Long noncoding RNAs implicated in embryonic development in Ybx1 knockout zebrafish

Chen Huang, Bo Zhu, Dongliang Leng, Wei Ge, Xiaohua Douglas Zhang

Research output: Contribution to journalArticlepeer-review

4 Scopus citations

Abstract

Y-box-binding protein 1 (Ybx1, YB-1), also known as Y-box transcription factor, is involved in a variety of biological processes (BPs) and pathways, including embryogenesis, reproduction and development in vertebrates. Several noncoding RNAs regulate Ybx1 signaling. However, the role of long noncoding RNAs (lncRNAs) in embryogenesis remains incompletely understood. Here, we investigated the possible involvement of lncRNAs in Ybx1-mediated regulation of vertebrate development by performing systematic transcriptome analysis of RNA sequencing data derived from ybx1 homozygous mutant zebrafish on day 5 (day5_ybx1−/−) and wild-type zebrafish on days 5 and 6 (day5_ybx1+/+ and day6_ybx1+/+). We identified several lncRNAs affected by ybx1 disruption that may target reduction–oxidation-related genes, such as duox (NADPH oxidase) and noxo1a (NADPH oxidase organizer). Knockdown of three selected lncRNAs led to morphological deformation of larvae, implying an involvement of these lncRNAs in zebrafish embryo development. In summary, our study provides new insights into the lncRNA-mediated mechanisms underlying development in Ybx1-deficient zebrafish larvae.

Original languageEnglish
Pages (from-to)1259-1276
Number of pages18
JournalFEBS Open Bio
Volume11
Issue number4
DOIs
StatePublished - Apr 2021

Bibliographical note

Funding Information:
The authors thank Kuan Cheok Lei for the suggestions of manuscript revision. A preprint version of this manuscript has been released at bioRxiv [42]. This work was funded by University of Macau through research grants MYRG2018-00071-FHS, EF005/FHS-ZXH/2018/GSTIC and FHS-CRDA-029-002-2017, and by the Science and Technology Development Fund, Macau SAR (File no. 0004/2019/AFJ and 0011/2019/AKP).

Publisher Copyright:
© 2020 The Authors. FEBS Open Bio published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.

Keywords

  • deep RNA sequencing
  • long noncoding RNAs
  • REDOX
  • YBX1
  • zebrafish embryo development

ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology (all)

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