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Reintroduction of the Archaic Variant of NOVA1

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Reintroduction of the Archaic Variant of NOVA1 RESEARCH ◥ protein-coding differences between modern RESEARCH ARTICLE SUMMARY human and archaic hominin genomes that could affect human neurodevelopment. HUMAN EVOLUTION RATIONALE: NOVA1 regulates alternative splic- Reintroduction of the archaic variant of NOVA1 in ing in the developing nervous system and is a master regulator of splicing genes responsible cortical organoids alters neurodevelopment for synapse formation. Altered NOVA1 splicing activity in humans is associated with neurolog- Cleber A. Trujillo, Edward S. Rice, Nathan K. Schaefer, Isaac A. Chaim, Emily C. Wheeler, Assael A. Madrigal, ical disorders, underscoring the role of NOVA1 in Justin Buchanan, Sebastian Preissl, Allen Wang, Priscilla D. Negraes, Ryan A. Szeto, Roberto H. Herai, neural function. Using CRISPR-Cas9 genome- Alik Huseynov, Mariana S. A. Ferraz, Fernando S. Borges, Alexandre H. Kihara, Ashley Byrne, editing technology in human induced pluripo- Maximillian Marin, Christopher Vollmers, Angela N. Brooks, Jonathan D. Lautz, Katerina Semendeferi, tent stem cells (iPSCs), we replaced the modern Beth Shapiro, Gene W. Yeo, Stephen E. P. Smith, Richard E. Green, Alysson R. Muotri* human allele of the NOVA1 gene with the ancestral allele found in Neanderthals and Denisovans, which contains a single-nucleotide INTRODUCTION: Current views of human evo- cies. Comparison of Neanderthal, Denisovan, substitution at position 200 that causes an lution, as supported by the fossil record, in- and extant human genomes has shown that isoleucine-to-valine change. To investigate the dicate that many hominin lineage branches many humans today carry genes introduced functional importance of this amino acid change arose, but only one survived to the present. through past admixture events and has allowed in humans, we followed iPSC neural develop- Downloaded from Neanderthals and Denisovans, two of these enumeration of human-specific genetic differ- ment through functional cortical organoids. extinctlineages,areourclosestevolutionary ences that may have been important for recent relatives and therefore provide the most subtle human evolution. Neuro-oncological ventral RESULTS: The reintroduction of the archaic genetic and phenotypic contrast to our spe- antigen 1 (NOVA1) includes one of the few version of NOVA1 into a human genetic back- ground causes changes in alternative splicing NOVA1 I200 in genes involved in neurodevelopment, pro- liferation, and synaptic connectivity. These http://science.sciencemag.org/ changes co-occur with differences in organoid NOVA1V200 morphology and neural network function, sug- gesting a functional role for the derived human- specific substitution in NOVA1.Furthermore, cortical organoids carrying the archaic NOVA1 displayed distinct excitatory synaptic changes, which may have led to the observed altera- Chicken Mouse Neanderthal Human tions in neural network development. Collec- Denisovan tively, our data suggest that expression of the NOVA1 archaic leads to modified synaptic on March 18, 2021 protein interactions, affects glutamatergic sig- naling, underlies differences in neuronal con- CRISPR NOVA1 to nectivity, and promotes higher heterogeneity archaic version of neurons regarding their electrophysiological Pluripotent stem cells Pluripotent stem cells profiles. NOVA1 Ar/Ar NOVA1 Hu/Hu CONCLUSION: A subset of genetic changes may underly the phenotypic traits that separate our species from these extinct relatives. We developed a platform to test the impact of human-specific genetic variants by reintroduc- Cortical organoids ing the archaic form found in Neanderthals and Denisovans and measuring its effects during neurodevelopment using human brain organoids. Our results suggest that the human- Molecular, cellular and neural network activity specific substitution in NOVA1, which became fixed in modern humans after divergence from Neanderthals, may have had functional con- sequences for our species’ evolution.▪ NOVA1 archaic variant in cortical organoids affects cellular, molecular, and neural network activity profiles. During human evolution, modern humans acquired a specific nucleotide substitution in the RNA binding domain of NOVA1. Using genome editing technology, the archaic version of NOVA1 was introduced in The list of author affiliations is available in the full article online. human iPSCs and differentiated into cortical organoids. The changes could be observed in different levels, from *Corresponding author. Email: [email protected] Cite this article as C. A. Trujillo et al., Science 371, eaax2537 altered proliferation, different gene expression, and splicing profiles to modified glutamatergic synapsis and (2021). DOI: 10.1126/science.aax2537 