Initial sequencing and analysis of the human genome - Vitagenes

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articleshave suggested that small deletions occur at a rate that is 75-foldhigher in ¯ies than in mammals; the half-life of such nonfunctionalDNA is estimated at 12 Myr for ¯ies and 800 Myr for mammals 167 .The rate of large deletions has not been systematically compared,but seems likely also to differ markedly.(3) Whereas in the human two repeat families (LINE1 and Alu)account for 60% of all interspersed repeat sequence, the otherorganisms have no dominant families. Instead, the worm, ¯y andmustard weed genomes all contain many transposon families, eachconsisting of typically hundreds to thousands of elements. Thisdifference may be explained by the observation that the verticallytransmitted, long-term residential LINE and SINE elements represent75% of interspersed repeats in the human genome, but only 5±25% in the other genomes. In contrast, the horizontally transmittedand shorter-lived DNA transposons represent only a small portionof all interspersed repeats in humans (6%) but a much largerfraction in ¯y, mustard weed and worm (25%, 49% and 87%,respectively). These features of the human genome are probablygeneral to all mammals. The relative lack of horizontally transmittedelements may have its origin in the well developed immune systemof mammals, as horizontal transfer requires infectious vectors, suchas viruses, against which the immune system guards.We also looked for differences among mammals, by comparingthe transposons in the human and mouse genomes. As with thehuman genome, care is required in calibrating the substitution clockfor the mouse genome. There is considerable evidence that the rateof substitution per Myr is higher in rodent lineages than in thehominid lineages 139,168,169 . In fact, we found clear evidence fordifferent rates of substitution by examining families of transposableelements whose insertions predate the divergence of the human andmouse lineages. In an analysis of 22 such families, we found that thesubstitution level was an average of 1.7-fold higher in mouse thanhuman (not shown). (This is likely to be an underestimate becauseof an ascertainment bias against the most diverged copies.) Thefaster clock in mouse is also evident from the fact that the ancientLINE2 and MIR elements, which transposed before the mammalianradiation and are readily detectable in the human genome, cannotbe readily identi®ed in available mouse genomic sequence (Fig. 18).We used the best available estimates to calibrate substitutionlevels and time 169 . The ratio of substitution rates varied from about1.7-fold higher over the past 100 Myr to about 2.6-fold higher overthe past 25 Myr.The analysis shows that, although the overall density of the fourtransposon types in human and mouse is similar, the age distributionis strikingly different (Fig. 18). Transposon activity in themouse genome has not undergone the decline seen in humans andproceeds at a much higher rate. In contrast to their possibleextinction in humans, LTR retroposons are alive and well in theProportion of interspersed repeats (%)1009080706050403020100HumanFlyWormMustardweed>25% Oldest
articlesProportion of genome comprised by each class (%)6050403020100SSRLINE2 MIRDNALINE1 ALULTR54GC content (%)Figure 22 Density of the major repeat classes as a function of local GC content, in windows of 50 kb.2.0100Frequency of Alu class relative to itsaverage density in the genome1.81.61.41.21.00.80.60.40.2Proportion of DNA transposonscomprised by each age group (%)80604020Nucleotidesubsitutionlevel24–30%21–23%16–20%14–15.5%0–13%0.054AluY < 1% ( 4% (5–30 Myr)GC content bins (%)AluSc (25–35 Myr)AluS (35–60 Myr)AluJ, FAM (60–100 Myr)052GC content bins (%)Figure 24 DNA transposon copies in AT-rich DNA tend to be younger than those in moreGC-rich DNA. DNA transposon families were grouped into ®ve age categories by theirmedian substitution level (see Fig. 19). The proportion attributed to each age class isshown as a function of GC content. Similar patterns are seen for LINE1 and LTR elements.Figure 23 Alu elements target AT-rich DNA, but accumulate in GC-rich DNA. This graphshows the relative distribution of various Alu cohorts as a function of local GC content. Thedivergence levels (including CpG sites) and ages of the cohorts are shown in the key.similarly resisted the insertion of transposable elements duringrodent evolution.Distribution by GC content. We next focused on the correlationbetween the nature of the transposons in a region and its GCcontent. We calculated the density of each repeat type as a functionof the GC content in 50-kb windows (Fig. 22). As has beenreported 142,173±176 , LINE sequences occur at much higher density inAT-rich regions (roughly fourfold enriched), whereas SINEs (MIR,Alu) show the opposite trend (for Alu, up to ®vefold lower in ATrichDNA). LTR retroposons and DNA transposons show a moreuniform distribution, dipping only in the most GC-rich regions.The preference of LINEs for AT-rich DNA seems like a reasonableway for a genomic parasite to accommodate its host, by targetinggene-poor AT-rich DNA and thereby imposing a lower mutationalburden. Mechanistically, selective targeting is nicely explained bythe fact that the preferred cleavage site of the LINE endonuclease isTTTT/A (where the slash indicates the point of cleavage), which isused to prime reverse transcription from the poly(A) tail of LINERNA 177 .The contrary behaviour of SINEs, however, is baf¯ing. How doSINEs accumulate in GC-rich DNA, particularly if they depend onthe LINE transposition machinery 178 ? Notably, the same pattern isseen for the Alu-like B1 and the tRNA-derived SINEs in mouse andfor MIR in human 142 . One possibility is that SINEs somehow targetGC-rich DNA for insertion. The alternative is that SINEs initiallyinsert with the same proclivity for AT-rich DNA as LINEs, but thatthe distribution is subsequently reshaped by evolutionaryforces 142,179 .We used the draft genome sequence to investigate this mystery bycomparing the proclivities of young, adolescent, middle-aged andold Alus (Fig. 23). Strikingly, recent Alus show a preference for ATrichDNA resembling that of LINEs, whereas progressively olderAlus show a progressively stronger bias towards GC-rich DNA.These results indicate that the GC bias must result from strongpressure: Fig. 23 shows that a 13-fold enrichment of Alus in GC-richDNA has occurred within the last 30 Myr, and possibly morerecently.These results raise a new mystery. What is the force that producesthe great and rapid enrichment of Alus in GC-rich DNA? Oneexplanation may be that deletions are more readily tolerated ingene-poor AT-rich regions than in gene-rich GC-rich regions,resulting in older elements being enriched in GC-rich regions.Such an enrichment is seen for transposable elements such as884 © 2001 Macmillan Magazines Ltd NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com
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