Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility
- Harvard University, United States
Abstract
Hundreds of long non-coding RNAs (lncRNAs) have been identified as potential regulators of gene expression, but their functions remain largely unknown. To study the role of lncRNAs during vertebrate development, we selected 25 zebrafish lncRNAs based on their conservation, expression profile or proximity to developmental regulators, and used CRISPR-Cas9 to generate 32 deletion alleles. We observed altered transcription of neighboring genes in some mutants, but none of the lncRNAs were required for embryogenesis, viability or fertility. Even RNAs with previously proposed non-coding functions (cyrano and squint) and other conserved lncRNAs (gas5 and lnc-setd1ba) were dispensable. In one case (lnc-phox2bb), absence of putative DNA regulatory-elements, but not of the lncRNA transcript itself, resulted in abnormal development. LncRNAs might have redundant, subtle, or context-dependent roles, but extrapolation from our results suggests that the majority of individual zebrafish lncRNAs have no overt roles in embryogenesis, viability and fertility.
Data availability
All data generated or analyzed during this study are included in the manuscript and supporting files.Previously published datasets used in this manuscript:SRP013950, GSE32880, GSE37453, GSE32898, GSE46512
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Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution.NCBI Gene Expression Omnibus, GSE32880.
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Extensive alternative polyadenylation during zebrafish development.NCBI Gene Expression Omnibus, GSE37453.
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Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis.NCBI Gene Expression Omnibus, GSE32898.
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Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs.NCBI Gene Expression Omnibus, GSE46512.
Article and author information
Author details
Alexander F Schier
Funding
NIH Office of the Director (R01HD076708)
- Alexander F Schier
Leopoldina (Postdoctorial fellowship LPDS2014-01)
- Mehdi Goudarzi
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2019, Goudarzi et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility
eLife 8:e40815.
https://doi.org/10.7554/eLife.40815
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