neuronal network connectivity. NOVA1I200, NOVA1 gene containing isoleucine archaic variant. NOVA1V200, NOVA1 gene containing valine human variant; NOVA1Ar/Ar, human cell line with homozygous reintroduction of the NOVA1 READ THE FULL ARTICLE AT archaic variant; NOVA1Hu/Hu, human cell line with NOVA1 human variant. Figure created with BioRender.com. https://doi.org/10.1126/science.aax2537 Trujillo et al., Science 371, 694 (2021) 12 February 2021 1of1 RESEARCH ◥ provide experimentally tractable candidates RESEARCH ARTICLE for genetic variation that might underlie human- specific phenotypes. HUMAN EVOLUTION Neuro-oncological ventral antigen 1 (NOVA1) is an RNA binding protein that contains a Reintroduction of the archaic variant of NOVA1 in nearly fixed, derived nonsynonymous change not seen in the Neanderthal or Denisovan cortical organoids alters neurodevelopment genomes or more distantly related species (an- cestral allele count is 0 in 1000 Genomes Proj- Cleber A. Trujillo1, Edward S. Rice2*†, Nathan K. Schaefer2‡, Isaac A. Chaim3, Emily C. Wheeler3, ect, 0 in SGDP, and 3 of 250,246 in gnomAD Assael A. Madrigal3, Justin Buchanan4, Sebastian Preissl4, Allen Wang4, Priscilla D. Negraes1, v2.1.1). NOVA1 regulates alternative splicing in Ryan A. Szeto1, Roberto H. Herai5, Alik Huseynov6, Mariana S. A. Ferraz7, Fernando S. Borges7, the developing nervous system (13, 14)andisa Alexandre H. Kihara7, Ashley Byrne8, Maximillian Marin2§, Christopher Vollmers2, Angela N. Brooks2, master regulator of splicing genes responsible Jonathan D. Lautz9,10, Katerina Semendeferi11, Beth Shapiro12,13, Gene W. Yeo4, for synapse formation (15). Altered NOVA1 Stephen E. P. Smith9,10, Richard E. Green2, Alysson R. Muotri1¶ splicing activity in humans is associated with neurological disorders (15–17), underscoring The evolutionarily conserved splicing regulator neuro-oncological ventral antigen 1 (NOVA1)playsa the role of NOVA1 in neural function. key role in neural development and function. NOVA1 also includes a protein-coding difference between the modern human genome and Neanderthal and Denisovan genomes. To investigate the Results Genomic comparison between modern and functional importance of an amino acid change in humans, we reintroduced the archaic allele archaic humans Downloaded from into human induced pluripotent cells using genome editing and then followed their neural development through cortical organoids. This modification promoted slower development and higher We compared human genetic data from the surface complexity in cortical organoids with the archaic version of NOVA1. Moreover, levels of 1000 Genomes Project and SGDP (11, 12)and synaptic markers and synaptic protein coassociations correlated with altered electrophysiological from two high-coverage Neanderthal genomes properties in organoids expressing the archaic variant. Our results suggest that the human-specific and one high-coverage Denisovan genome (3, 4). substitution in NOVA1, which is exclusive to modern humans since divergence from Neanderthals, may We found a set of 61 positions in which all have had functional consequences for our species’ evolution. humans carry an autosomal fixed derived mu- http://science.sciencemag.org/ tation (table S1). We measured the length of the human- any hominin lineage branches are re- both Neanderthals and Denisovans or to each specific haplotype around each fixed human- presented in the fossil record, but only lineagethatwereintroducedintoancestralto specific site, i.e., the largest genome region one survived to the present (1). Nean- modern humans through admixture around in which no humans carry any substitutions M derthals and Denisovans, two of these 60,000 years ago (1) and not lost by drift or observed in the archaic genomes (Fig. 1A). extinct lineages, are our closest evolu- selection in descendants. However, some re- Among the 61 nonsynonymous differences, tionary relatives and therefore provide the gions of modern human genomes are devoid the human-specific NOVA1 substitution is on subtlest genetic and phenotypic contrast to of Neanderthal or Denisovan ancestry and the third-largest human-specific haplotype: NOVA1 our own species. High-quality genomes are carryonlymodernhuman-specificgenetic 4.4 kb (Fig. 1A). This archaic variant on March 18, 2021 available for both, inferred from DNA recov- variants (4, 5, 9, 10). These regions can result was identified in the comparison using data ered from bone remains (2–5). Comparison of from negative selection on archaic variants, from phase I of the 1000 Genomes Project (4). Neanderthal, Denisovan, and extant human positive selection on human-specific variants, The olfactory receptor gene OR8B2 and the genomes has shown that many humans today or drift. Comparisons with data from phase I nuclear receptor coactivator gene NCOA6 were carry genes introduced
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