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Genome Res. 2016 Jul;26(7):1000-9. doi: 10.1101/gr.200386.115. Epub 2016 Apr 28.

The mRNA-bound proteome of the early fly embryo.

Author information

1
Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany;
2
Department of Biology, New York University, New York, New York 10003, USA;
3
Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany; Department of Biology, Humboldt University, 10115 Berlin, Germany.

Abstract

Early embryogenesis is characterized by the maternal to zygotic transition (MZT), in which maternally deposited messenger RNAs are degraded while zygotic transcription begins. Before the MZT, post-transcriptional gene regulation by RNA-binding proteins (RBPs) is the dominant force in embryo patterning. We used two mRNA interactome capture methods to identify RBPs bound to polyadenylated transcripts within the first 2 h of Drosophila melanogaster embryogenesis. We identified a high-confidence set of 476 putative RBPs and confirmed RNA-binding activities for most of 24 tested candidates. Most proteins in the interactome are known RBPs or harbor canonical RBP features, but 99 exhibited previously uncharacterized RNA-binding activity. mRNA-bound RBPs and TFs exhibit distinct expression dynamics, in which the newly identified RBPs dominate the first 2 h of embryonic development. Integrating our resource with in situ hybridization data from existing databases showed that mRNAs encoding RBPs are enriched in posterior regions of the early embryo, suggesting their general importance in posterior patterning and germ cell maturation.

PMID:
27197210
PMCID:
PMC4937569
DOI:
10.1101/gr.200386.115
[Indexed for MEDLINE]
Free PMC Article

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