Initial sequencing and analysis of the human genome - Vitagenes

articleschromosome Y is unusually young, probably owing to a hightolerance for gain of new material by insertion and loss of oldmaterial by deletion. Several lines of evidence support this picture.For example, LINE elements on chromosome Yare on average muchyounger than those on autosomes (not shown). Similarly, MaLRfamilyretroposons on chromosome Y are younger than those onautosomes, with the representation of subfamilies showing a stronginverse correlation with the age of the subfamily. Moreover, chromosomeY has a relative over-representation of the younger retroviralclass II (ERVK) and a relative under-representation of theprimarily older class III (ERVL) compared with other chromosomes.Overall, chromosome Y seems to maintain a youthfulappearance by rapid turnover.Interspersed repeats on chromosome Y can also be used toestimate the relative mutation rates, a m and a f , in the male andfemale germlines. Chromosome Y always resides in males, whereaschromosome X resides in females twice as often as in males. Thesubstitution rates, m Y and m X , on these two chromosomes shouldthus be in the ratio m Y :m X =(a m ):(a m +2a f )/3, provided that oneconsiders equivalent neutral sequences. Several authors have estimatedthe mutation rate in the male germline to be ®vefold higherthan in the female germline, by comparing the rates of evolution ofX- and Y-linked genes in humans and primates. However, Page andcolleagues 192 have challenged these estimates as too high. Theystudied a 39-kb region that is apparently devoid of genes and resideswithin a large segmental duplication from X to Y that occurred 3±4Myr ago in the human lineage. On the basis of phylogenetic analysisof the sequence on human Yand human, chimp and gorilla X, theyobtained a much lower estimate of m Y :m X = 1.36, corresponding toa m :a f = 1.7. They suggested that the other estimates may have beenhigher because they were based on much longer evolutionaryperiods or because the genes studied may have been under selection.Our database of human repeats provides a powerful resource foraddressing this question. We identi®ed the repeat elements fromrecent subfamilies (effectively, birth cohorts dating from the past50 Myr) and measured the substitution rates for subfamily memberson chromosomes X and Y (Fig. 29). There is a clear linear relationshipwith a slope of m Y :m X = 1.57 corresponding to a m :a f = 2.1. Theestimate is in reasonable agreement with that of Page et al., althoughit is based on much more total sequence (360 kb on Y, 1.6 Mb on X)and a much longer time period. In particular, the discrepancy withearlier reports is not explained by recent changes in the humanlineage. Various theories have been proposed for the higher mutationrate in the male germline, including the greater number of celldivisions in the formation of sperm than eggs and different repairmechanisms in sperm and eggs.Median substitution level ofrepeat subfamily on Y (%)10500 5 10Median substitution level ofrepeat subfamily on X (%)Figure 29 Higher substitution rate on chromosome Y than on chromosome X. Wecalculated the median substitution level (excluding CpG sites) for copies of the most recentL1 subfamilies (L1Hs±L1PA8) on the X and Y chromosomes. Only the 39 UTR of the L1element was considered because its consensus sequence is best established.Active transposons. We were interested in identifying the youngestretrotransposons in the draft genome sequence. This set shouldcontain the currently active retrotransposons, as well as the insertionsites that are still polymorphic in the human population.The youngest branch in the phylogenetic tree of human LINE1elements is called L1Hs (ref. 158); it differs in its 39 untranslatedregion (UTR) by 12 diagnostic substitutions from the next oldestsubfamily (L1PA2). Within the L1Hs family, there are twosubsets referred to as Ta and pre-Ta, de®ned by a diagnostictrinucleotide 193,194 . All active L1 elements are thought to belong tothese two subsets, because they account for all 14 known cases ofhuman disease arising from new L1 transposition (with 13 belongingto the Ta subset and one to the pre-Ta subset) 195,196 . Thesesubsets are also of great interest for population genetics because atleast 50% are still segregating as polymorphisms in the humanpopulation 194,197 ; they provide powerful markers for tracingpopulation history because they represent unique (non-recurrentand non-revertible) genetic events that can be used (along withsimilarly polymorphic Alus) for reconstructing human migrations.LINE1 elements that are retrotransposition-competent shouldconsist of a full-length sequence and should have both ORFs intact.Eleven such elements from the Ta subset have been identi®ed,including the likely progenitors of mutagenic insertions into thefactor VIII and dystrophin genes 198±202 . A cultured cell retrotranspositionassay has revealed that eight of these elements remainretrotransposition-competent 200,202,203 .We searched the draft genome sequence and identi®ed 535 LINEsbelonging to the Ta subset and 415 belonging to the pre-Ta subset.These elements provide a large collection of tools for probinghuman population history. We also identi®ed those consisting offull-length elements with intact ORFs, which are candidate activeLINEs. We found 39 such elements belonging to the Ta subset and22 belonging to the pre-Ta subset; this substantially increases thenumber in the ®rst category and provides the ®rst known examplesin the second category. These elements can now be tested forretrotransposition competence in the cell culture assay. Preliminaryanalysis resulted in the identi®cation of two of these elements as thelikely progenitors of mutagenic insertions into the b-globin andRP2 genes (R. Badge and J. V. Moran, unpublished data). Similaranalyses should allow the identi®cation of the progenitors of most,if not all, other known mutagenic L1 insertions.L1 elements can carry extra DNA if transcription extends throughthe native transcriptional termination site into ¯anking genomicDNA. This process, termed L1-mediated transduction, provides ameans for the mobilization of DNA sequences around the genomeand may be a mechanism for `exon shuf¯ing' 204 . Twenty-one percent of the 71 full-length L1s analysed contained non-L1-derivedsequences before the 39 target-site duplication site, in cases in whichthe site was unambiguously recognizable. The length of the transducedsequence was 30±970 bp, supporting the suggestion that 0.5±1.0% of the human genome may have arisen by LINE-basedtransduction of 39 ¯anking sequences 205,206 .Our analysis also turned up two instances of 59 transduction(145 bp and 215 bp). Although this possibility had been suggestedon the basis of cell culture models 195,203 , these are the ®rst documentedexamples. Such events may arise from transcription initiatingin a cellular promoter upstream of the L1 elements. L1transcription is generally con®ned to the germline 207,208 , buttranscription from other promoters could explain a somatic L1retrotransposition event that resulted in colon cancer 206 .Transposons as a creative force. The primary force for the originand expansion of most transposons has been selection for theirability to create progeny, and not a selective advantage for the host.However, these sel®sh pieces of DNA have been responsible forimportant innovations in many genomes, for example by contributingregulatory elements and even new genes.Twenty human genes have been recognized as probably derivedNATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com © 2001 Macmillan Magazines Ltd887