The amount of noncoding genomic DNA sequence that aligns between human and mouse varies substantially in different regions of their genomes, and the amount of repetitive DNA also varies. In this report, we show that divergence in noncoding nonrepetitive DNA is strongly correlated with the amount of repetitive DNA in a region. We investigated aligned DNA in four large genomic regions with finished human sequence and almost or completely finished mouse sequence. These regions, totaling 5.89 Mb of DNA, are on different chromosomes and vary in their base composition. An analysis based on sliding windows of 10 kb shows that the fraction of aligned noncoding nonrepetitive DNA and the fraction of repetitive DNA are negatively correlated, both at the level of an entire region and locally within it. This conclusion is strongly supported by a randomization study, in which repetitive elements are removed and randomly relocated along the sequences. Thus, regions of noncoding genomic DNA that accumulated fewer point mutations since the primaterodent divergence also suffered fewer retrotransposition events. These results indicate that some regions of the genome are more ''flexible'' over the time scale of mammalian evolution, being able to accommodate many point mutations and insertions, whereas other regions are more ''rigid'' and accumulate fewer changes. Stronger conservation is generally interpreted as indicating more extensive or more important function. The evidence presented here of correlated variation in the rates of different evolutionary processes across noncoding DNA must be considered in assessing such conservation for evidence of selection. T he rate of fixation of nucleotide substitutions and small insertions͞deletions, collectively referred to as point mutations, varies substantially in different regions of mammalian genomes. The 1,000-fold difference in nonsynonymous substitution rates among genes has long been recognized as a reflection of different levels of selection on the protein products of genes (reviewed in refs. 1 and 2). However, the rate of fixation of synonymous substitutions, which seem to be effectively neutral, also varies about 10-fold locus to locus (3). The synonymous and nonsynonymous substitution rates are significantly correlated (4, 5). The variation in synonymous substitution rates has been attributed to differences in the rate and pattern of mutation in different regions of the genome (6). Recently, Matassi et al. (7) showed that the synonymous substitution rate is significantly more similar for neighboring genes than for randomly chosen genes, which argues for regional differences in substitution rates. Regional differences in point mutation rates are also indicated by comparisons of long genomic DNA sequences. Examination of several loci reveals dramatic differences in the amount of noncoding nonrepetitive DNA that aligns between species in different mammalian orders (8, 9). Substantial differences are seen even for two loci that encode functionally equivalent proteins, the ␣-and ␤-globin subunits of hemoglobin (10). The amount of conservation in noncoding nonrepetitive DNA varies about 10-fold (11). Thus, a similar range of variation is seen both for the amount of aligning noncoding DNA and for synonymous substitution rates in coding DNA, showing local variation in the rate of fixation of substitutions and small insertions͞deletions. Striking differences in the distribution of repetitive DNA are also seen across the human genome (12) (13) (14) . At one extreme are HOX gene clusters, which contain only about 2% interspersed repeats within 100 kb, whereas a 525-kb region of chromosome Xp11 has a repeat density of 89% (14). Thus, the frequency of fixation of these transposable elements varies enormously in different segments of the human genome. Some potential explanations for these regional differences focus on particular sequences, such as target-site preference for transposition or base-composition biases in substitutions (6, 15). These explanations do not require a correlation between amount of point mutation and amount of transposition. A different model is that some segments of the genome are more tolerant of changes of any sort, whether they are point mutations or transpositions. In this case, a correlation should be seen between the number of point mutations (revealed by alignments of noncoding nonrepetitive DNA) and the amount of repetitive DNA in a locus. We demonstrate such a correlation in four loci on different chromosomes for which substantial continuous DNA sequence is available in human and mouse. Quantitative and statistical analyses confirm a significant association between amount of divergence in noncoding nonrepetitive DNA and frequency of interspersed repeats in all four loci. Our results show that overall rates of evolution vary in different segments of the genome, with more ''flexible'' regions able to accommodate many point mutations and insertions, whereas more ''rigid'' regions tend to accumulate fewer changes of both types. Sources of Sequences. Information about the sources, chromosomal locations, and characteristics of the human and mouse sequences is summarized in Table 1 . The human sequences for all four loci and parts of the mouse sequence homologous to the CD4 and velocardiofacial syndrome (VCFS) regions are finished. Other mouse sequences were compiled from searches of mouse draft sequences in GenBank. The PIPMAKER server can align a finished first sequence with multiple unordered and unoriented contigs from the second sequence (16). Annotation. To discriminate coding from noncoding sequences with high accuracy, we exhaustively reannotated the human sequences in a multistep process. First, the annotations from the authors were downloaded from GenBank or the Sanger Center (for the MHC, http:͞͞www.sanger.ac.uk͞HGP͞Chr6͞MHC.shtml). Then additional genes were identified by matches to known genes and to spliced expressed sequence tags (ESTs) by using the program
In REF the authors compare observed and randomized histograms of local correlation coefficients to relate the divergence in non-coding non-repetive DNA with the amount of repetitve DNA.
Association between divergence and interspersed repeats in mammalian noncoding genomic DNA
Proceedings of the National Academy of Sciences of the United States of America
Proceedings of the National Academy of Sciences of the United States of America
Medicine Biology