Studies of differences between the chimpanzee and human genomes have focused on protein-coding genes. However, examples of amino acid changes between chimp and human have not been able to explain most of the phenotypic differences between us and our fellow hominoids. King and Wilson (1975) proposed that the main differences between chimps and humans will be found in non-coding regulatory DNA. Consistent with this hypothesis, recent whole-genome scans for evolutionarily conserved DNA elements that have evolved rapidly since our divergence from the chimp-human ancestor have discovered largely non-coding regions. The authors investigate a carefully screened set of 202 such human accelerated regions (HARs). Most of these HARs do not code for proteins, but instead are located in introns and intergenic regions near protein-coding genes. The set of genes near HARs is enriched for transcription factors, suggesting that the HARs may play important roles in gene regulation. This study also discovers a striking adenine and thymine to guanine and cytosine bias among the human-specific changes in HARs. This suggests the involvement of biased gene conversion or a selective force to increase guanine and cytosine content. Some HARs may also have been under positive selection. Hence, there is likely more than one evolutionary force shaping the fastest evolving regions of the human genome.

In order to convert the genetic information encoded in an organism's genomic sequence into the functional features, the genomic sequence must be transcribed. According to the current genome annotation, the human genome encodes 20,000–25,000 protein-coding transcripts and a smaller number of non-coding transcripts. There is, however, a growing body of evidence indicating that a much greater proportion of the human genome is transcribed than is accounted for by the existing annotation. Much of this evidence has been found using tiling arrays, microarrays that enable the measurement of transcription regardless of existing annotation. Although some have suggested that these transcripts represent previously unidentified functional RNAs as well as extensions of known genes, the extent of their functionality remains unknown. In this study, Khaitovich et al. assess the functionality of these novel transcripts by testing the extent to which their expression is conserved between humans and chimpanzees in different tissues. The results suggest that, surprisingly, the expression of both known and novel transcripts was affected by the same functional constraints during human and chimpanzee evolution.