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The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches

Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological...

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Autores principales: Gerovac, Milan, Vogel, Jörg, Smirnov, Alexandre
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8058203/
https://www.ncbi.nlm.nih.gov/pubmed/33898526
http://dx.doi.org/10.3389/fmolb.2021.661448
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author Gerovac, Milan
Vogel, Jörg
Smirnov, Alexandre
author_facet Gerovac, Milan
Vogel, Jörg
Smirnov, Alexandre
author_sort Gerovac, Milan
collection PubMed
description Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological function. Whether those are dynamic regulatory ribonucleoproteins (RNPs) or integrated molecular machines involved in gene expression, the comprehensive knowledge of these units is critical to our understanding of key molecular mechanisms and cell physiology phenomena. Such is the goal of diverse complexomic approaches and in particular of the recently developed gradient profiling by sequencing (Grad-seq). By separating cellular protein and RNA complexes on a density gradient and quantifying their distributions genome-wide by mass spectrometry and deep sequencing, Grad-seq charts global landscapes of native macromolecular assemblies. In this review, we propose a function-based ontology of stable RNPs and discuss how Grad-seq and related approaches transformed our perspective of bacterial and eukaryotic ribonucleoproteins by guiding the discovery of new RNA-binding proteins and unusual classes of noncoding RNAs. We highlight some methodological aspects and developments that permit to further boost the power of this technique and to look for exciting new biology in understudied and challenging biological models.
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spelling pubmed-80582032021-04-22 The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches Gerovac, Milan Vogel, Jörg Smirnov, Alexandre Front Mol Biosci Molecular Biosciences Macromolecular complexes of proteins and RNAs are essential building blocks of cells. These stable supramolecular particles can be viewed as minimal biochemical units whose structural organization, i.e., the way the RNA and the protein interact with each other, is directly linked to their biological function. Whether those are dynamic regulatory ribonucleoproteins (RNPs) or integrated molecular machines involved in gene expression, the comprehensive knowledge of these units is critical to our understanding of key molecular mechanisms and cell physiology phenomena. Such is the goal of diverse complexomic approaches and in particular of the recently developed gradient profiling by sequencing (Grad-seq). By separating cellular protein and RNA complexes on a density gradient and quantifying their distributions genome-wide by mass spectrometry and deep sequencing, Grad-seq charts global landscapes of native macromolecular assemblies. In this review, we propose a function-based ontology of stable RNPs and discuss how Grad-seq and related approaches transformed our perspective of bacterial and eukaryotic ribonucleoproteins by guiding the discovery of new RNA-binding proteins and unusual classes of noncoding RNAs. We highlight some methodological aspects and developments that permit to further boost the power of this technique and to look for exciting new biology in understudied and challenging biological models. Frontiers Media S.A. 2021-04-07 /pmc/articles/PMC8058203/ /pubmed/33898526 http://dx.doi.org/10.3389/fmolb.2021.661448 Text en Copyright © 2021 Gerovac, Vogel and Smirnov. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Molecular Biosciences
Gerovac, Milan
Vogel, Jörg
Smirnov, Alexandre
The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches
title The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches
title_full The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches
title_fullStr The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches
title_full_unstemmed The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches
title_short The World of Stable Ribonucleoproteins and Its Mapping With Grad-Seq and Related Approaches
title_sort world of stable ribonucleoproteins and its mapping with grad-seq and related approaches
topic Molecular Biosciences
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8058203/
https://www.ncbi.nlm.nih.gov/pubmed/33898526
http://dx.doi.org/10.3389/fmolb.2021.661448
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