Phylogenetic Shadowing of Primate Sequences to Find Functional Regions of the Human Genome

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Science  28 Feb 2003:
Vol. 299, Issue 5611, pp. 1391-1394
DOI: 10.1126/science.1081331


Nonhuman primates represent the most relevant model organisms to understand the biology of Homo sapiens. The recent divergence and associated overall sequence conservation between individual members of this taxon have nonetheless largely precluded the use of primates in comparative sequence studies. We used sequence comparisons of an extensive set of Old World and New World monkeys and hominoids to identify functional regions in the human genome. Analysis of these data enabled the discovery of primate-specific gene regulatory elements and the demarcation of the exons of multiple genes. Much of the information content of the comprehensive primate sequence comparisons could be captured with a small subset of phylogenetically close primates. These results demonstrate the utility of intraprimate sequence comparisons to discover common mammalian as well as primate-specific functional elements in the human genome, which are unattainable through the evaluation of more evolutionarily distant species.

Genomic sequence comparisons between distant species have been extensively used to identify genes and determine their intron-exon boundaries, as well as to identify regulatory elements present in the large noncoding fraction of the genome (1–3). This strategy has been successful in human-mouse comparisons, because the ∼75 million years (My) of separation from their last common ancestor have provided sufficient time for a large fraction of nucleotides to have been exposed to considerable mutation and selection pressure. Although such comparisons readily identify regions of the human genome performing general biological functions shared with evolutionarily distant mammals, they will invariably miss recent changes in DNA sequence that account for uniquely primate biological traits.

As a consequence of their short evolutionary separation (apes 6 to 14 My, Old World monkeys 25 My, New World monkeys 40 My) (4), there is a paucity of sequence variation between humans and each of their nearest primate relatives. This lack makes it difficult to distinguish functional from passive conservation on the basis of pairwise comparisons, thus limiting the usefulness of such comparisons. However, the additive collective divergence of higher primates as a group (fig. S1) is comparable to that of humans and mice. This suggests that deep sequence comparisons of numerous primate species should be sufficient to identify important regions of conservation that encode functional elements. Phylogenetic footprinting (5, 6) has been used to identify highly conserved putative regulatory elements, exploiting alignments across numerous evolutionarily distant species. We developed a variant of phylogenetic footprinting, which we termed phylogenetic shadowing. In contrast to footprinting, phylogenetic shadowing examines sequences of closely related species and takes into account the phylogenetic relationship of the set of species analyzed. This approach enabled the localization of regions of collective variation and complementary regions of conservation, facilitating the identification of coding as well as noncoding functional regions.

We first examined the ability of this strategy to identify functional regions with precise locations within the human genome, such as intron-exon boundaries. The lack of clone-based libraries for multiple primate species limited us to sequencing orthologous regions from a large set of primates, using genomic DNA as template (7). The sole criterion used in the selection of the four different regions that we studied was that each should contain at least one annotated exon. The sequences were generated (8) for a set of 13 to 17 primate species that included those evolutionarily closest to humans, such as Old World and New World monkeys and hominoids, but not distant primates such as prosimians. The resulting sequences were analyzed to determine the likelihood ratio under a fast- versus slow-mutation regime for each aligned nucleotide site across all four regions analyzed (supporting online text) (8). This ratio represents the relative likelihood that any given nucleotide site was subjected to a faster or slower rate of accumulation of variation and is related to functional constraints imposed on each site. The corresponding likelihood ratio curves were used to describe the variation profile of the four genomic intervals analyzed.

In all regions examined, the exon-containing sequences displayed the least amount of cross-species variation, in agreement with the constraint imposed by their functional role (Fig. 1, A to D). A limited number of short regions of minimal variation similar to the exon-containing sequences appeared in the likelihood plots. These regions, however, were all less than 50 base pairs (bp) long, making them unlikely to be candidate exons for alternative splicing (the vast majority of internal exons predominantly range between 50 and 200 bp in length) (9). These regions may represent previously unidentified regulatory elements. In agreement with observations from other parts of the genome (10), the four sequenced regions have evolved at different rates, as indicated by their differing absolute likelihoods. Comparison of human-mouse versus the multiple-primate visualization plots (Fig. 1, a to d) yields similar results, with exons showing the highest level of conservation in all regions studied. The primate sequence comparisons illustrate the effectiveness of phylogenetic shadowing in yielding a precise identification of the exon boundaries. In the case of the cholesteryl ester transfer protein gene (Fig. 1, B and b), the human-mouse comparison is unavailable, because this gene has been inactivated in the mouse. This inactivation represents an extreme example of the frequently encountered situation where the mouse genome, owing to the lack of meaningful alignments between human and mouse sequences, fails to localize functional elements in the human genome (11).

