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Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs

During eukaryotic translation, mRNAs may form intra-molecular interactions between distant domains. The 5′-cap and the polyA tail were shown to interact through their associated proteins, and this can induce physical compaction of the mRNA in vitro. However, the stability of this intra-molecular ass...

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Detalles Bibliográficos
Autores principales: Eldad, Naama, Yosefzon, Yahav, Arava, Yoav
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2008
Materias:
RNA
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588509/
https://www.ncbi.nlm.nih.gov/pubmed/18948291
http://dx.doi.org/10.1093/nar/gkn754
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author Eldad, Naama
Yosefzon, Yahav
Arava, Yoav
author_facet Eldad, Naama
Yosefzon, Yahav
Arava, Yoav
author_sort Eldad, Naama
collection PubMed
description During eukaryotic translation, mRNAs may form intra-molecular interactions between distant domains. The 5′-cap and the polyA tail were shown to interact through their associated proteins, and this can induce physical compaction of the mRNA in vitro. However, the stability of this intra-molecular association in translating mRNAs and whether additional contacts exist in vivo are largely unknown. To explore this, we applied a novel approach in which several endogenous polysomal mRNAs from Saccharomyces cerevisiae were cleaved near their stop codon and the resulting 3′-UTR fragments were tested either for co-sedimentation or co-immunoprecipitation (co-IP) with their ORFs. In all cases a significant fraction of the 3′-UTR fragments sedimented similarly to their ORF-containing fragments, yet the extent of co-sedimentation differed between mRNAs. Similar observations were obtained by a co-IP assay. Interestingly, various treatments that are expected to interfere with the cap to polyA interactions had no effect on the co-sedimentation pattern. Moreover, the 3′-UTR appeared to co-sediment with different regions from within the ORF. Taken together, these results indicate extensive physical associations between 3′-UTRs and their ORFs that vary between genes. This implies that polyribosomal mRNAs are in a compact configuration in vivo.
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spelling pubmed-25885092009-03-04 Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs Eldad, Naama Yosefzon, Yahav Arava, Yoav Nucleic Acids Res RNA During eukaryotic translation, mRNAs may form intra-molecular interactions between distant domains. The 5′-cap and the polyA tail were shown to interact through their associated proteins, and this can induce physical compaction of the mRNA in vitro. However, the stability of this intra-molecular association in translating mRNAs and whether additional contacts exist in vivo are largely unknown. To explore this, we applied a novel approach in which several endogenous polysomal mRNAs from Saccharomyces cerevisiae were cleaved near their stop codon and the resulting 3′-UTR fragments were tested either for co-sedimentation or co-immunoprecipitation (co-IP) with their ORFs. In all cases a significant fraction of the 3′-UTR fragments sedimented similarly to their ORF-containing fragments, yet the extent of co-sedimentation differed between mRNAs. Similar observations were obtained by a co-IP assay. Interestingly, various treatments that are expected to interfere with the cap to polyA interactions had no effect on the co-sedimentation pattern. Moreover, the 3′-UTR appeared to co-sediment with different regions from within the ORF. Taken together, these results indicate extensive physical associations between 3′-UTRs and their ORFs that vary between genes. This implies that polyribosomal mRNAs are in a compact configuration in vivo. Oxford University Press 2008-12 2008-10-23 /pmc/articles/PMC2588509/ /pubmed/18948291 http://dx.doi.org/10.1093/nar/gkn754 Text en © 2008 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle RNA
Eldad, Naama
Yosefzon, Yahav
Arava, Yoav
Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs
title Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs
title_full Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs
title_fullStr Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs
title_full_unstemmed Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs
title_short Identification and characterization of extensive intra-molecular associations between 3′-UTRs and their ORFs
title_sort identification and characterization of extensive intra-molecular associations between 3′-utrs and their orfs
topic RNA
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2588509/
https://www.ncbi.nlm.nih.gov/pubmed/18948291
http://dx.doi.org/10.1093/nar/gkn754
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