Many human accelerated regions are developmental enhancers

Abstract

The genetic changes underlying the dramatic differences in form and function between humans and other primates are largely unknown, although it is clear that gene regulatory changes play an important role. To identify regulatory sequences with potentially human-specific functions, we and others used comparative genomics to find non-coding regions conserved across mammals that have acquired many sequence changes in humans since divergence from chimpanzees. These regions are good candidates for performing human-specific regulatory functions. Here, we analysed the DNA sequence, evolutionary history, histone modifications, chromatin state and transcription factor (TF) binding sites of a combined set of 2649 non-coding human accelerated regions (ncHARs) and predicted that at least 30% of them function as developmental enhancers. We prioritized the predicted ncHAR enhancers using analysis of TF binding site gain and loss, along with the functional annotations and expression patterns of nearby genes. We then tested both the human and chimpanzee sequence for 29 ncHARs in transgenic mice, and found 24 novel developmental enhancers active in both species, 17 of which had very consistent patterns of activity in specific embryonic tissues. Of these ncHAR enhancers, five drove expression patterns suggestive of different activity for the human and chimpanzee sequence at embryonic day 11.5. The changes to human non-coding DNA in these ncHAR enhancers may modify the complex patterns of gene expression necessary for proper development in a human-specific manner and are thus promising candidates for understanding the genetic basis of human-specific biology.

Comprehensive identification and analysis of human accelerated regulatory DNA

“…An elegant and powerful way to identify evolutionary changes in noncoding DNA of potential significance, originally described by Pollard et al (2006b) and extensively used thereafter (Pollard et al 2006a,b;Prabhakar et al 2006;Kim and Pritchard 2007;Bush and Lahn 2008;McLean et al 2010;Lindblad-Toh et al 2011;Pertea et al 2011), focuses on the discovery of sequences that are rapidly evolving or lost on the human lineage but that are otherwise phylogenetically conserved and thus likely functional. This approach has led to the discovery of several regions with species-specific enhancer activity (Prabhakar et al 2008;Capra et al 2013;Kamm et al 2013), as well as human-specific deletion of regulatory DNA (McLean et al 2011).…”

An evolving view of epigenetic complexity in the brain

“…One example of functional genomic elements involved in this nuclear choreography is developmental enhancers, which exhibit tissue-specific regulatory activity. Intriguingly, many of these developmental enhancers represent 'human accelerated regions' that have served as substrates for evolutionary innovations in the human lineage, including those underpinning brain structure and activity [86,87]. Mobile genetic elements (i.e.…”

Genomic approaches to studying human-specific developmental traits

“…Interestingly, HARs are enriched for substitutions that predate the divergence from Neanderthals and Denisovans, suggesting that our genome did not evolve particularly rapidly during the emergence of modern humans (Burbano et al, 2012;Hubisz and Pollard, 2014). From a developmental perspective, HARs have a particularly interesting genomic distribution: they cluster nearby transcriptional factors and other regulatory genes expressed in embryos (Capra et al, 2013;Kamm et al, 2013b), suggesting that HAR mutations could be responsible for the evolution of human traits through modification of developmental gene regulatory networks.…”

“…A second use of functional genomics data is to generate information about the tissue-and stage-specificity of human-specific non-coding sequences. Comparing chromatin states, transcription factor binding profiles and gene expression across multiple cell types predicts that one-third or more of HARs are gene regulatory enhancers active in various embryonic tissues (Capra et al, 2013). Such predictions can help identify the phenotypes in which a humanspecific non-coding mutation is involved (Trynka et al, 2013).…”

“…Multiple HARs have also been tested in this manner: HAR2/HANCS1 (which drives expression in the limb, pharyngeal arches, ear and eye; Prabhakar et al, 2008); a cluster of 14 HARs near the gene encoding the transcription factor NPAS3 (11 of which drive expression in the nervous system; Kamm et al, 2013a); 23 HARs tested by the VISTA Enhancer Browser project (17 in the nervous system, three in limb, two in heart, eight in other tissues; Visel et al, 2007); 29 HARs with epigenetic signatures of active developmental enhancers (20 in the nervous system, eight in limb, four in heart, eight in other tissues; Capra et al, 2013); and HARE5/ANC516 (Bird et al, 2007), a non-coding region located upstream of the Wnt receptor frizzled 8 gene (FZD8) that is apparently neocortex specific (Boyd et al, 2015). Supporting the hypothesis that human-specific mutations in HARs may have altered their developmental regulatory functions, several show expression differences between reporter constructs carrying the chimpanzee and human HAR sequences (Boyd et al, 2015;Capra et al, 2013;Kamm et al, 2013a,b;Prabhakar et al, 2008). These include human gains of enhancer activity for NPAS3-associated 2xHAR.142 in forebrain at embryonic day (E) 12.5 (Kamm et al, 2013a) and for HAR2/ HANCS1 at the base of the limb bud at E11.5 (Prabhakar et al, 2008), which may have resulted from the destruction of a repressorbinding site (Sumiyama and Saitou, 2011).…”