Small RNA Expression And Function In Zebrafish Early Embryonic Development

During zebrafish early embryogenesis, a large number of small noncoding RNAs are maternally inherited or expressed upon activation of zygotic transcription. However, the exact identity, expression levels, and function for most of these noncoding RNAs remain largely unknown. Herein, we utilized next-generation sequencing technology to determine temporal expression patterns for noncoding RNAs in zebrafish gametes and early embryos of16-cell (cleavage stage), lk-cell (blastula stage),5.7hr (gastrula-stage). The results show miRNAs (microRNAs) and piRNAs (piwi-interacting RNAs) and other small RNAs are abundant in both gametes and all examined early embryos. Relative amount of miRNAs increases significantly in post-MBT5.7hr embryos which may facilitate the degradation of maternal deposite factors upon zygotic gene activation. Especially, in5.7hr embryos, miR-430family themselves accounted for20%of the total expressed small RNAs which has been shown to degrade maternal deposit genes. Additionally, we identified that piRNAs is highly expressed not only in the sperm and egg, but also in early embryos. piRNA clusters are significantly enriched in anti-sense strand of transposon elements which is consistent with its function in repression of transposon. Meanwhile, a striking amount of piRNAs also map to CpG island, genetic regions, and non-coding RNA regions. We also found that some rRNA and tRNA derived small RNAs show temporal expression pattern during early embryogenesis. Further investigation is needed to explore their functions. Taken together, our study systematically explored the temporal expression of small RNAs in zebrafish gametes and early embryos which set a stage for further studies on the function of small RNA in zebrafish early embryogenesis.