title: Characterization of small RNAs in X. tropicalis gastrulae.
abstract: Here, we report and characterize deep sequencing data and bioinformatics analysis of small RNAs from X. tropicalis gastrula. A total of 17,553,124 reads with perfect match to the genome derived from 2,616,053 unique sequences were identified. Seventy-seven percent of theses sequences were not found in previous reports from X. tropicalis oocytes and somatic tissues. Bioinformatics analyses indicate that a large fraction of the small RNAs are PIWI-interacting RNAs. Up to 23.9% of small RNAs mapped to transposable elements and 27% to genic regions. Most of the abundant transposon-derived small RNAs are found in oocyte and gastrula libraries, suggesting that transposons also need to be silenced during early embryonic development. Importantly, novel clusters of piRNAs whose expression is activated after zygotic transcription begins were identified in the genome of X. tropicalis. Additionally, miRNAs were also identified and many of them are not present in oocytes, suggesting that miRNA expression is stage-specific. To the best of our knowledge, this is the first high throughput data release and bioinformatics characterization of small RNAs during Xenopus early embryonic development.
authors.affiliation: Center for Aging and Regeneration and Millennium Nucleus in Regenerative Biology, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, Chile. ffaunes@uc.cl
authors.forename: Fernando
authors.initials: F
authors.lastname: Faunes
authors.forename: Leonardo I
authors.initials: LI
authors.lastname: Almonacid
authors.forename: Francisco
authors.initials: F
authors.lastname: Melo
authors.forename: Juan
authors.initials: J
authors.lastname: Larrain
mesh_terms: D000818:Animals; D001483:Base Sequence; D002874:Chromosome Mapping; D019295:Computational Biology; D004251:DNA Transposable Elements; D004625:Embryo, Nonmammalian; D047108:Embryonic Development; D005775:Gastrula / Q000378:metabolism*; D054262:Gastrulation / Q000235:genetics*; D018507:Gene Expression Regulation, Developmental; D015698:Genomic Library; D059014:High-Throughput Nucleotide Sequencing; D008969:Molecular Sequence Data; D009865:Oocytes / Q000502:physiology; D058727:RNA, Small Untranslated / Q000737:chemistry / Q000235:genetics* / Q000302:isolation & purification; D017422:Sequence Analysis, DNA; D014981:Xenopus / Q000235:genetics*
chemical_list: D004251:DNA Transposable Elements; D058727:RNA, Small Untranslated