Sequencing of the human genome was first formally proposed in 1985, but at the time the idea was met with mixed reactions in the scientific community. Then in1990 the Human Genome Project (HGP), under the direction by the N.I.H. and the Dept. of Energy, launched a 15-year, $3 billion plan for sequencing the complete human genome. Their progress was slow however and the HGP did not appear to be on pace to finish by the projected date in 2005. Half way through their planned time period, in early 1998, the HGP had sequenced less than 5% of the entire genome.
Then, in the same year that the HGP was reevaluating its progress, Celera, headed by Craig Venter, announced its intention to sequence the entire human genome over a three year period. After cutting their teeth on the Drosophila genome (which was done in collaboration with Gerald Rubin and the Berkley Drosophila Genome Project), Celera initiated the whole-genome shotgun sequencing of the human genome on September 8th, 1999. Less than a year later, on 17 June 2000, the first draft of the genome was completed. Today 99.9% of the human genome is 'finished', meaning less than 1 bp error per 10,000 base pairs.
The method Celera used, termed shotgun sequencing, is conceptually straightforward, but requires large amounts of computer processing power to complete. The protocol (in great oversimplification) is as follows: 1) cut up the genomic DNA into small pieces of known and regular size, 2) clone the pieces of genomic DNA into plasmids for purification and amplification purposes, 3) randomly sequence the DNA fragments from the plasmids while screening the results for contamination, 4) and then load the whole sequenced mess into the computer and let the computer sort it all out. The computer essentially plays a giant matching game building up larger and larger overlapping sequences until the whole genome is finally laid out in entirety. The process is, of course, not nearly this simple. One major complication worth mentioning is that the human genome is particularly replete with repeat sequences that could easily create numerous misleading matches. Computing the set of all overlaps required approx. 10,000 CPU hours on a suite of four-processor Alpha SMPs with 4 gigabytes of RAM (4-5 days in elapsed time using 40 such machines).
Celera's surprising and controversial success was due to several factors. First off, Celera was able to build upon the knowledge that previous sequencing efforts had gained through years of research and experience, including the Human Genome Project and The Institute for Genome Research (TIGR). Second, Celera's sequencing facilities were unparalleled in their sheer size. Celera's sequencing facilities had 50x the sequencing capacity of TIGR. Finally, because the results of the HGP were public, Celera was able to use their data to help align their shotgun sequences in the whole genome.
The human genome is 2.91-billion base pairs in length. Celera estimated that approx. 26,383 genes exist in the human genome, but this number has been a source of continued controversy with other estimates reaching as high as 150,000 genes (which is almost certainly much too high). Of the estimate 26,383 genes, 42% have an unknown function. The average number of exons in the predicted genes range between 4-5 and the typical exon length is around 100-300 base pairs. The average size of a human gene is around 27,000bp, with typical ranges between 20,000 and 50,000bp. A quick calculation will demonstrate that human genes are mostly intronic in composition. The average intron can be thousands of base pairs in size and can be as large as tens of thousands of base pairs (compare this to the typical exon with a paltry size of ~200bp). Coding regions in the human genome are estimated to account for only around 3% of the total DNA sequence, intronic sequences contribute ~30%, and intergenic regions ~67%.
The expansion of non-coding DNA in humans is particularly striking when compared to other metazoan eukaryotes. For example, the human genome is 30x larger than the C. elegans and the Drosophila genome, but has only ~2-3x as many genes. Furthermore, human genes are 10x larger than fly and worm genes, but the vast majority of this increase in size is due to intronic expansion; their exons are essentially the same size. Repeat sequences are another very prominent feature of the human genome. 35% of the entire human genome (including coding regions) is classified as repetitive, which is quite high already, but if we examine non-coding regions the proportion of repetitive DNA climbs to 46%. Compare these numbers to Arabidopsis which has a relatively low percentage of repeat sequences in the genome, 10%. But you should also keep in mind that Vivia faba, or the humble broadbean, is composed of upwards of 80% repetitive DNA.
Another important feature of the human (and other mammalian) genomes is CpG islands. A CpG island is a region of DNA that has a higher relative proportion of CpG dinucleotides when compared to the entire genome. This increased CpG density is significant because these regions tend to be unmethylated and therefore are believed to promote the initiation of transcription. This belief is drawn mainly from two observations: 1) most of the housekeeping genes (which are constitutively expressed genes) have CpG islands at the 5' end of the transcript, and 2) CpG island methylation is known to correlate with gene inactivation during gene imprinting and tissue specific gene expression.
GNN: Quick Guide to Sequenced Genomes
