GBE Human Accelerated Regions and Other Human-Specific Sequence Variations in the Context of Evolution and Their Relevance for Brain Development Anastasia Levchenko1,*, Alexander Kanapin1,2, Anastasia Samsonova1,2, and Raul R. Gainetdinov1,3 1Institute of Translational Biomedicine, Saint Petersburg State University, Russia 2Department of Oncology, University of Oxford, United Kingdom 3Skolkovo Institute of Science and Technology, Skolkovo, Moscow, Russia *Corresponding author: E-mail: [email protected]. Accepted: November 14, 2017 Abstract The review discusses, in a format of a timeline, the studies of different types of genetic variants, present in Homo sapiens,but absent in all other primate, mammalian, or vertebrate species, tested so far. The main characteristic of these variants is that they are found in regions of high evolutionary conservation. These sequence variations include single nucleotide substitutions (called human accelerated regions), deletions, and segmental duplications. The rationale for finding such variations in the human genome is that they could be responsible for traits, specific to our species, of which the human brain is the most remarkable. As became obvious, the vast majority of human-specific single nucleotide substitutions are found in noncoding, likely regulatory regions. A number of genes, associated with these human-specific alleles, often through novel enhancer activity, were in fact shown to be implicated in human-specific development of certain brain areas, including the prefrontal cortex. Human-specific deletions may remove regulatory sequences, such as enhancers. Segmental duplications, because of their large size, create new coding sequences, like new functional paralogs. Further functional study of these variants will shed light on evolution of our species, as well as on the etiology of neurodevelopmental disorders. Key words: substitutions, duplications, deletions, neurodevelopmental disorders, psychiatry, genes. Introduction The human brain is indeed much more sophisticated when Human accelerated regions (HARs) and human-specific geno- compared with our closest living relative, the chimpanzee, mic rearrangements, including deletions and segmental dupli- from whom we diverged 8 Ma and with whom we share cations, are among the most interesting sequences in the 99% of our genome (The Chimpanzee Sequencing and human genome to study, because they seem to shed light on Analysis Consortium 2005; Moorjani et al. 2016). As con- the appearance of Homo sapiens as a species, especially in the cluded by the classic study by King and Wilson (King and sense of the exceptionally developed human brain (O’Bleness Wilson 1975), functionally new protein-coding genes cannot et al. 2012a; Sassa 2013; Hubisz and Pollard 2014; Zhang and account for all obvious morphological differences between Long 2014; Bae et al. 2015; Franchini and Pollard 2015; Dennis humans and chimpanzees, because human protein-coding and Eichler 2016; Silver 2016; Namba and Huttner 2017). The genes are very similar to chimpanzee genes and constitute human brain appeared in evolution probably as a result of nat- only 1.5% of the human genome. The genetic basis of ural selection among the intellectually developed members of the morphological differences must therefore primarily the Homo genus. Only Homo sapiens survived, by presenting come from noncoding, regulatory sequences. One of the an exceptionally developed telencephalon, the prefrontal cor- most appealing ways to demonstrate that evolutionarily tex in particular, that gave us the capacity to invent more so- new regulatory regions play an important role in the function phisticated tools and to plan ahead. of the human brain was the discovery of HARs of 2006, An obvious question is: which evolutionarily new sequence followed by a number of similar studies (Pollard et al. variations determined the new pattern of brain development? 2006a; Prabhakar et al. 2006; Bird et al. 2007; Bush and ß The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact [email protected] 166 Genome Biol. Evol. 10(1):166–188. doi:10.1093/gbe/evx240 Advance Access publication November 14, 2017 Human Accelerated Regions and Other Human-Specific Sequence Variations GBE Lahn 2008; Lindblad-Toh et al. 2011; Gittelman et al. 2015). 