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Youn_et_al_RNAbodies_SAINT3090

ABSTRACT: Youn et al., High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies. Dataset related to APMS, SAINTexpress ID 3090.

INSTRUMENT(S): TripleTOF 6600

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Anne-Claude Gingras

PROVIDER: MSV000081414 | MassIVE | Sun Aug 06 09:15:00 BST 2017

REPOSITORIES: MassIVE

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Publications

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies.

Youn Ji-Young JY Dunham Wade H WH Hong Seo Jung SJ Knight James D R JDR Bashkurov Mikhail M Chen Ginny I GI Bagci Halil H Rathod Bhavisha B MacLeod Graham G Eng Simon W M SWM Angers Stéphane S Morris Quaid Q Fabian Marc M Côté Jean-François JF Gingras Anne-Claude AC

Molecular cell 20180125 3

mRNA processing, transport, translation, and ultimately degradation involve a series of dedicated protein complexes that often assemble into large membraneless structures such as stress granules (SGs) and processing bodies (PBs). Here, systematic in vivo proximity-dependent biotinylation (BioID) analysis of 119 human proteins associated with different aspects of mRNA biology uncovers 7424 unique proximity interactions with 1,792 proteins. Classical bait-prey analysis reveals connections of hundr ...[more]

PMID: 29395067

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Global Analysis of Yeast mRNPs

Project description:Proteins regulate gene expression by controlling mRNA biogenesis, localization, translation and decay. Identifying the composition, diversity and function of mRNPs (mRNA protein complexes) is essential to understanding these processes. In a global survey of S. cerevisiae mRNA binding proteins we identified 120 proteins that cross-link to mRNA, including 66 new mRNA binding proteins. These include kinases, RNA modification enzymes, metabolic enzymes, and tRNA and rRNA metabolism factors. These proteins show dynamic subcellular localization during stress, including assembly into stress granules and P-bodies (Processing-bodies). CLIP (cross-linking and immunoprecipitation) analyses of the P-body components Pat1, Lsm1, Dhh1 and Sbp1 identified sites of interaction on specific mRNAs revealing positional binding preferences and co-assembly preferences. Taken together, this work defines the major yeast mRNP proteins, reveals widespread changes in their subcellular location during stress, and begins to define assembly rules for P-body mRNPs. CLIP-seq analysis of Dhh1, Lsm1, Pat1 and Sbp1

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Youn_et_al_RNAbodies_SAINT3105_Set2

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Project description:This set of submissions contains the mass spectrometry files acquired using Data-Dependent Acquisition mode (DDA), which were paired with Data-Independent Acquisition mode (DIA) files (MSV000081414) for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA bodies. These DDA files were used to generate spectral library in MSPLIT analysis of both DDA and DIA files. The paired SAINT 3090 set entails APMS experiments of stress granule baits treated or untreated briefly with sodium arsenite and these were were performed from Flp-In T-REx HEK293 cells and MS files were acquired on AbSciex Triple TOF 6600 instrument in data-independent acquisition mode.

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