Initial sequencing and analysis of the human genome - Vitagenes

articlesposable elements in categories re¯ecting equal amounts of sequencedivergence. In Fig. 18b the data are grouped into four binscorresponding to successive 25-Myr periods, on the basis of anapproximate clock. Figure 19 shows the mean ages of varioussubfamilies of DNA transposons. Several facts are apparent fromthese graphs. First, most interspersed repeats in the human genomepredate the eutherian radiation. This is a testament to the extremelyslow rate with which nonfunctional sequences are cleared fromvertebrate genomes (see below concerning comparison with the ¯y).Second, LINE and SINE elements have extremely long lives. Themonophyletic LINE1 and Alu lineages are at least 150 and 80 Myrold, respectively. In earlier times, the reigning transposons wereLINE2 and MIR 148,158 . The SINE MIR was perfectly adapted forreverse transcription by LINE2, as it carried the same 50-basesequence at its 39 end. When LINE2 became extinct 80±100 Myrago, it spelled the doom of MIR.Third, there were two major peaks of DNA transposon activity(Fig. 19). The ®rst involved Charlie elements and occurred longbefore the eutherian radiation; the second involved Tigger elementsand occurred after this radiation. Because DNA transposons canproduce large-scale chromosome rearrangements 159±162 , it is possiblethat widespread activity could be involved in speciation events.Fourth, there is no evidence for DNA transposon activity in thepast 50 Myr in the human genome. The youngest two DNAtransposon families that we can identify in the draft genomesequence (MER75 and MER85) show 6±7% divergence from theirrespective consensus sequences representing the ancestral element(Fig. 19), indicating that they were active before the divergence ofhumans and new world monkeys. Moreover, these elements wererelatively unsuccessful, together contributing just 125 kb to the draftgenome sequence.Number of kb covered by family8,0007,0006,0005,0004,0003,0002,0001,000CharliePiggyBac-likeMarinerTc2TiggerUnclassifiedZaphod00 0.05 0.1 0.15 0.2 0.25 0.3 0.35 0.4Average nucleotide substitution level for familyFigure 19 Median ages and per cent of the genome covered by subfamilies of DNAtransposons. The Charlie and Zaphod elements were hobo-Activator-Tam3 (hAT) DNAtransposons; Mariner, Tc2 and Tigger were Tc1-like elements. Unlike retroposons, DNAtransposons are thought to have a short life span in a genome. Thus, the average ormedian divergence of copies from the consensus is a particularly accurate measure of theage of the DNA transposon copies.Finally, LTR retroposons appear to be teetering on the brink ofextinction, if they have not already succumbed. For example, themost proli®c elements (ERVL and MaLRs) ¯ourished for more than100 Myr but appear to have died out about 40 Myr ago 163,164 . Only asingle LTR retroposon family (HERVK10) is known to have transposedsince our divergence from the chimpanzee 7 Myr ago, withonly one known copy (in the HLA region) that is not sharedbetween all humans 165 . In the draft genome sequence, we canidentify only three full-length copies with all ORFs intact (the®nal total may be slightly higher owing to the imperfect state ofthe draft genome sequence).More generally, the overall activity of all transposons has declinedmarkedly over the past 35±50 Myr, with the possible exception ofLINE1 (Fig. 18). Indeed, apart from an exceptional burst of activityof Alus peaking around 40 Myr ago, there would appear to havebeen a fairly steady decline in activity in the hominid lineage sincethe mammalian radiation. The extent of the decline must be evengreater than it appears because old repeats are gradually removed byrandom deletion and because old repeat families are harder torecognize and likely to be under-represented in the repeat databases.(We con®rmed that the decline in transposition is not an artefactarising from errors in the draft genome sequence, which, inprinciple, could increase the divergence level in recent elements.First, the sequence error rate (Table 9) is far too low to have asigni®cant effect on the apparent age of recent transposons; andsecond, the same result is seen if one considers only ®nishedsequence.)What explains the decline in transposon activity in the lineageleading to humans? We return to this question below, in the contextof the observation that there is no similar decline in the mousegenome.Comparison with other organisms. We compared the complementof transposable elements in the human genome with those of theother sequenced eukaryotic genomes. We analysed the ¯y, wormand mustard weed genomes for the number and nature of repeats(Table 12) and the age distribution (Fig. 20). (For the ¯y, weanalysed the 114 Mb of un®nished `large' contigs produced by thewhole-genome shotgun assembly 166 , which are reported to representeuchromatic sequence. Similar results were obtained by analysing30 Mb of ®nished euchromatic sequence.) The human genomestands in stark contrast to the genomes of the other organisms.(1) The euchromatic portion of the human genome has a muchhigher density of transposable element copies than the euchromaticDNA of the other three organisms. The repeats in the otherorganisms may have been slightly underestimated because therepeat databases for the other organisms are less complete thanfor the human, especially with regard to older elements; on the otherhand, recent additions to these databases appear to increase therepeat content only marginally.(2) The human genome is ®lled with copies of ancient transposons,whereas the transposons in the other genomes tend to be of morerecent origin. The difference is most marked with the ¯y, but is clearfor the other genomes as well. The accumulation of old repeats islikely to be determined by the rate at which organisms engage in`housecleaning' through genomic deletion. Studies of pseudogenesTable 12 Number and nature of interspersed repeats in eukaryotic genomesPercentageof basesHuman Fly Worm Mustard weedApproximatenumber offamiliesPercentageof basesApproximatenumber offamiliesPercentageof basesApproximatenumber offamiliesPercentageof basesApproximatenumber offamiliesLINE/SINE 33.40% 6 0.70% 20 0.40% 10 0.50% 10LTR 8.10% 100 1.50% 50 0.00% 4 4.80% 70DNA 2.80% 60 0.70% 20 5.30% 80 5.10% 80Total 44.40% 170 3.10% 90 6.50% 90 10.50% 160...................................................................................................................................................................................................................................................................................................................................................................The complete genomes of ¯y, worm, and chromosomes 2 and 4 of mustard weed (as deposited at ncbi.nlm.nih.gov/genbank/genomes) were screened against the repeats in RepBase Update 5.02(September 2000) with RepeatMasker at sensitive settings.882 © 2001 Macmillan Magazines Ltd NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com