Convergent Function of Retrotransposons in Octopus Brain Drive Sophisticated Cognitive Capabilities

By: William Brown, Biophysicist at the Resonance Science Foundation

Compared to humans the Octopus is in many ways alien, it is an invertebrate with the only hard part being a chitinous beak, it has eight arms where most of its neuronal tissue—or brain—is located, and in many species, it can shape-shift and change the color of its integument to match its surrounding with near perfect adaptive camouflage. However, despite the many differences, many octopus species do share one similarity with that of humans: sophisticated cognitive capabilities, including problem solving, fore-thought, and creative ingenuity.

Since Octopus species have a rather large evolutionary distance from humans, mammals, or even vertebrates, a study of the cellular and molecular underpinning of their sophisticated cognitive capabilities can give us insight into what specific mechanisms enable and drive intelligence in animals. Interestingly, the molecular underpinnings of neuronal plasticity and intelligence are found all the way through to the core of the cell, in the genome.

In the neurons that are most associated with learning and memory, such as those found in the hippocampus of human and mammalian brains [1], there is found some of the highest activity in any tissue of transposable elements—what are popularly referred to as mobile genetic elements or jumping genes—so much so that the genomic heterogeneity produced by transposable element-generated recombination produces genomic mosaicism in the adult brain [2].

While the exact function of the somatic cell (adult cell) nuclear recombination driven by transposons and retrotransposons is unknown, particularly in functions of learning, memory, and intelligence, it is obvious that the generation of such genomic heterogeneity will produce more dynamic neuronal plasticity—neurons with a wider array of unique phenotypes and variations that can facilitate greater adaptive information processing. Here at the Resonance Science Foundation, we are researching whether such somatic cell nuclear recombination may play direct roles in information processing, where memory functions are taking place at the molecular (quantum) level including DNA recombination events.

What is being discovered is that it is the non-coding regions of the genome that contribute most to what makes us unique individuals, and underpin processes involved in intelligence and cognitive capabilities. Approximately 80% of the mammalian genome is transcribed in a cell-specific manner, and the majority of that cell-specific transcription is of noncoding regions—only a small portion is transcribed into protein-coding mRNAs, and the vast majority produces numerous long noncoding RNAs (lncRNAs), which come from transposable elements. These lncRNAs are emerging as important regulators in gene expression networks by controlling nuclear architecture and transcription in the nucleus and by modulating mRNA stability, translation, and post-translational modifications in the cytoplasm [3].

Mammalian genomes encode tens of thousands of long-noncoding RNAs (lncRNAs), which are capable of interactions with DNA, RNA and protein molecules, thereby enabling a variety of transcriptional and post transcriptional regulatory activities. Strikingly, about 40% of lncRNAs are expressed specifically in the brain with precisely regulated temporal and spatial expression patterns. In stark contrast to the highly conserved repertoire of protein-coding genes, thousands of lncRNAs have newly appeared during primate nervous system evolution with hundreds of human-specific lncRNAs. Their evolvable nature and the myriad of potential functions make lncRNAs ideal candidates for drivers of human brain evolution. The human brain displays the largest relative volume of any animal species and the most remarkable cognitive abilities. In addition to brain size, structural reorganization and adaptive changes represent crucial hallmarks of human brain evolution. lncRNAs are increasingly reported to be involved in neurodevelopmental processes suggested to underlie human brain evolution, including proliferation, neurite outgrowth and synaptogenesis, as well as in neuroplasticity. Hence, evolutionary human brain adaptations are proposed to be essentially driven by lncRNAs, which will be discussed in this review. [4] G. Zimmer-Bensch, “Emerging Roles of Long Non-Coding RNAs as Drivers of Brain Evolution,” Cells, 2019.

