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Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

ABSTRACT: Here we report on genome-wide small RNA and transcriptome profiling of blastula, gastrula and neurula-stage Xenopus tropicalis embryos using deep sequencing. By combining bioinformatic analysis of the small RNA-seq dataset with experimental validation, we identify novel microRNAs and Piwi-interacting RNAs. We show that microRNA expression is highly dynamic and spatially localized in early embryos in contrast to Piwi-interacting RNAs, and we validate a novel microRNA prediction pipeline. We go on to identify a new class of small intronic non-coding RNAs, that we name sincRNAs. On a genome-wide scale we find that genes containing sincRNA clusters are transcriptionally repressed. Our data suggest a novel mechanism of sincRNA-mediated gene silencing in vertebrates.

ORGANISM(S): Xenopus tropicalis

PROVIDER: GSE38605 | GEO | 2013/09/23

SECONDARY ACCESSION(S): PRJNA168208

REPOSITORIES: GEO

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Genome-wide small RNA profiling and mRNA profiling of Xenopus embryos

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