Transcriptomics,Genomics

Dataset Information

35

Pumilio regulates mRNA decay during the late maternal-to-zygotic transition in Drosophila melanogaster


ABSTRACT: Pumilio (PUM) is a Drosophila member of a conserved family of sequence-specific RNA-binding proteins that have been shown to regulate mRNA stability and/or translation in a variety of organisms. PUM has been shown to repress the translation of several mRNAs in the Drosophila early embryo; failure to repress these targets leads to lethal developmental defects. Here we use a combination of microarray-based gene expression profiling and next-generation sequencing to identify more than 200 mRNAs that are associated with full-length PUM protein in early embryos and to define a global role for PUM in mRNA decay. Surprisingly, despite the fact that PUM is maternally supplied and thus is present from the beginning of embryogenesis, the vast majority of PUM-directed decay occurs only after zygotic genome activation. We show that the smaug mRNA, which itself encodes an RNA-binding protein that directs transcript decay, is a direct target of PUM via binding sites in the smg 3'UTR. Whereas the endogenous smaug mRNA and the transgenic reporter mRNA that carries the smaug 3'UTR undergo decay after zygotic genome activation, a reporter with an array of PUM-binding sites decays before zygotic genome activation. These data support a model in which additional cis-elements in the smg 3'UTR delay decay until after zygotic genome activation. Overall design: Comparison of mRNA expression levels between cold-sensitive pum13/pumMsc embryos and corresponding wild-type controls at 18°C; and between pumET7/pumMsc embryos and corresponding wild-type controls at 25°C. The comparison of pum13/pumMsc embryos with their corresponding wild-type controls was done in two replicates: one was a direct comparison between pum13/pumMsc and wild-type samples at corresponding time points; the replicate was a comparison of pum13/pumMsc and corresponding wild-type time points through a common reference, wild-type stage 14 oocytes. The comparison of pumET7/pumMsc and corresponding wild-type samples was done with two replicates, each of which used a common reference (wild-type stage 14 oocytes).

INSTRUMENT(S): Agilent-019871 Hughes Fly 44K v1.0 array (Feature Number version)

SUBMITTER: Howard D Lipshitz  

PROVIDER: GSE48645 | GEO | 2017-07-01

SECONDARY ACCESSION(S): PRJNA211092

REPOSITORIES: GEO

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