Enhancer RNA like function of intergenic inherited lncRNAs during maternal to zygotic transition in zebrafish

The maternal-to-zygotic transition (MZT) is a major developmental event during which inherited transcripts are remodeled and zygotic transcription is established. Although parentally inherited long noncoding RNAs (lncRNAs) are present in early embryos, they have been thought to be dispensable. We have identified more than 2000 inherited lncRNAs in zebrafish embryos, but how these RNAs participate in regulatory programs during early development has remained unexplored. Here, the inheritance of selected zebrafish lncRNAs spanning a broad expression range were confirmed at the pre-MZT stage and full-length sequences were captured by Direct RNA nanopore sequencing. We show that 30% inherited intergenic lncRNAs are preferentially associated with active enhancers, annotated as such in DANIO CODE, whereas non-inherited intergenic lncRNAs rarely overlap with enhancers. Perturbation of five inherited intergenic lncRNAs, individually, using antisense oligonucleotides reduced the expression of their respective neighboring genes at 2.5, 4.3, and/or 6 hours post fertilization, indicating that these RNAs act as positive local regulators during MZT. Together, these findings identify inherited intergenic lncRNAs as enhancer-associated regulators with elncRNA-like properties during early embryogenesis.