Dataset Information

Drosophila mRNA Interactome - Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila

ABSTRACT: The maternal-to-zygotic transition (MZT) is a process that occurs in animal embryos at the earliest developmental stages, during which maternally deposited mRNAs and other molecules are degraded and replaced by products of the zygotic genome. The zygotic genome is not activated immediately upon fertilization, therefore post-transcriptional mechanisms control the first steps of development in the early, pre-MZT embryo. To perform unbiased organism-wide identification of Drosophila RNA binding proteins (RPBs), crucial players of post-transcriptional control, we applied the recently developed RNA interactome capture method, which involves cross-linking of RNAs and their direct protein partners by UV light, purification of RNA under stringent conditions and identification of proteins by mass spectrometry. Our analysis yielded 523 high confidence RBP hits, half of which were not previously reported to bind RNA. Our comparison of the RNA interactomes of pre- and post-MZT embryos reveals a highly dynamic behavior of the RNA-bound proteome during early development, and suggests active regulation of RNA binding of some RBPs. This resource provides the first evidence of RNA binding for hundreds of Drosophila proteins, and opens new avenues for study of molecular mechanisms of early development.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Drosophila Melanogaster (fruit Fly)

TISSUE(S): Embryo

SUBMITTER: Christian Frese

LAB HEAD: Jeroen Krijgsveld

PROVIDER: PXD003882 | Pride | 2016-07-11

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	140519_CF_v_proteome_fr0_30p.raw	Raw
	140519_CF_v_proteome_fr1_30p.raw	Raw
	140519_CF_v_proteome_fr2_30p.raw	Raw
	140519_CF_v_proteome_fr3_30p.raw	Raw
	140519_CF_v_proteome_fr4_30p.raw	Raw

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Publications

Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in Drosophila.

Sysoev Vasiliy O VO Fischer Bernd B Frese Christian K CK Gupta Ishaan I Krijgsveld Jeroen J Hentze Matthias W MW Castello Alfredo A Ephrussi Anne A

Nature communications 20160705

The maternal-to-zygotic transition (MZT) is a process that occurs in animal embryos at the earliest developmental stages, during which maternally deposited mRNAs and other molecules are degraded and replaced by products of the zygotic genome. The zygotic genome is not activated immediately upon fertilization, and in the pre-MZT embryo post-transcriptional control by RNA-binding proteins (RBPs) orchestrates the first steps of development. To identify relevant Drosophila RBPs organism-wide, we ref ...[more]

PMID: 27378189

Similar Datasets

Project description:Background: During the maternal-to-zygotic transition (MZT) vast changes in the embryonic transcriptome are produced by a combination of two processes: elimination of maternally provided mRNAs and synthesis of new transcripts from the zygotic genome. Previous genome-wide analyses of the MZT have been restricted to whole embryos. Here we report the first such analysis for primordial germ cells (PGCs), the progenitors of the germ-line stem cells. Results: We purified PGCs from Drosophila embryos, defined their proteome and transcriptome, and assessed the content, scale and dynamics of their MZT. Transcripts encoding proteins that implement particular types of biological functions group into nine distinct expression profiles, reflecting coordinate control at the transcriptional and posttranscriptional levels. mRNAs encoding germ-plasm components and cell-cell signaling molecules are rapidly degraded while new transcription produces mRNAs encoding the core transcriptional and protein synthetic machineries. The RNA-binding protein, Smaug, is essential for the PGC MZT, clearing transcripts encoding proteins that regulate stem cell behavior, transcriptional and posttranscriptional processes. Computational analyses suggest that Smaug and AU-rich element binding-proteins function independently to control transcript elimination. Conclusion: The scale of the MZT is similar in the soma and PGCs. However, the timing and content of their MZTs differ, reflecting the distinct developmental imperatives of these cell types. The PGC MZT is delayed relative to that in the soma, likely because relief of PGC-specific transcriptional silencing is required for zygotic genome activation as well as for efficient maternal transcript clearance. There are 26 samples in total, including 1-to-3 hour, 3-to-5 hour, 5-to-7 hour PGCs in wild type and smaug mutant flies and 1-to-3 hour somatic cells in wild type flies. Except for the 1-to-3 hour and 3-to-5 hour smaug mutant PGCs which have three replicates, all the other samples have four replicates.