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Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae
BACKGROUND: Protein-RNA interactions are integral components of nearly every aspect of biology, including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast l...
Autores principales: | , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053964/ https://www.ncbi.nlm.nih.gov/pubmed/23409723 http://dx.doi.org/10.1186/gb-2013-14-2-r13 |
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author | Freeberg, Mallory A Han, Ting Moresco, James J Kong, Andy Yang, Yu-Cheng Lu, Zhi John Yates, John R Kim, John K |
author_facet | Freeberg, Mallory A Han, Ting Moresco, James J Kong, Andy Yang, Yu-Cheng Lu, Zhi John Yates, John R Kim, John K |
author_sort | Freeberg, Mallory A |
collection | PubMed |
description | BACKGROUND: Protein-RNA interactions are integral components of nearly every aspect of biology, including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions. RESULTS: Here, we describe the gPAR-CLIP (global photoactivatable-ribonucleoside-enhanced crosslinking and immunopurification) approach for capturing regions of the untranslated, polyadenylated transcriptome bound by RNA-binding proteins (RBPs) in budding yeast. We report over 13,000 RBP crosslinking sites in untranslated regions (UTRs) covering 72% of protein-coding transcripts encoded in the genome, confirming 3' UTRs as major sites for RBP interaction. Comparative genomic analyses reveal that RBP crosslinking sites are highly conserved, and RNA folding predictions indicate that secondary structural elements are constrained by protein binding and may serve as generalizable modes of RNA recognition. Finally, 38% of 3' UTR crosslinking sites show changes in RBP occupancy upon glucose or nitrogen deprivation, with major impacts on metabolic pathways as well as mitochondrial and ribosomal gene expression. CONCLUSIONS: Our study offers an unprecedented view of the pervasiveness and dynamics of protein-RNA interactions in vivo. |
format | Online Article Text |
id | pubmed-4053964 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-40539642014-06-12 Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae Freeberg, Mallory A Han, Ting Moresco, James J Kong, Andy Yang, Yu-Cheng Lu, Zhi John Yates, John R Kim, John K Genome Biol Research BACKGROUND: Protein-RNA interactions are integral components of nearly every aspect of biology, including regulation of gene expression, assembly of cellular architectures, and pathogenesis of human diseases. However, studies in the past few decades have only uncovered a small fraction of the vast landscape of the protein-RNA interactome in any organism, and even less is known about the dynamics of protein-RNA interactions under changing developmental and environmental conditions. RESULTS: Here, we describe the gPAR-CLIP (global photoactivatable-ribonucleoside-enhanced crosslinking and immunopurification) approach for capturing regions of the untranslated, polyadenylated transcriptome bound by RNA-binding proteins (RBPs) in budding yeast. We report over 13,000 RBP crosslinking sites in untranslated regions (UTRs) covering 72% of protein-coding transcripts encoded in the genome, confirming 3' UTRs as major sites for RBP interaction. Comparative genomic analyses reveal that RBP crosslinking sites are highly conserved, and RNA folding predictions indicate that secondary structural elements are constrained by protein binding and may serve as generalizable modes of RNA recognition. Finally, 38% of 3' UTR crosslinking sites show changes in RBP occupancy upon glucose or nitrogen deprivation, with major impacts on metabolic pathways as well as mitochondrial and ribosomal gene expression. CONCLUSIONS: Our study offers an unprecedented view of the pervasiveness and dynamics of protein-RNA interactions in vivo. BioMed Central 2013 2013-02-14 /pmc/articles/PMC4053964/ /pubmed/23409723 http://dx.doi.org/10.1186/gb-2013-14-2-r13 Text en Copyright © 2013 Freeberg et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Freeberg, Mallory A Han, Ting Moresco, James J Kong, Andy Yang, Yu-Cheng Lu, Zhi John Yates, John R Kim, John K Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae |
title | Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae |
title_full | Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae |
title_fullStr | Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae |
title_full_unstemmed | Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae |
title_short | Pervasive and dynamic protein binding sites of the mRNA transcriptome in Saccharomyces cerevisiae |
title_sort | pervasive and dynamic protein binding sites of the mrna transcriptome in saccharomyces cerevisiae |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053964/ https://www.ncbi.nlm.nih.gov/pubmed/23409723 http://dx.doi.org/10.1186/gb-2013-14-2-r13 |
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