title: Transcriptome-wide analysis of small RNA expression in early zebrafish development.
abstract: During early vertebrate development, a large number of noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. The exact identity, expression levels, and function for most of these noncoding RNAs remain largely unknown. miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) are two classes of small noncoding RNAs that play important roles in gene regulation during early embryonic development. Here, we utilized next-generation sequencing technology to determine temporal expression patterns for both miRNAs and piRNAs during four distinct stages of early vertebrate development using zebrafish as a model system. For miRNAs, the expression patterns for 198 known miRNAs within 122 different miRNA families and eight novel miRNAs were determined. Significant sequence variation was observed at the 5' and 3'ends of miRNAs, with most extra nucleotides added at the 3' end in a nontemplate directed manner. For the miR-430 family, the addition of adenosine and uracil residues is developmentally regulated and may play a role in miRNA stability during the maternal zygotic transition. Similar modification at the 3' ends of a large number of miRNAs suggests widespread regulation of stability during early development. Beside miRNAs, we also identified a large and unexpectedly diverse set of piRNAs expressed during early development.
authors.affiliation: Department of Biological Sciences, Vanderbilt University, Nashville, Tennessee 37235, USA.
authors.forename: Chunyao
authors.initials: C
authors.lastname: Wei
authors.forename: Leonidas
authors.initials: L
authors.lastname: Salichos
authors.forename: Carli M
authors.initials: CM
authors.lastname: Wittgrove
authors.forename: Antonis
authors.initials: A
authors.lastname: Rokas
authors.forename: James G
authors.initials: JG
authors.lastname: Patton
mesh_terms: D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D015870:Gene Expression; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D035683:MicroRNAs / Q000737:chemistry / Q000378:metabolism*; D011110:Polymorphism, Genetic; D034741:RNA, Small Interfering / Q000737:chemistry / Q000378:metabolism*; D012343:RNA, Transfer / Q000737:chemistry; D017423:Sequence Analysis, RNA; D059467:Transcriptome; D015027:Zebrafish / Q000235:genetics* / Q000378:metabolism
chemical_list: D035683:MicroRNAs; D034741:RNA, Small Interfering; D012343:RNA, Transfer