So, we see the integral and critical role of transposable elements, retrotransposons, and lncRNAs in evolution, development, and intelligence of animals—with striking and significant examples in the human lineage, where transposable element insertions have strongly affected human evolution [5]:

The aim of this paper is an explanation for the high speed of evolution of the human lineage, which has been exceptional compared with other animals. The high speed of evolution of human lineage brain size is recognized by comparison of fossil brain sizes... Evolution of the lineage leading to humans during the last several million years was striking. In this period the brain in our lineage tripled in mass... The function of the brain also changed rapidly but there are few useful fossils. What we know is that the result was the modern human brain, which has been called the most complex thing in the universe. We believe the brain evolution was due to natural selection and genomic variation.

Now, an international team of researchers led by Remo Sanges from SISSA of Trieste and by Graziano Fiorito from Stazione Zoologica Anton Dohrn of Naples, have conducted a comprehensive study of the Octopus’ neuronal transcriptome—sequencing the body of RNA molecules within the neurons of Octopus species, which includes retrotransposable elements and long non-coding RNAs—and have characterized a remarkable similarity with the mobile genetic landscape of humans and other mammals with high cognitive functionality [6].

_{Top: phylogenetic tree of cadherin genes in the California two-spot octopus (blue), Homo sapiens (red), Drosophila melanogaster (orange), Nematostella vectensis (mustard yellow), Amphimedon queenslandica (yellow), Capitella teleta (green), Lottia gigantea (teal), and Saccoglossus kowalevskii (purple). I – Type I classical cadherins; II – calsyntenins; III – octopus protocadherin expansion (168 genes); IV – human protocadherin expansion (58 genes); V – dachsous; VI – fat-like; VII – fat; VIII – CELSR; IX – Type II classical cadherins. Asterisk denotes a novel cadherin with over 80 extracellular cadherin domains found in the California two-spot octopus and Capitella teleta. Bottom: schematic of California two-spot octopus anatomy, highlighting the tissues sampled for transcriptome analysis: viscera (heart, kidney and hepatopancreas) – yellow; gonads (ova or testes) – peach; retina – orange; optic lobe (OL) – maroon; supraesophageal brain (Supra) – bright pink; subesophageal brain (Sub) – light pink; posterior salivary gland (PSG) – purple; axial nerve cord (ANC) – red; suckers – grey; skin – mottled brown; stage 15 (St15) embryo – aquamarine. Skin sampled for transcriptome analysis included the eyespot, shown in light blue. Image credit: Caroline B. Albertin et al.}

The research is highly salient to understanding the molecular underpinnings of intelligence capabilities in animals because it involves a species that is evolutionarily far-removed from mammals, and yet there is a convergence of the molecular genetic mechanisms underlying neuronal plasticity and adaptive information processing. Since the octopus is a veritable alien species compared to humans, the expression and function of retrotransposons and long non-coding RNAs cannot be an extant trait that results from a shared lineage, but instead has arisen, at least to a certain degree, independently—which is a strong indication of the universality of the mechanism and its importance to cellular and molecular information processing underlying intelligence and cognition.

…We report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. [6] G. Petrosino et al., “Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain,” BMC Biol, 2022.

The finding is a trifecta of salience, as it reveals (1) a new and deeper understanding of the critical role of non-coding DNA, which comprises more than 98% of the human genome; (2) The molecular mechanisms underlying intelligence and cognitive capabilities of animals, and (3) how intelligence and cognitive capabilities emerged evolutionarily. At least one take-away to highlight from the study is that it confronts a conventional perspective on the evolution of intelligence that it must be a very slow and gradual process. The reasoning being that something as complex and sophisticated as intelligence must take a very long time to develop. However, the strong link that is developing in our understanding between intelligence and the role of transposable genetic elements also points to how sophisticated cognitive capabilities can develop rapidly, in punctuated or even salutatory evolutionary leaps, as mobile genetic elements are also integral to accelerating evolvability and rapidly generating genomic recombination events and novel phenotypes.

A retrotransposon that we have focused much of our investigations on here at the Resonance Science Foundation is the primate specific Alu retrotransposon family (around 10% of the human genome is Alu elements). It has diverse roles in generating novel genes by introducing alternative splice sites and direct regulation of gene expression by inserting in gene promoter regions, and it has myriad functions in regulating the RNA transcriptome. One remarkable function is what is known as RNA editing, that enables the code of mRNA transcripts to be changed, allowing the diversification of proteomes beyond the genomic blueprint.

