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Evidence of Abundant Purifying Selection in Humans for Recently Acquired Regulatory Functions

No More Junk DNA The majority of the human genome is transcribed at some level, but the function and evolutionary constraint among regions that do not regulate gene expression or code for genes are generally unknown. Examining data from the 1000 Genomes Project and ENCODE, Ward and Kellis (p. 1675, published online 5 September) examined regions of the human genome that did not show conservation among mammals and found evidence for a human lineage-specific constraint spanning approximately 4% of the genome that is biochemically active but not directly associated with genes. Interestingly, these regions showed lower numbers of single-nucleotide polymorphisms, heterozygosity, and derived allele frequencies, suggesting that they are under constraint and may be functional. Diversity in human-specific regions of the genome has been reduced by functional constraints. Although only 5% of the human genome is conserved across mammals, a substantially larger portion is biochemically active, raising the question of whether the additional elements evolve neutrally or confer a lineage-specific fitness advantage. To address this question, we integrate human variation information from the 1000 Genomes Project and activity data from the ENCODE Project. A broad range of transcribed and regulatory nonconserved elements show decreased human diversity, suggesting lineage-specific purifying selection. Conversely, conserved elements lacking activity show increased human diversity, suggesting that some recently became nonfunctional. Regulatory elements under human constraint in nonconserved regions were found near color vision and nerve-growth genes, consistent with purifying selection for recently evolved functions. Our results suggest continued turnover in regulatory regions, with at least an additional 4% of the human genome subject to lineage-specific constraint.