MicroRNAs are deeply linked to the emergence of the complex octopus brain

MicroRNAs are deeply linked to the emergence of the complex octopus brain. Grigoriy Zolotarov et al. Science Advances, Nov 25 2022, Vol 8, Issue 47. DOI: 10.1126/sciadv.add99

Abstract: Soft-bodied cephalopods such as octopuses are exceptionally intelligent invertebrates with a highly complex nervous system that evolved independently from vertebrates. Because of elevated RNA editing in their nervous tissues, we hypothesized that RNA regulation may play a major role in the cognitive success of this group. We thus profiled messenger RNAs and small RNAs in three cephalopod species including 18 tissues of the Octopus vulgaris. We show that the major RNA innovation of soft-bodied cephalopods is an expansion of the microRNA (miRNA) gene repertoire. These evolutionarily novel miRNAs were primarily expressed in adult neuronal tissues and during the development and had conserved and thus likely functional target sites. The only comparable miRNA expansions happened, notably, in vertebrates. Thus, we propose that miRNAs are intimately linked to the evolution of complex animal brains.

DISCUSSION

Coleoid cephalopods are unusual among invertebrates in having a nervous system comparable to the central nervous system of vertebrates, at least in terms of the neuronal number and anatomical specialization (3) and hence in terms of its complexity (32, 33). Nonetheless, the complexity of the coleoid nervous system belies the generality of its protein-encoding genomic content, in particular its set of transcription factors (table S2). Aside from independent expansions of the C2H2 zinc finger–encoding and protocadherin-encoding genes in the squid and octopus lineages, the octopus has a canonical repertoire of transcription factors similar to other lophotrochozoans (5, 6). Coupling this generalized protein-encoding repertoire with the reported elevated rates of A-to-I editing in coleoid neural tissues (8, 9) led us to hypothesize that RNA regulation in general might be involved in driving an apparent increase in the complexity of the coleoid nervous system. Our data and analyses argue that in terms of alternative splicing diversity and rates (including back-splicing that generates circRNAs), as well as mRNA cleavage and polyadenylation patterns, there is no major departure from other invertebrates. Further, we find no evidence for substantial editing in miRNA seed sequences nor in potential target sites either in the abrogation of a genetically encoded site or in the creation of a newly relevant site (figs. S7 and S8). Furthermore, a recent study in O. bimaculoides and squid Doryteuthis pealeii reports no enrichment of A-to-I editing in any particular protein domain genome-wide with the vast majority of editing events found outside of coding regions (34). Of course, A-to-I editing may still be functionally important in individual cases (35), but the main function of this process in coleoids remains elusive.

On the other hand, a clear distinction in RNA regulation between coleoid cephalopods and all other known invertebrates is reflected in the marked expansion of their miRNA repertoire. The conservation of more than 50 miRNA loci in both the squid and octopus lineages since they diverged from one another nearly 300 million years ago (20) coupled with the 3′UTR (Fig. 2B), miRNA expression (Figs. 3 and 4), and target site (Fig. 5) analyses discussed above all strongly suggest that these miRNAs are functionally important during the development of the coleoid nervous system. In stark contrast to Octopus that evolved 90 novel miRNA families since its last common ancestor with the oyster Crassosstrea, the genus Crassostrea evolved only five novel miRNA families over the same span of geological time (36) as assessed through comparable levels and samples of small RNA sequencing data. Like in virtually all other increases to a miRNA repertoire, both the source and evolutionary pressures for the rise of these novel miRNA loci are not known; whole-genome duplications can be ruled out (5, 6), and scenarios may apply where novel miRNAs arise from the extensive genomic reorganizations found in coleoid taxa (5, 37). Whatever their source, once under selection, miRNAs in general are believed to improve the robustness of the developmental processes (38–42), increasing the heritability of the interaction (43–45), which might then allow for the evolution of new cell types (46) and ultimately morphological and behavior complexity (32, 47). With respect to the development of the nervous system, we note that at least in vertebrates, miRNAs are known to have highly complex expression patterns with, for example, miRNA transcripts localized to the synapse and modulating their function (48). Although it remains to be seen whether these types of pathways operate in coleoids, the notable explosion of the miRNA gene repertoire in coleoid cephalopods may indicate that miRNAs and, perhaps, their specialized neuronal functions are deeply linked and possibly required for the emergence of complex brains in animals.