Figure 1

Likelihood ratios under a fast- versus slow-mutation regime for genomic intervals containing apo-B exon 19 (A), CETP exon 8 (B), LXR-α exon 3 (C), and plasminogen exon 6 (D). The x axis represents the position in the multiple alignment consensus sequence, and they axis the log likelihood ratio at that position. The plot is smoothed by means of a 20%-trimmed mean over the 50-base window centered at each aligned site. A lower ratio indicates a higher degree of constraint on mutability of that site. The position of the exon in each sequence is shown by the magenta line under the green ratio curve. The LXR-α plot (C) contains a fragment of an additional exon at the right end of the plot. Panels (a) to (d) show the VISTA conservation plots for the corresponding orthologous regions in human and mouse. They axis represents the percentage of sequence conservation and the blue area the position of the exon.

We next analyzed the sequence data for the four regions studied to assess the contribution of additional species to the discriminative power of phylogenetic shadowing and to identify the most informative minimum subset of species (8). The sequences from the most informative subset of only four to seven species, depending on the genomic locus, were calculated to be sufficient to capture ∼75% of the total available discriminative power of this approach (Table 1). We were able to unequivocally identify the position of exon 3 of liver X receptor–α from the five most informative species (Homo, Saguinis, Colobus,Callicebus, Allenopithecus), as indicated by the likelihood curve (fig. S2). Comparison with Fig. 1C shows that additional species only marginally improve this plot. As would be predicted, the species included in the set maximizing the discriminative power of phylogenetic shadowing include representatives of the different clades that compose the primate phylogenetic tree and therefore constitute the least related species in the set studied (fig. S1).

Table 1

The discriminative power of phylogenetic shadowing at increasing species subset sizes. Each row is an exonic region under study. Each column shows, by region, the percentage of total phylogenetic divergence in a complete species set of that region that is captured by the most-divergent subset of the indicated size. The minimum number of species required to capture at least 75% of the full power of the approach is highlighted in bold for each gene.

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To investigate the ability of phylogenetic shadowing to discover primate-specific gene-regulatory elements, we studied apolipoprotein (a) [apo(a)], a recently evolved primate gene whose orthologous distribution is limited to Old World monkeys and hominoids (12). Defining the regulatory sequences determining apo(a) expression levels is of considerable biomedical relevance, because high plasma levels of this protein serve as an important cardiovascular disease risk predictor (13, 14). The sparse distribution of this gene among mammals precludes classical comparative genomic approaches. Sequence comparison of the apo(a) locus in humans, chimps, and baboons revealed a region of extreme conservation of ∼1.6 kb adjacent to the transcription start site, surrounded by ∼8 kb of reduced conservation on either side, owing to the different patterns of repetitive-element insertion in the three species. We sequenced and analyzed this 1.6-kb region in 18 Old World monkeys and hominoids (8). Phylogenetic shadowing revealed regions of varying conservation similar to that observed for the intron-exon regions described previously (Fig. 2A). In addition to the region containing the first exon of apo(a) (region E) (15), the remaining regions with the lowest variation include the apo(a) promoter's TATA box (region C9) and a critical hepatocyte nuclear factor (HNF)–1α transcription factor binding site (region C10), both of which have been functionally described (16). Eight additional regions, varying in size between 40 and 70 bp, show levels of conservation comparable to that of these three functional regions, suggesting they are also biologically important.

Figure 2

Analysis of the apo(a) 1.6-kb region. (A) Likelihood ratios under a fast- versus slow-mutation regime for the genomic interval containing the apo(a) exon 1 and 5′-flanking sequence. The x axis represents the position in the multiple alignment consensus sequence, and the y axis the log likelihood ratio at that position. The plot is smoothed using a 20%-trimmed mean over the 50-base window centered at each aligned site. The position of the exon (E) is shown by the magenta arrow. The blue (C1 to C10) and red (N1 to N7) rectangles show the sequence intervals that were selected as the representatives of conserved and nonconserved regions, respectively. Delineation of regions C9 and C10 was based on previous knowledge of their functional role. These regions were investigated by gel-shift and transfection analysis. (B) Electrophoretic mobility–shift patterns of the conserved (C1 to C10) and nonconserved (N1 to N7) intervals. Region C10, being too long (97 bp) for gel-shift analysis, was split into two 60-bp overlapping oligonucleotides (C10.1 and C10.2). (C) Densitometric analysis of the electrophoretic mobility–shift patterns. The y axis represents the amount of shifted oligonucleotide normalized to the total amount of oligonucleotide in the lane. Columns and error bars represent the mean and 1 SD, respectively, of five (C1 to C10.2) and three (N1 to N7) independent gel-shift experiments. The dotted line indicates the median electrophoretic mobility–shift of the conserved and nonconserved regions.

