The mRNA-bound proteome of the early fly embryo
- Hans-Hermann Wessels1,4,
- Koshi Imami1,4,
- Alexander G. Baltz1,
- Marcin Kolinski1,
- Anastasia Beldovskaya2,
- Matthias Selbach1,
- Stephen Small2,
- Uwe Ohler1,3 and
- Markus Landthaler1
- 1Berlin Institute for Medical Systems Biology, Max-Delbrück-Center for Molecular Medicine, 13125 Berlin, Germany;
- 2Department of Biology, New York University, New York, New York 10003, USA;
- 3Department of Biology, Humboldt University, 10115 Berlin, Germany
- Corresponding authors: uwe.ohler{at}mdc-berlin.de, markus.landthaler{at}mdc-berlin.de
-
↵4 These authors contributed equally to this work.
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.
Footnotes
-
[Supplemental material is available for this article.]
-
Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.200386.115.
-
Freely available online through the Genome Research Open Access option.
- Received September 30, 2015.
- Accepted April 26, 2016.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