2014), abnormal spindle-like microcephaly associated HARs are short, 260 bp on an average, stretches of DNA, to (ASPM) that bears a number of human-specific synonymous 97% noncoding. They are conserved in vertebrates, including and nonsynonymous substitutions (Zhang 2003; Evans et al. Pan troglodytes, but not in Homo sapiens, in whom the con- 2004; Buchman et al. 2011; Jayaraman et al. 2016)and served sequences were subjected to significantly, in many Abelson helper integration site 1 (AHI1) that also underwent cases dramatically, higher rates of single nucleotide substitu- positive selection in humans (Ferland et al. 2004; Cheng et al. tions (Hubisz and Pollard 2014). An example of a HAR is given 2012). The reader is referred to reviews that describe these on figure 1a. Because conserved noncoding sequences are genes in further detail (Vallender et al. 2008; O’Bleness et al. most likely regions regulating gene expression, new substitu- 2012a; Bae et al. 2015). tions in these regions imply new patterns of regulation. A Taken together, currently available scientific data indicate fraction of HARs affect noncoding RNA genes (Pollard et al. that both noncoding regulatory regions, modified by single 2006b),whichareoftenalsoimplicatedinregulationofgene nucleotide substitutions and deletions, and new coding expression. In fact, a meta-analysis (Haygood et al. 2010), that sequences, created by segmental duplications, are important used data from Pollard et al. (2006a), Prabhakar et al. (2006) in human evolution and seem to shape the human brain. Only and a study that investigated positive selection in human pro- genomic regions and genes that were discovered in genome- moters (Haygood et al. 2007), indicated that human genes wide studies of human evolution will be dealt with in this regulating neurodevelopment were subjected, during evolu- review. Table 1 summarizes these regions and genes. tion, to the most prominent positive selection only within their Figure 2 presents the timeline of the studies. noncoding sequences. This tendency is exclusive to neurode- velopmental genes, whereas positive selection in coding sequences is characteristic for evolution of human genes im- Original Studies Describing HARs plicated in other functions, such as immune system and ol- faction (Haygood et al. 2010). Similar results were obtained by The First Discovery of HARs two other scientific teams that showed that substitutions in The two pioneering studies, in which HARs were de- the coding sequence of human brain-expressed genes were scribed, appeared in 2006 (Pollard et al. 2006a, 2006b). not numerous enough to indicate positive selection (Shi et al. The studies used a biostatistical method, which aimed at 2006; Wang et al. 2007). Finally, coding sequences of genes detecting any significant acceleration in the rate of nucle- associated with schizophrenia and autism were not subjected otide substitutions in human. First, Pollard et al. (2006a) to accelerated nonsynonymous substitutions in humans aligned genomes of chimpanzee, mouse, and rat, in order (Ogawa and Vallender 2014). to define regions of at least 96% conservation over As became clear starting in 2003 (Locke et al. 2003), the 100 bp; second, they aligned the orthologous conserved human genome is also subject to an important number of sequences of the total of 17 vertebrates, including hu- complex genomic rearrangements, including segmental dupli- man. Software MultiZ and PhastCons from the PHAST cations, that can also, because of their large size, affect cod- package (Blanchette et al. 2004; Siepel et al. 2005; ing genes (Fortna et al. 2004), in particular, create new Hubisz et al. 2011) and a likelihood ratio test were used functional paralogs (Charrier et al. 2012; Dennis et al. 2012, to this end. This method was different from the approach 2017). An example is given on figure 1b. Human-specific where the rate of substitutions in the genome of a species deletions may also remove regulatory sequences (McLean was compared with theoretical neutral expectations. In et al. 2011). An example is shown on figure 1c. The study other words, Pollard et al. (2006a)reliedonlyonfactual of the patterns of human-specific large structural variants is sequences of a number of different vertebrates, to directly currently in its infancy (Dennis and Eichler 2016), but it has compare them with Homo sapiens. Pollard et al. (2006a) already become clear that the impact of these variants in the discovered a more stringent data set of 49 HARs, at a false context of human evolution is paramount. discovery rate (FDR)-corrected P value <0.05, and a The majority of single nucleotide substitutions relevant to broader data set of 202 HARs in the human genome. As human brain evolution are in noncoding regions and affected an example, the top five HARs had substitution rates 26 coding genes are