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PMID: 20858238 Published · ppublish English Journal Article Research Support, Non-U.S. Gov't

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

Genome biology ·Vol. 11 ·No. 9 ·2010-00-00 ·Pages R93

Thomsen S, Anders S, Janga SC, Huber W, Alonso CR

Abstract

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. 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. 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.

MeSH Terms
Animals Drosophila Proteins/metabolism Drosophila melanogaster/embryology,genetics,metabolism Embryo, Nonmammalian/embryology,metabolism Embryonic Development/genetics Gene Expression Regulation, Developmental Genome, Insect MicroRNAs/genetics,metabolism Oligonucleotide Array Sequence Analysis Ovum Polymerase Chain Reaction RNA Stability RNA, Messenger/genetics,metabolism Regulatory Sequences, Ribonucleic Acid Transcription, Genetic
Chemicals
Drosophila Proteins MicroRNAs RNA, Messenger Regulatory Sequences, Ribonucleic Acid
Authors & Affiliations
5 authors, click to expand affiliations / ORCID
Thomsen Stefan
Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK. S.Thomsen@sussex.ac.uk
Anders Simon
Janga Sarath Chandra
Huber Wolfgang
Alonso Claudio R
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Article Info
Journal
Genome biology
Abbr.
Genome Biol
ISSN
1474-760X
DOI
10.1186/gb-2010-11-9-r93
Email
s.thomsen@sussex.ac.uk
Published
2010-00-00
Epub
2010-00-21
Pages
R93
Language
English
Region
England
NLM ID
100960660
PMCID
PMC2965385
Subset
IM
Grants
Biotechnology and Biological Sciences Research Council · United Kingdom
Medical Research Council · United Kingdom
External Links
PubMed source DOI: 10.1186/gb-2010-11-9-r93 PMC Full Text View journal details
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