Small RNAs and gene silencing in zebrafish

Abstract

Small noncoding RNAs including miRNAs and siRNAs play significant roles in gene regulation via the mechanism of RNA interference (RNAi) and have been exploited to conduct loss-of-function studies. The discovery that these small RNAs can regulate genes at the post-transcriptional level by interacting with mRNA targets has enabled researchers to understand their importance in normal cellular processes as well as disease processes. Although extensive findings have been illuminated at the post- transcriptional level, there are still some questions regarding roles of small RNAs at the level of transcription (DNA) using higher vertebrate models. Using zebrafish, we explored a novel transcriptional gene silencing method and found that introduction of transgenes containing convergent transcription units in zebrafish embryos induced stable silencing in cis and trans for reporter (mCherry) and endogenous (One-Eyed Pinhead (OEP) and miR-27a/b) genes. Silencing was mediated by the RNAi enzyme, Dicer and ChIP analyses detected an enrichment of the heterochromatin mark H3K9me3 in the two convergently arranged promoters and in the intervening reading frame. Our work demonstrates that convergent transcription can induce gene silencing in zebrafish providing another tool to create specific temporal and spatial control of gene expression.