Transcriptome-wide analysis of small RNA expression in early zebrafish development
- Authors
- Wei, C., Salichos, L., Wittgrove, C.M., Rokas, A., and Patton, J.G.
- ID
- ZDB-PUB-120315-2
- Date
- 2012
- Source
- RNA (New York, N.Y.) 18(5): 915-929 (Journal)
- Registered Authors
- Patton, James G.
- Keywords
- microRNA, zebrafish, piRNA, development
- Datasets
- GEO:GSE27722
- MeSH Terms
-
- Animals
- Base Sequence
- Cluster Analysis
- Gene Expression
- Gene Expression Profiling
- Gene Expression Regulation, Developmental*
- MicroRNAs/chemistry
- MicroRNAs/metabolism*
- Polymorphism, Genetic
- RNA, Small Interfering/chemistry
- RNA, Small Interfering/metabolism*
- RNA, Transfer/chemistry
- Sequence Analysis, RNA
- Transcriptome*
- Zebrafish/genetics*
- Zebrafish/metabolism
- PubMed
- 22408181 Full text @ RNA
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 52 and 32ends of miRNAs, with most extra nucleotides added at the 32 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 32 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.