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Genome-wide analysis of mRNA decay patterns during early Drosophila development
BACKGROUND: The modulation of mRNA levels across tissues and time is key for the establishment and operation of the developmental programs that transform the fertilized egg into a fully formed embryo. Although the developmental mechanisms leading to differential mRNA synthesis are heavily investigat...
Autores principales: | , , , , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2010
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965385/ https://www.ncbi.nlm.nih.gov/pubmed/20858238 http://dx.doi.org/10.1186/gb-2010-11-9-r93 |
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author | Thomsen, Stefan Anders, Simon Janga, Sarath Chandra Huber, Wolfgang Alonso, Claudio R |
author_facet | Thomsen, Stefan Anders, Simon Janga, Sarath Chandra Huber, Wolfgang Alonso, Claudio R |
author_sort | Thomsen, Stefan |
collection | PubMed |
description | BACKGROUND: The modulation of mRNA levels across tissues and time is key for the establishment and operation of the developmental programs that transform the fertilized egg into a fully formed embryo. Although the developmental mechanisms leading to differential mRNA synthesis are heavily investigated, comparatively little attention is given to the processes of mRNA degradation and how these relate to the molecular programs controlling development. RESULTS: Here we combine timed collection of Drosophila embryos and unfertilized eggs with genome-wide microarray technology to determine the degradation patterns of all mRNAs present during early fruit fly development. Our work studies the kinetics of mRNA decay, the contributions of maternally and zygotically encoded factors to mRNA degradation, and the ways in which mRNA decay profiles relate to gene function, mRNA localization patterns, translation rates and protein turnover. We also detect cis-regulatory sequences enriched in transcripts with common degradation patterns and propose several proteins and microRNAs as developmental regulators of mRNA decay during early fruit fly development. Finally, we experimentally validate the effects of a subset of cis-regulatory sequences and trans-regulators in vivo. CONCLUSIONS: Our work advances the current understanding of the processes controlling mRNA degradation during early Drosophila development, taking us one step closer to the understanding of mRNA decay processes in all animals. Our data also provide a valuable resource for further experimental and computational studies investigating the process of mRNA decay. |
format | Text |
id | pubmed-2965385 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2010 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-29653852010-10-28 Genome-wide analysis of mRNA decay patterns during early Drosophila development Thomsen, Stefan Anders, Simon Janga, Sarath Chandra Huber, Wolfgang Alonso, Claudio R Genome Biol Research BACKGROUND: The modulation of mRNA levels across tissues and time is key for the establishment and operation of the developmental programs that transform the fertilized egg into a fully formed embryo. Although the developmental mechanisms leading to differential mRNA synthesis are heavily investigated, comparatively little attention is given to the processes of mRNA degradation and how these relate to the molecular programs controlling development. RESULTS: Here we combine timed collection of Drosophila embryos and unfertilized eggs with genome-wide microarray technology to determine the degradation patterns of all mRNAs present during early fruit fly development. Our work studies the kinetics of mRNA decay, the contributions of maternally and zygotically encoded factors to mRNA degradation, and the ways in which mRNA decay profiles relate to gene function, mRNA localization patterns, translation rates and protein turnover. We also detect cis-regulatory sequences enriched in transcripts with common degradation patterns and propose several proteins and microRNAs as developmental regulators of mRNA decay during early fruit fly development. Finally, we experimentally validate the effects of a subset of cis-regulatory sequences and trans-regulators in vivo. CONCLUSIONS: Our work advances the current understanding of the processes controlling mRNA degradation during early Drosophila development, taking us one step closer to the understanding of mRNA decay processes in all animals. Our data also provide a valuable resource for further experimental and computational studies investigating the process of mRNA decay. BioMed Central 2010 2010-09-21 /pmc/articles/PMC2965385/ /pubmed/20858238 http://dx.doi.org/10.1186/gb-2010-11-9-r93 Text en Copyright ©2010 Thomsen 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 Thomsen, Stefan Anders, Simon Janga, Sarath Chandra Huber, Wolfgang Alonso, Claudio R Genome-wide analysis of mRNA decay patterns during early Drosophila development |
title | Genome-wide analysis of mRNA decay patterns during early Drosophila development |
title_full | Genome-wide analysis of mRNA decay patterns during early Drosophila development |
title_fullStr | Genome-wide analysis of mRNA decay patterns during early Drosophila development |
title_full_unstemmed | Genome-wide analysis of mRNA decay patterns during early Drosophila development |
title_short | Genome-wide analysis of mRNA decay patterns during early Drosophila development |
title_sort | genome-wide analysis of mrna decay patterns during early drosophila development |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2965385/ https://www.ncbi.nlm.nih.gov/pubmed/20858238 http://dx.doi.org/10.1186/gb-2010-11-9-r93 |
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