NEW YORK (GenomeWeb) – A team of Dutch researchers has annotated cis-regulatory elements in primate brains to uncover human-specific changes that might have had a role in brain evolution.
Using ChIP-seq, researchers led by the University Medical Center Utrecht's Menno Creyghton annotated cis-regulatory elements in human, chimpanzee, and rhesus macaque brains to find that many of these elements were similarly located, even in the more distantly related rhesus macaques and humans. As the researchers reported in Nature Neuroscience today, this suggests that many cis-regulatory elements (CREs) were present in a common ancestor, though they also uncovered a number of human-specific elements.
"We found that the overall positional conservation of CREs is high, but observed differences in their usage," Creyghton and his colleagues wrote in their paper. "Furthermore, we show that most regulatory changes occurred before the divergence of human and chimpanzee."
Since the locations of active cis-regulatory elements can be gauged by whether or not histone modifications like H3 lysine 27 acetylation (H3K27ac) are present, the researchers used a ChIP-seq approach to annotate these regions in eight anatomical regions of the brain — including the cerebellum, putamen, prefrontal cortex, and more — in three humans, three rhesus macaques, and two chimpanzees.
The analysis identified some 60,000 significant H3K27ac-enriched regions each in humans, chimpanzees, and rhesus macaque. More than 90 percent of the predicted CREs in the human cortex contained enhancer or promoter states, based on ChromHMM chromatin signatures. In addition, for 93 percent of these putative cis-regulatory elements, the researchers uncovered sequence orthologs in the human, chimpanzee, and rhesus reference genomes. In addition, they noted that genes near predicted brain-specific enhancers were often linked to neural processes.
Creyghton and his colleagues compared the differences in active chromatin at CREs in humans and rhesus for each anatomical subdivision of the brain. Most predicted CREs, they noted, were either enriched in both species or had no significant difference between the two. This, the researchers said, suggests that the positional information of the regulatory landscape in the brain is largely conserved.
However, they noted that a PhastCons analysis showed little sequence conservation at these sites, despite this positional conservation.
At the same time, the researchers found that a sizeable portion of the regulatory elements differed between humans and rhesus macaque, based on a quantitative analysis of H3K27ac. Further, they noted that gene expression changes corresponded to differences in H3K27ac enrichment for both predicted enhancers and promoters.
A functional analysis of these genes indicated that they are associated with neuronal processes linked to the particular anatomical subdivision. This, Creyghton and his colleagues said, indicates that existing CRE activity has been altered across brain regions in humans and rhesus macaques, preferentially affecting enhancers.
Only a few of these regulatory changes occurred after the human-chimpanzee split, the researchers reported. That was further confirmed as the expression levels of genes close to enhancers were more similar between humans and chimpanzees than between humans and rhesus macaque. On average, the researchers noted, 22.5 percent of the differences between human and rhesus macaque were also present between human and chimpanzee.
Still, the team uncovered nearly 1,400 enhancers and 89 promoters that appeared to be new within the human brain. Though these predicted elements were enriched across the human brain, they were less frequently seen in multiple regions of the brain, the researchers noted. This supports the notion that enhancers are "more amenable to evolutionary change" since they tend to be tissue-specific, Creyghton and his colleagues wrote.
"[O]ur data allow the identification of regulatory changes that occurred in the brain during the final stages of human evolution," the researchers added. "Combined with genomic and transcriptomic data, this work represents a framework from which single predicted regulatory elements can be further assessed using more targeted approaches."