The Genom of Homo sapiens.pdf

PREDICTING GENE REGULATORY REGIONS 337count for at most 2% of the human genome, and they areobviously under selective constraint. The other 38% ofthe human genome that does not code for protein but stillaligns with mouse should include gene regulatory sequencesand other functional noncoding sequences. However,these alignments also include much neutral DNA;e.g., about one-fourth of all the ancestral repeats in humansalign with orthologs in mouse. All the sequencesthat align between mouse and human are conserved in thesense that they are present in both species, but the goal isto identify the sequences that are subject to purifying selection.It is the latter sequences that are playing a role insome conserved function.A major complication to answering this question is thatthe rate of neutral evolution varies across the genome.The distribution of nucleotide substitutions per site in ancestralrepeats (computed on 1-Mb nonoverlapping windows)is quite wide (Fig. 1), reflecting substantial regionalvariation in the underlying neutral substitutionrate. In addition, the amount of DNA inferred to bedeleted from mouse and the amount of transposable elementsinserted and retained show substantial variation(Fig. 1). Furthermore, the amounts of neutral substitution,deletion, insertion (of LTR repeats), recombination, andsingle-nucleotide polymorphisms (SNPs) covary dramatically(Fig. 2A). Because the substitutions are measuredin neutral DNA, different levels of selection cannot exonecan draw an informative inference about the nonaligningpart of the ancestral portion of a genome—it isnot likely to be present in the other genome. Because wedo not align lineage-specific insertions, and lineage-specificduplicates can align, the simplest explanation for thesequences not being in the comparison genome is thatthey were deleted. Other analyses based on a relativelyconstant genome size in mammals also argue that thenonaligning fraction reveals deletions in the comparisongenome (Waterston et al. 2002).Genome sequences of additional species, such as rat (InternationalRat Genome Sequencing Consortium, in prep.),are being assembled as large-scale genomic sequence andanalysis projects move into more functional and analyticalstudies (Collins et al. 2003). Pair-wise and multiple alignmentsof these sequences are regularly updated and madeavailable on the UCSC Genome Browser (Kent et al. 2002)at http://genome.ucsc.edu. Additional mammalian genomesequences substantially improve the power of sequencealignment techniques to resolve functional from nonfunctionalDNA sequences (Thomas et al. 2003).CONSERVATION AND SELECTIONAbout 40% of the human genome aligns with sequencesin the mouse genome. As expected, almost all(99%) of the genes align between the genomes. These ac-A.correlation coefficient0.50.40.30.20.1OriginalResiduals onGC parametersB.0.0deletions SNPs recombinationLTR insertionssubstitutions per AR site versusBase positionGata1HumanConsRepeat Masker4130000 4135000Primitive erythropoiesisDefinitive erythropoiesis40Figure 2. Covariation in divergence rates and application of an alignment score that accounts for local rate variation. (A) Correlationamong the amounts of neutral substitution (in ARs) with large deletions (based on human–mouse alignments), insertions of LTR repeats,recombination, and SNPs in human. Correlations are shown for the original data and for residuals after the quadratic effects offraction G+C, change in fraction G+C, and CpG island density have been removed (Hardison et al. 2003). The correlations of variousdivergence processes with insertion and retention of different classes of repeats is the subject of ongoing work. (B) The HumanCons track plots the L score giving the log-likelihood that alignments reflect selection for the mouse Gata1 gene. The gene is transcribedfrom right to left. The upstream and intronic noncoding regions with high L scores correspond to previously described strongerythroid enhancers (Onodera et al. 1997).