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Genome-wide analysis of mRNA decay patterns during early Drosophila development

Stefan Thomsen12, Simon Anders34, Sarath Chandra Janga56, Wolfgang Huber34 and Claudio R Alonso12*

Author Affiliations

1 Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK

2 John Maynard Smith Building, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QG, UK

3 European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK

4 European Molecular Biology Laboratory (EMBL), Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

5 MRC Laboratory of Molecular Biology, (LMB-MRC) Hills Road, Cambridge CB2 0QH, UK

6 Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Drive, Urbana, IL, 61801, USA

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Genome Biology 2010, 11:R93  doi:10.1186/gb-2010-11-9-r93

Published: 21 September 2010

Abstract

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.