The lncRNAs Implicated in Redox Regulation in Ybx1 Deficient Zebrafish Larvae

Abstract

Ybx1 has been demonstrated as a crucial gene in embryogenesis, reproduction as well as development in various vertebrates such as mouse and zebrafish. However, the underlying lncRNA-mediated mechanisms require deep investigation. Particularly, the importance of lncRNA to vertebrate development is controversial and questionable since many studies have yielded contradictory conclusions for the same lncRNAs. In the present study, in order to disclose the lncRNAs implicated in vertebrate development, a systematic transcriptome analysis is conducted based on the RNA sequencing data derived from ybx1 homozygous mutant zebrafish on day5 (day5_ybx1-/-) as well as wild type zebrafish on day5 and day6 (day5_ybx1+/+, day6_ybx1+/+). A high-confidence dataset of zebrafish lncRNAs is detected using a stepwise filtering pipeline. Differential expression analysis and co-expression network analysis reveal that several lncRNAs probably act on duox and noxo1a, the genes related to redox (reduction-oxidation reaction) processes which are triggered by ybx1 disruption. Validation by an experimental study on three selected lncRNAs indicates that knockdown of all selected lncRNAs leads to morphological deformation of larvae. In addition, our experiments effectively support the prediction of network analysis in many interaction patterns between the selected lncRNAs and the two redox genes (duox, noxo1a). In short, our study provides new insights into the function and mechanism of lncRNAs implicated in zebrafish embryonic development and demonstrates the importance of lncRNAs in vertebrate development.\n\nAuthor SummaryLncRNAs has been emerged as key regulatory layers because of their multiple functions in diverse biological processes and pathways. However, there is disagreement about the roles of lncRNAs in vertebrate development Some cases demonstrated that lncRNAs was important to development. Others showed that lncRNAs just have feeble functions in development. On the other hand, Ybx1 processing multi-functions has been well demonstrated as a key protein to most vertebrate in development. Hence, aimed at disclosure of key lncRNAs implicated in vertebrate development as well as their possible roles, we performed a systematic transcriptome analysis based on the deep RNA sequencing data of ybx1 homozygous mutant zebrafish and wild type zebrafish. Our analysis successfully revealed several lncRNAs probably target on the redox-related genes. Furthermore, our experiments validated the importance of these lncRNAs to zebrafish embryo development. This study is the first to utilize Ybx1 as breakpoint to identify key lncRNA related to vertebrate development and provides new insights into underlying mechanisms of lncRNAs in development.