Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach
RNA binding proteins (RBPs) bind RNAs through specific RNA-binding domains, generating multi-molecular complexes known as ribonucleoproteins (RNPs). Various post-translational modifications (PTMs) have been described to regulate RBP structure, subcellular localization, and interactions with other pr...
Main Authors: | , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2021-09-01
|
Series: | Frontiers in Molecular Biosciences |
Subjects: | |
Online Access: | https://www.frontiersin.org/articles/10.3389/fmolb.2021.688973/full |
id |
doaj-3255b4b505a94da3a097aa84a37e14d3 |
---|---|
record_format |
Article |
spelling |
doaj-3255b4b505a94da3a097aa84a37e14d32021-09-07T04:54:44ZengFrontiers Media S.A.Frontiers in Molecular Biosciences2296-889X2021-09-01810.3389/fmolb.2021.688973688973Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic ApproachMarianna Maniaci0Marianna Maniaci1Francesca Ludovica Boffo2Enrico Massignani3Enrico Massignani4Tiziana Bonaldi5Laboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, ItalyEuropean School of Molecular Medicine (SEMM), Milan, ItalyLaboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, ItalyLaboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, ItalyEuropean School of Molecular Medicine (SEMM), Milan, ItalyLaboratory of Nuclear Proteomics to Study Gene Expression Regulation in Cancer, European Institute of Oncology (IEO) IRCSS, Department of Experimental Oncology (DEO), Milan, ItalyRNA binding proteins (RBPs) bind RNAs through specific RNA-binding domains, generating multi-molecular complexes known as ribonucleoproteins (RNPs). Various post-translational modifications (PTMs) have been described to regulate RBP structure, subcellular localization, and interactions with other proteins or RNAs. Recent proteome-wide experiments showed that RBPs are the most representative group within the class of arginine (R)-methylated proteins. Moreover, emerging evidence suggests that this modification plays a role in the regulation of RBP-RNA interactions. Nevertheless, a systematic analysis of how changes in protein-R-methylation can affect globally RBPs-RNA interactions is still missing. We describe here a quantitative proteomics approach to profile global changes of RBP-RNA interactions upon the modulation of type I and II protein arginine methyltransferases (PRMTs). By coupling the recently described Orthogonal Organic Phase Separation (OOPS) strategy with the Stable Isotope Labelling with Amino acids in Cell culture (SILAC) and pharmacological modulation of PRMTs, we profiled RNA-protein interaction dynamics in dependence of protein-R-methylation. Data are available via ProteomeXchange with identifier PXD024601.https://www.frontiersin.org/articles/10.3389/fmolb.2021.688973/fullproteomicsPTMsprotein-R-methylationPRMTsSILACOOPS |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Marianna Maniaci Marianna Maniaci Francesca Ludovica Boffo Enrico Massignani Enrico Massignani Tiziana Bonaldi |
spellingShingle |
Marianna Maniaci Marianna Maniaci Francesca Ludovica Boffo Enrico Massignani Enrico Massignani Tiziana Bonaldi Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach Frontiers in Molecular Biosciences proteomics PTMs protein-R-methylation PRMTs SILAC OOPS |
author_facet |
Marianna Maniaci Marianna Maniaci Francesca Ludovica Boffo Enrico Massignani Enrico Massignani Tiziana Bonaldi |
author_sort |
Marianna Maniaci |
title |
Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach |
title_short |
Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach |
title_full |
Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach |
title_fullStr |
Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach |
title_full_unstemmed |
Systematic Analysis of the Impact of R-Methylation on RBPs-RNA Interactions: A Proteomic Approach |
title_sort |
systematic analysis of the impact of r-methylation on rbps-rna interactions: a proteomic approach |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Molecular Biosciences |
issn |
2296-889X |
publishDate |
2021-09-01 |
description |
RNA binding proteins (RBPs) bind RNAs through specific RNA-binding domains, generating multi-molecular complexes known as ribonucleoproteins (RNPs). Various post-translational modifications (PTMs) have been described to regulate RBP structure, subcellular localization, and interactions with other proteins or RNAs. Recent proteome-wide experiments showed that RBPs are the most representative group within the class of arginine (R)-methylated proteins. Moreover, emerging evidence suggests that this modification plays a role in the regulation of RBP-RNA interactions. Nevertheless, a systematic analysis of how changes in protein-R-methylation can affect globally RBPs-RNA interactions is still missing. We describe here a quantitative proteomics approach to profile global changes of RBP-RNA interactions upon the modulation of type I and II protein arginine methyltransferases (PRMTs). By coupling the recently described Orthogonal Organic Phase Separation (OOPS) strategy with the Stable Isotope Labelling with Amino acids in Cell culture (SILAC) and pharmacological modulation of PRMTs, we profiled RNA-protein interaction dynamics in dependence of protein-R-methylation. Data are available via ProteomeXchange with identifier PXD024601. |
topic |
proteomics PTMs protein-R-methylation PRMTs SILAC OOPS |
url |
https://www.frontiersin.org/articles/10.3389/fmolb.2021.688973/full |
work_keys_str_mv |
AT mariannamaniaci systematicanalysisoftheimpactofrmethylationonrbpsrnainteractionsaproteomicapproach AT mariannamaniaci systematicanalysisoftheimpactofrmethylationonrbpsrnainteractionsaproteomicapproach AT francescaludovicaboffo systematicanalysisoftheimpactofrmethylationonrbpsrnainteractionsaproteomicapproach AT enricomassignani systematicanalysisoftheimpactofrmethylationonrbpsrnainteractionsaproteomicapproach AT enricomassignani systematicanalysisoftheimpactofrmethylationonrbpsrnainteractionsaproteomicapproach AT tizianabonaldi systematicanalysisoftheimpactofrmethylationonrbpsrnainteractionsaproteomicapproach |
_version_ |
1717764771679305728 |