Human-specific loss of regulatory DNA and the evolution of human-specific traits

Abstract

Humans differ from other animals in many aspects of anatomy, physiology, and behaviour; however, the genotypic basis of most human-specific traits remains unknown. Recent whole-genome comparisons have made it possible to identify genes with elevated rates of amino acid change or divergent expression in humans, and non-coding sequences with accelerated base pair changes. Regulatory alterations may be particularly likely to produce phenotypic effects while preserving viability, and are known to underlie interesting evolutionary differences in other species. Here we identify molecular events particularly likely to produce significant regulatory changes in humans: complete deletion of sequences otherwise highly conserved between chimpanzees and other mammals. We confirm 510 such deletions in humans, which fall almost exclusively in non-coding regions and are enriched near genes involved in steroid hormone signalling and neural function. One deletion removes a sensory vibrissae and penile spine enhancer from the human androgen receptor (AR) gene, a molecular change correlated with anatomical loss of androgen-dependent sensory vibrissae and penile spines in the human lineage. Another deletion removes a forebrain subventricular zone enhancer near the tumour suppressor gene growth arrest and DNA-damage-inducible, gamma (GADD45G), a loss correlated with expansion of specific brain regions in humans. Deletions of tissue-specific enhancers may thus accompany both loss and gain traits in the human lineage, and provide specific examples of the kinds of regulatory alterations and inactivation events long proposed to have an important role in human evolutionary divergence.

Fig. 1. Hundreds of sequences highly conserved between chimpanzee and other species are deleted in humans

a, Computational approach used to discover human-specific deletions of functional DNA: identification of ancestral chimpanzee genomic sequences deleted in human; discovery of chimpanzee genomic sequences highly conserved in other species; and detection of human-specific deletions that remove one or more chimpanzee conserved sequences. Total chimpanzee sequence identified in each step is displayed beneath each graphic. b, Human genomic locations of the 583 hCONDELs. hCONDELs are displayed as blue ticks above the many locations where they are missing. c, Size distribution of hCONDELs.

Fig. 2. Transgenic analysis of a chimpanzee and mouse AR enhancer region missing in humans

a, Upper panel: 1.1 Mb region of the chimpanzee X chromosome. The red bar shows the position of a 60.7 kb human deletion removing a well-conserved chimpanzee enhancer between the AR and OPHN1 genes. Lower panel: Multiple species comparison of the deleted region, showing sequences alignable between chimpanzee and other mammals. Blue and orange bars represent chimpanzee and mouse sequences tested for enhancer activity in transgenic mice. The chimpanzee sequence drives lacZ expression in, b, facial vibrissae (arrows); and c, genital tubercle (dotted line) of E16.5 mouse embryos. Histological sections reveal strongest staining in superficial mesenchyme of d, the prospective glans of the genital tubercle; and e, dermis surrounding the base of sensory vibrissae. The mouse enhancer also drives consistent expression in f, facial vibrissae; g, genital tubercle; and hair follicles of E16.5 embryos. h, Endogenous AR is expressed in the genital tubercle (dotted line) as demonstrated by in situ hybridization. i, Histological section of a 60-day-old transgenic mouse penis showing postnatal lacZ expression in dermis of penile spines. Vibrissae and penile spines are androgen-dependent, as shown by, j, changes in vibrissae length in castrated and testosterone-treated mice and, k, loss and recovery of penile spines of a castrated and testosterone-treated primate (Galago crassicaudatus) (modified from refs. and 24). l, Model depicting multiple conserved tissue-specific enhancers (colored shapes) surrounding AR coding sequences (black bars) of different species. Loss of an ancestral vibrissae/penile spine enhancer in humans is correlated with corresponding loss of sensory vibrissae and penile spines.

Fig. 3. Transgenic analysis of a chimpanzee and mouse forebrain enhancer missing from a tumor suppressor gene in humans

a, Upper panel: 1.3 Mb region of the chimpanzee chromosome 9. The red bar illustrates a 3,181 bp human-specific deletion removing a conserved chimpanzee enhancer located downstream of GADD45g. Lower panel: Multiple species comparison of the deleted region, showing sequences alignable between chimpanzee and other mammals. The green bar represents a mouse forebrain-specific p300 binding site, and the blue and orange bars represent chimpanzee and mouse sequences tested for enhancer activity in transgenic mice. The chimpanzee (b,c,d,e) and mouse sequence (f,g,h,i) both drive consistent lacZ expression in E14.5 mouse embryos in the ventral thalamus (c, g), the SVZ of the septum (d, h), and the preoptic area (e, i). Increased production of neuronal subtypes from these regions may contribute to thalamic and cortical expansion in humans-. All sections are sagittal with anterior to right. Th, thalamus; Se, septum; POA, preoptic area.