_{Cytidine and adenosine deaminases are critical RNA editors that play important functions in physiological events. a The vital role of APOBEC1 editing can be observed in the production of apolipoprotein B in the gut. The C-to-U editing at residue 2153 of hepatic Apo-B100 transforms the glutamate to a stop codon and produces a truncated protein Apo-B48 in intestinal cells [4]. b In neurons, mRNA editing of the glutamate receptor 2 (GluR2) at position 607 by ADAR2 results in an adenosine to inosine change. This transforms the CAG codon for glutamine (Q) to CIG for arginine (R) as (CGG), since ribosomes read inosine (I) as guanosine (G). This neutralizes the diffusion of divalent cations and makes the receptor impermeable to calcium [7]}

This is a highly advanced genomic adaptation for rapid proteomic plasticity (generating adaptive phenotypes outside of what is included in the protein-code of the genome), and is observed comparatively sparingly in most taxa of the animal kingdom. The Alu element is specific to the majority of adenosine-to-inosine mRNA transcript modifications in the human transcriptome (at least 4.6 million modification sites identified to date). This specific retrotransposon element is not found in octopus species (or any non-primate species), however the recent study by Sanges et alia has identified a long ineterspersed element (LINE) L1 and other TEs that are potentially involved in the widespread mRNA editing observed in behaviorally sophisticated coleoid cephalopods, serving a similar function to the Alu family of retrotransposons in the human genome. Interestingly, the two class of animals where RNA editing is undoubtedly highly prevalent, with dynamic epitranscriptomic regulation, are in humans [8] and cephalopod species like the octopus [9]—adding another interesting piece to the puzzle.

References

[1] S. Bachiller, Y. Del-Pozo-Martín, and Á. M. Carrión, “L1 retrotransposition alters the hippocampal genomic landscape enabling memory formation,” Brain Behav. Immun., vol. 64, pp. 65–70, Aug. 2017, doi: 10.1016/j.bbi.2016.12.018

[2] S. R. Richardson, S. Morell, and G. J. Faulkner, “L1 Retrotransposons and Somatic Mosaicism in the Brain,” Annual Review of Genetics, vol. 48, no. 1, pp. 1–27, 2014, doi: 10.1146/annurev-genet-120213-092412

[3] R.-W. Yao, Y. Wang, and L.-L. Chen, “Cellular functions of long noncoding RNAs,” Nat Cell Biol, vol. 21, no. 5, pp. 542–551, May 2019, doi: 10.1038/s41556-019-0311-8

[4] G. Zimmer-Bensch, “Emerging Roles of Long Non-Coding RNAs as Drivers of Brain Evolution,” Cells, vol. 8, no. 11, p. 1399, Nov. 2019, doi: 10.3390/cells8111399

[5] R. J. Britten, “Transposable element insertions have strongly affected human evolution,” Proc. Natl. Acad. Sci. U.S.A., vol. 107, no. 46, pp. 19945–19948, Nov. 2010, doi: 10.1073/pnas.1014330107

[6] G. Petrosino et al., “Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain,” BMC Biol, vol. 20, no. 1, p. 116, Dec. 2022, doi: 10.1186/s12915-022-01303-5

[7] T. Christofi and A. Zaravinos, “RNA editing in the forefront of epitranscriptomics and human health,” Journal of Translational Medicine, vol. 17, no. 1, p. 319, Sep. 2019, doi: 10.1186/s12967-019-2071-4

[8] C. Lo Giudice et al., “Quantifying RNA Editing in Deep Transcriptome Datasets,” Frontiers in Genetics, vol. 11, 2020, Accessed: Jul. 11, 2022. [Online]. Available: https://www.frontiersin.org/articles/10.3389/fgene.2020.00194

[9] N. Liscovitch-Brauer et al., “Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods,” Cell, vol. 169, no. 2, pp. 191-202.e11, Apr. 2017, doi: 10.1016/j.cell.2017.03.025