Proteomics

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The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

ABSTRACT: The data presented here was produced using XRNAX - a novel extraction method for protein-crosslinked RNA from UV-crosslinked cells. We apply XRNAX for three proteomic downstream applications. First, we purify ribonucleotide-crosslinked peptides from XRNAX extracts and use their identification as direct evidence for protein-RNA interfaces. Second, we use SILAC, XRNAX and silica enrichment in order to derive high-confidence RNA-binding proteomes from the three human cell lines MCF7, HEK293 and HeLa. Third, using SILAC we quantify total proteomes and RNA-binding proteomes differentially during a time course experiment of arsenite stress in MCF7 cells.

INSTRUMENT(S): Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Permanent Cell Line Cell

DISEASE(S): Cervix Carcinoma,Disease Free,Breast Cancer

SUBMITTER: Sophia Foehr  

LAB HEAD: Jeroen Krijgsveld

PROVIDER: PXD010520 | Pride | 2018-12-06

REPOSITORIES: Pride

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Dataset's files

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Action DRS
20160530_QE1_JT_XRNAXpep_Trp_hydro.mzML Mzml
20160530_QE1_JT_XRNAXpep_Trp_hydro.tsv Tabular
20161223_QE1_JT_dXRNAX_LAsH_10min_F1.raw Raw
20161223_QE1_JT_dXRNAX_LAsH_10min_F2.raw Raw
20161223_QE1_JT_dXRNAX_LAsH_10min_F3.raw Raw
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The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest.

Trendel Jakob J   Schwarzl Thomas T   Horos Rastislav R   Prakash Ananth A   Bateman Alex A   Hentze Matthias W MW   Krijgsveld Jeroen J  

Cell 20181206 1-2

Proteins and RNA functionally and physically intersect in multiple biological processes, however, currently no universal method is available to purify protein-RNA complexes. Here, we introduce XRNAX, a method for the generic purification of protein-crosslinked RNA, and demonstrate its versatility to study the composition and dynamics of protein-RNA interactions by various transcriptomic and proteomic approaches. We show that XRNAX captures all RNA biotypes and use this to characterize the sub-pr  ...[more]

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