoplexy. TMPRSS2-ERG gene fusions found in human prostate tumors are a hallmark of chromoplexy. TMPRSS2-ERG fusions have been linked to androgen signaling and depend on androgen receptor (AR)-coupled gene transcription. Here, we show that dimethylation of KDM1A at K114 (to form K114me2) by the histone methyltransferase EHMT2 is a key event controll ...[more]

PMID: 26751641

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Project description:Measuring the properties of endogenous cell proteins, such as expression level, subcellular localization and turnover rates, on a whole proteome level remains a major challenge in the post-genome era. Quantitative methods for measuring mRNA expression do not reliably predict corresponding protein levels and provide little or no information on other protein properties. Here we describe a combined pulse-labelling, spatial proteomics and data analysis strategy to characterize the expression, localization, synthesis, degradation and turnover rates of endogenously expressed, untagged human proteins in different subcellular compartments. Using quantitative mass spectrometry and SILAC, a total of 80,098 peptides from 8,041 HeLa proteins were quantified, and their spatial distribution between the cytoplasm, nucleus and nucleolus determined and visualised using specialised software tools developed in PepTracker. Using information from ion intensities and rates of change in isotope ratios, protein abundance levels and protein synthesis, degradation and turnover rates were calculated for the whole cell and for the respective cytoplasmic, nuclear and nucleolar compartments. Expression levels of endogenous HeLa proteins varied by up to seven orders of magnitude. The average turnover rate for HeLa proteins was approximately 20 hours. Turnover rate did not correlate with either molecular weight or net charge, but did correlate with abundance, with highly abundant proteins showing longer than average half-lives. Fast turnover proteins had overall a higher frequency of PEST motifs than slow turnover proteins but no general correlation was observed between amino or carboxy terminal amino acid identities and turnover rates. A subset of proteins was identified that exist in pools with different turnover rates depending on their subcellular localization. This strongly correlated with subunits of large, multi-protein complexes, suggesting a general mechanism whereby their assembly is controlled in a different subcellular location to their main site of function.