New article by IIMCB scientists in Nature Communications

The key message of the article is the discovery of the phenomenon of A-to-I RNA editing, which entails the modification of the RNA genetic code from that encoded in the DNA, in the zebrafish. It was also found that this process is necessary for proper embryonic development in the early life of the zebrafish, while it is required for regulating the innate immune response at a later stage of life.

A-to-I editing is necessary for regulating the innate immune system in human and mammals and it is implicated in human diseases, including autoimmune conditions – that’s according to a study conducted by a group of researchers, e.g. Cecilia Winata, PhD Dsc Habil and prof. dr hab. Matthias Bochtler from the International Institute of Molecular and Cell Biology in Warsaw (among others).

The discovery of a conserved role in zebrafish  opens up new possibilities for modelling related human diseases in this model organism to better understand disease mechanism and inform future developments of therapy. Moreover, precise editing of nucleic acid using RNA editing enzymes such as ADAR could potentially be exploited for developing targeted genetic therapy.

In this manuscript, the authors report distinct maternal and zygotic functions of  ADAR-mediated RNA editing in embryonic patterning along the zebrafish antero-posterior and dorso-ventral axes, and in the regulation of innate immune response, respectively.

A-to-I editing entails the deamination of adenosine (A) at the C6 position, giving rise to an inosine (I). Enzymes known as Adenosine Deaminase Acting on RNA (ADAR) are responsible for catalyzing this process. Zebrafish adar is highly expressed in the earliest stages of embryogenesis. Through Adar loss- or gain-of-function experiments, we demonstrated that maternal Adar function is essential for establishing the anteroposterior and dorsoventral body axes, as well as embryonic patterning along these axes. This function is dependent on an intact deaminase domain. Genome-wide editing discovery by combined analyses of parental genome and embryonic transcriptome uncovered prevalent A-to-I editing in maternal as well as the earliest zygotic transcripts, the majority of which occurred in the 3’-UTR region. Transcripts known to play a role in gastrulation and embryonic patterning were found to contain multiple editing sites, suggesting that Adar may exert their function through them. Knockdown or overexpression of Adar affected global editing patterns and transcriptome profile observable by 12 hpf, coinciding with the timing when the earliest embryonic patterns start to emerge. Finally, analysis of adar zygotic mutants revealed distinct zygotic function of Adar in regulating the innate immune response, a role which is conserved to that in mammals. Collectively, our study established a novel function of Adar-mediated A-to-I editing in regulating embryonic patterning, and reveals a conservation of zygotic Adar function between zebrafish and mammals.

Figure 1. (A-C) Phenotypic defects at 24 hpf caused by adar knockdown and overexpression. Adar MO-injected embryos develop abnormal phenotype in the posterior part with disturbed body axis, shortened tail and crooked, disorganized notochord. MO phenotype can be fully rescued with wild-type mRNA injection. (D-I) tbx2b expression  marking diencephalon (DE), R, epiphysis (EP), trigeminal ganglion (TG), and otic vesicle (OV) in Adar morpholino knockdown and adar mRNA overexpression. (J-L) expression of tbxta marks the notochord. (M) Mismatches between RNA and DNA sequencing data. As RNA libraries were not strand selective, mismatches were read as their complement (i.e. T->C instead of A->G, or C->T as G->A) in roughly half of all cases. (N) Selected transcripts of developmental signaling pathway genes implicated in dorsoventral and/or anteroposterior patterning containing two or more RNA editing sites detected at their 3’-UTR region. Gene names in red denotes those that are commonly edited at all three stages. (O) Association of editing sites with genomic features. A large fraction of RNA editing is classified as `genic_other` due to overlap between introns/exons/UTRs from multiple transcripts.