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Researchers ID Copy Number Differences in Human, Chimp Genomes

NEW YORK (GenomeWeb News) – The copy number variation in human and chimpanzee genomes may provide clues about differences between the two species that sequence data alone cannot explain, new research suggests.
A team of researchers from the UK and the US used array-comparative genomic hybridization on human arrays to compare the copy number variations present in 30 human and 30 chimp genomes. The research, appearing in the November issue of Genome Research, uncovered both shared and distinct CNVs in the two species. In particular, the team found that genes involved in processes such as inflammatory response and cell proliferation tend to be gained or lost more often than other genes.
“This is the first study of this scale, comparing directly the genomes of many humans and chimpanzees,” senior author Richard Redon, a Wellcome Trust Sanger Institute researcher, said in a statement. “By looking at one ‘reference’ sequence for human or chimpanzee, as has been done previously, it is not possible to tell which differences occur only among individual chimpanzees or humans and which are differences between the two species.”
Thousands of copy number variants have been detected in human genomes. Although some have been linked to disease states, many have no obvious phenotypic consequences. And little research has been done looking at CNV patterns in different individuals or between humans and closely related species.
In an effort to remedy that, Redon and his team did array-CGH on a whole-genome tiling path platform to compare copy number variations in 30 chimpanzees (29 from West Africa and one from East Africa) and 30 humans (ten Yoruba individuals from Nigeria, ten Biaka rainforest hunter-gatherers from the Central African Republic and ten Mbuti rainforest hunter-gatherers from the Democratic Republic of Congo).
Their results suggest that, on average, individuals within the human and chimp groups had about 70 to 80 CNVs each. Overall, the researchers found 353 autosomal CNVs in humans and 438 CNVs in chimpanzees — with 229 of the CNVs present in two or more chimps and 223 CNVs present in two or more humans.
Although individuals in the two species had a similar number of CNVs, the sets of genes that were amplified or deleted in each varied: the researchers detected 355 autosomal copy number differences between humans and chimpanzees.
They also discovered that genes involved in the inflammatory response and cell proliferation seem to have been duplicated or deleted more often than other genes.
“[I]nflammatory response and cell proliferation function categories were both characterized by a relative excess of fixed [copy number differences], suggesting that some of these duplications or deletions may have been fixed by positive selection,” the authors wrote. “Therefore, the affected genes will be of particular interest for subsequent studies focusing on the evolution of adaptive phenotypic-level differences between humans and chimpanzees.”
For instance, they found that many genes involved in inflammatory response in humans — such as APOL1, APOL4, CARD18, ILIF7, and ILIF8 — are no longer present in chimpanzee genomes. That, in turn, suggests that humans and chimps regulate certain inflammatory responses differently.
Similarly, the team detected copy number differences in a gene called TBC1D3, which is involved in cell proliferation. The humans tested usually had eight copies of the gene, while most chimpanzees had just one. In contrast, there were no obvious copy number differences in a nearby gene called CCL3L1. CNVs in that gene have previously been shown to influence HIV susceptibility in humans, with fewer copies of the gene increasing susceptibility.
“It is evident that there has been striking turnover in gene content between humans and chimpanzees, and some of these changes have resulted from exceptional selection pressures,” lead author George Perry, a researcher affiliated with Arizona State University and Boston’s Brigham and Women’s Hospital, said in a statement.
Even so, the team detected other instances in which human and chimpanzee genomes had CNVs that appear to have sprung up in orthologous regions — possibly because of similarities in their overall genome sequence or structure. “[S]equence motifs or architectures shared between the human and chimpanzee genomes may predispose certain chromosomal regions to structural instability in both extant species,” Redon and his colleagues wrote.

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