The Long Noncoding RNA Landscape of Cardiac Regeneration in Zebrafish

Abstract

Background: Novel therapeutic targets of heart failure (HF) are needed. Long noncoding RNAs (lncRNAs) are engaged during cardiac regeneration. Unlike in humans, zebrafish naturally undergo cardiac regeneration after HF. We aimed to describe the landscape of lncRNAs during regeneration in a zebrafish model of HF and to investigate their human homologs.

Methods: HF was established in adult zebrafish through thrice-weekly incubations with an anemia-inducing drug, phenylhydrazine hydrochloride (PHZ). After 5 weeks, PHZ treatment ceased and the fish were followed through a regeneration period of 14 days. Total RNA was extracted from the hearts of adult zebrafish after establishment of HF and at 2, 5, and 9 days after treatment cessation (9 hearts per condition at each time point). Gene regulation patterns were characterized with the use of bioinformatics and validated with the use of quantitative polymerase chain reaction.

Results: We obtained 14,340 lncRNAs from the reannotated Affymetrix zebrafish microarray. Of these, 187 lncRNAs were found to be differentially expressed (false discovery rate < 0.05 and fold change ≥ 2) at at least 1 time point. 85% of differentially expressed lncRNAs overlapped or were close to (distance < 10 kb) protein-coding genes which were mostly related to muscle development in Gene Ontology analyses. Fifty-seven lncRNAs had human homologs, according to orientation relative to their conserved protein-coding neighbours.

Conclusions: LncRNAs are differentially expressed during regeneration after HF in adult zebrafish and could be potential future therapeutic targets. The extent to which lncRNAs contribute to cardiac regeneration is a worthy avenue for future research.