Individual long non-coding RNAs have no overt functions in zebrafish embryogenesis, viability and fertility.

Mehdi Goudarzi,Alexander F Schier,Lindsey M Pieper,Kathryn Berg

doi:10.7554/elife.40815

Mehdi Goudarzi, Alexander F Schier + Show 2 more

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https://doi.org/10.7554/elife.40815

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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.

Highlights

Long non-coding RNAs comprise a heterogeneous group of transcripts longer than 200 nucleotides that do not encode proteins
Morpholinos targeting the evolutionarily conserved Long non-coding RNAs (lncRNAs) megamind (TUNA (Lin et al, 2014)) and cyrano resulted in embryonic defects (Ulitsky et al, 2011)
These conflicting results have led to a controversy about the importance of lncRNAs for vertebrate development (Sauvageau et al, 2013), (Han et al, 2018)

Summary

Introduction

Long non-coding RNAs (lncRNAs) comprise a heterogeneous group of transcripts longer than 200 nucleotides that do not encode proteins. Chromosomes and Gene Expression Developmental Biology a group of selected zebrafish lncRNAs using CRISPR-Cas9, and assay their roles in embryogenesis, viability and fertility. For our mutant analysis we selected 24 bona fide lncRNAs based on synteny (conserved relative position on at least one other vertebrate genome), sequence conservation, expression dynamics (expression levels, onset and pattern) and proximity to developmental regulatory genes (see Table 1).

Results

Conclusion