Initial sequencing and analysis of the human genome - Vitagenes

articleslong introns are more likely than short introns to be interrupted bygaps in the draft genome sequence. Nonetheless, there may be someresidual bias against long genes and long introns.There is considerable variation in overall gene size and intron size,with both distributions having very long tails. Many genes are over100 kb long, the largest known example being the dystrophin gene(DMD) at 2.4 Mb. The variation in the size distribution of codingsequences and exons is less extreme, although there are still someremarkable outliers. The titin gene 276 has the longest currentlyknown coding sequence at 80,780 bp; it also has the largestnumber of exons (178) and longest single exon (17,106 bp).It is instructive to compare the properties of human genes withthose from worm and ¯y. For all three organisms, the typical lengthof a coding sequence is similar (1,311 bp for worm, 1,497 bp for ¯yand 1,340 bp for human), and most internal exons fall within acommon peak between 50 and 200 bp (Fig. 35a). However, theworm and ¯y exon distributions have a fatter tail, resulting in alarger mean size for internal exons (218 bp for worm versus 145 bpfor human). The conservation of preferred exon size across all threespecies supports suggestions of a conserved exon-based componentof the splicing machinery 277 . Intriguingly, the few extremely shorthuman exons show an unusual base composition. In 42 detectedhuman exons of less than 19 bp, the nucleotide frequencies of A, G,T and C are 39, 33, 15 and 12%, respectively, showing a strongpurine bias. Purine-rich sequences may enhance splicing 278,279 , and itis possible that such sequences are required or strongly selected forto ensure correct splicing of very short exons. Previous studies haveshown that short exons require intronic, but not exonic, splicingenhancers 280 .In contrast to the exons, the intron size distributions differsubstantially among the three species (Fig. 35b, c). The worm and¯y each have a reasonably tight distribution, with most introns nearthe preferred minimum intron length (47 bp for worm, 59 bp for¯y) and an extended tail (overall average length of 267 bp for wormand 487 bp for ¯y). Intron size is much more variable in humans,with a peak at 87 bp but a very long tail resulting in a mean of morethan 3,300 bp. The variation in intron size results in great variationin gene size.The variation in gene size and intron size can partly be explainedby the fact that GC-rich regions tend to be gene-dense with manycompact genes, whereas AT-rich regions tend to be gene-poor withmany sprawling genes containing large introns. The correlation ofgene density with GC content is shown in Fig. 36a, b; the relativedensity increases more than tenfold as GC content increases fromaFrequency0.200.180.160.140.120.100.080.060.040.020.000.300.320.340.360.380.400.420.440.460.480.500.520.540.560.580.600.620.640.66GC contentGenomeGenes0.680.70b 20Relative gene density1816141210864200.300.320.340.360.380.400.420.440.460.480.500.520.54GC content0.560.580.600.620.640.660.680.70c2,500140Median intron length2,0001,5001,0001201008060Median exon length50040200IntronExon0.3 0.35 0.4 0.45 0.5 0.55 0.6 0.65GC content0Figure 36 GC content. a, Distribution of GC content in genes and in the genome. For9,315 known genes mapped to the draft genome sequence, the local GC content wascalculated in a window covering either the whole alignment or 20,000 bp centred aroundthe midpoint of the alignment, whichever was larger. Ns in the sequence were notcounted. GC content for the genome was calculated for adjacent nonoverlapping 20,000-bp windows across the sequence. Both the gene and genome distributions have beennormalized to sum to one. b, Gene density as a function of GC content, obtained by takingthe ratio of the data in a. Values are less accurate at higher GC levels because thedenominator is small. c, Dependence of mean exon and intron lengths on GC content. Forexons and introns, the local GC content was derived from alignments to ®nished sequenceonly, and were calculated from windows covering the feature or 10,000 bp centred on thefeature, whichever was larger.NATURE | VOL 409 | 15 FEBRUARY 2001 | www.nature.com © 2001 Macmillan Magazines Ltd897