ABSTRACT: Youn et al. High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies . Files related to SAINT 3115.
Project description:Youn et al. High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies (SAINTexpress 3108)
Project description:Youn et al., High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies.
MassIVE title: Youn_et_al_RNAbodies_SAINT3112
Project description:Youn et al., High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies. Dataset related to APMS, SAINTexpress ID 3090.
Project description:Youn et al. High-density proximity mapping reveals the subcellular organization of mRNA-associated granules and bodies (SAINTexpress 3073)
Sample information related to MASSIVE submission Youn_et_al_RNAbodies_SAINT 3073 (data -indendent acquisition, MSPLIT analysis).
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
Project description:This set of submissions contains the mass spectrometry files for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA bodies. BioID experiments were performed from Flp-In T-REx HEK293 cells and MS files were acquired on Orbitrap Elite and Orbitrap Velos. Different MassIVE submissions corresponding to SAINT 3105 (see list below) have been made and this is set 3.
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.
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 (MSV000081419) 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 3108 set entails BioID experiments of stress granule and Processing-body baits expressed in Flp-In T-REx HEK293 cells, treated or untreated with sodium arsenite during labeling period.
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 (MSV000081422) for the manuscript by Ji-Young Youn et al. that describes the high-density proximity mapping of RNA bodies