Because these elements were located immediately upstream of the apo(a) promoter, we tested these sequences for their ability to be recognized by DNA binding proteins. The highly conserved regions were predicted to interact with such proteins more efficiently than were regions characterized by a low degree of conservation. We performed electrophoretic mobility–shift assays on 10 oligonucleotides spanning the most-conserved regions and, as putative negative controls, seven similarly sized oligonucleotides representing regions with the least conservation (Fig. 2A, regions N1 to N7). In this assay, nuclear extracts from a liver cell line were mixed with radiolabeled oligonucleotides and separated by electrophoresis (8). All oligonucleotides from the conserved regions interacted with one or more DNA binding proteins, as reflected by the slower electrophoretic mobility of the protein-bound oligonucleotides relative to the mobility of the pure oligonucleotides (Fig. 2B, lower bands). Conversely, oligonucleotides from nonconserved regions showed only weak or no protein binding. Overall, binding of oligonucleotides from conserved regions with hepatic nuclear proteins was more than six times as strong as binding of oligonucleotides from regions with lower conservation (Fig. 2C, regions C1 to C10.2 versus N1 to N7).

Consistent with the prediction that conserved regions interact preferentially with DNA binding proteins is the prediction that these regions are involved in transcriptional regulation activity. To explore this possibility, we developed an assay for in vitro enhancer activity based on transient transfection of a human liver cell line. The 10 most conserved regions, as well as the 7 least conserved regions, were individually deleted from the whole 1.6-kb region (8). These constructs were compared with the intact 1.6-kb region construct for their ability to drive the expression of a luciferase reporter gene. Three independent experimental determinations reproducibly indicated that conserved regions had a much larger functional impact than did nonconserved regions in these reporter-gene expression assays (8). The deletions of the conserved sequence elements reduced the expression of the full reporter by 25 to 55% (17), with the exception of the construct carrying the deletion of region 6 (Fig. 3). In contrast, deletions of all but one of the seven nonconserved regions had a minimal effect on the expression of the full reporter construct, reducing its levels by a median value of only 4%.

Figure 3

Transfection analysis of conserved and nonconserved regions in the 1.6-kb apo(a) region. The colored bars represent expression values of luciferase reporter vectors carrying individual deletions from the whole 1.6-kb apo(a) region of one of the conserved (blue bars) or nonconserved (red bars) regions. Luciferase values are normalized by β-galactosidase expression and reported as percentages of the expression of the whole 1.6-kb apo(a) region. Each bar represents the average of three independent transfection experiments, each determined in quadruplicate. Error bars indicate 1 SD. The dotted line indicates the median expression of the conserved and nonconserved regions.

The analysis of closely related primates facilitates the discovery of functional elements specific to primates as well as elements shared with evolutionarily distant mammals. The high absolute degree of similarity minimizes ambiguity in the computation of the multiple alignment, which in turn greatly facilitates the subsequent construction of the phylogenetic tree (18). Furthermore, the generalization of gene-finding algorithms to multiple organism annotation is simplified, which results in more accurate predictions (supporting online text). The facility of sequence alignments and the possibility of comparative assembly for nonhuman primates, with human as the reference sequence, have important practical relevance, because they considerably diminish the depth of sequence coverage required for an organism to be informative in annotating the human genome.

Evaluation of our data suggests that sequence from as few as four to six primate species in addition to humans is sufficient for the identification of a large fraction of functional elements in the human genome, many of which are likely to be missed by human-mouse comparisons. With the goal of annotating the human genome, these studies indicate that the generation of a limited amount of sequence from a few additional properly selected primate genomes will provide information previously unavailable from comparisons of humans with more evolutionarily distant species.

Supporting Online Material

Materials and Methods

SOM Text

Figs. S1 and S2


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