The sequencing of whole genomes means that genetic information is increasingly considered in functional rather than structural terms. But for the moment, the principal structural element of genomes — the chromosome — remains the predominant unit by which to measure progress in the Human Genome Project.

On page 311 of this issue1, a multinational consortium reports the complete sequence of chromosome 21, the smallest human chromosome. The results indicate that previous estimates of the total number of human genes may need to be revised downwards. Meanwhile, the small number of genes, and a catalogue that identifies them, provide a boost for those endeavouring to define all of the primary molecular players in Down syndrome. Affecting one in 700 live births, Down syndrome occurs when three copies of chromosome 21 are inherited instead of two (Fig 1, top). The condition is the most common known genetic cause of mental retardation and the leading cause of congenital heart disease, and results in a wide variety of other developmental and health problems.

Figure 1: Chromosome 21 in context.
figure 1


Top, triplication of chromosome 21 is the genetic defect underlying Down syndrome. Bottom, transmission electron micrograph of chromosome 21, showing the long and short arms.

The consortium's report1 describes several new technical achievements. The total length of the sequence reported is 33.55 million base pairs (or megabases, Mb). This covers 99.7% of the long arm of chromosome 21 (Fig 1, bottom), and just exceeds the 33.46 Mb reported for the slightly larger long arm of chromosome 22 (ref. 2). The paper includes the longest continuous DNA sequence reported to date, extending 28.5 Mb. The entire chromosome sequence has only three gaps (totalling 100 kilobases), compared with the ten gaps (totalling about 1 Mb) for the long arm of chromosome 22.

The new sequence also includes 281 kilobases from chromosome 21's short arm — mapping and cloning of which posed a challenge because it contains several classes of highly repetitive sequences3. The length of this short arm can vary greatly among individuals. So this sequence is the first example of a large genome region that can expand or contract on a scale of many megabases.

The sequencing of the long arm of chromosome 21 provides a somewhat arbitrary, but nonetheless worthwhile, basis for deriving conclusions about the general organization of the human genome. The most striking difference is the reduced gene content of chromosome 21 — 225 genes identified, compared with 545 on chromosome 22. The two consortia responsible for these sequences used somewhat different criteria to identify the genes within their respective chromosomes (Box 1, overleaf). But the differences may well balance each other out, meaning that a comparison of gene numbers is valid.

Chromosome 21 was expected to be relatively gene-poor, but it seems that it is even more impoverished than anticipated. The long arm of chromosome 21 represents about 1% of the human genome, but was predicted to contain less than 1% of the total number of human genes. The Unigeneproject4 suggested that chromosome 21 would contain only 80% of the number of genes that would be expected on the basis of its size. If the total number of human genes were 100,000, as predicted, chromosome 21 would still be expected to contain 800–1,000 genes. The 225 genes now identified1 stand in stark contrast to this prediction.

Combining data from the long arms of the two completely sequenced chromosomes, the chromosome 21 consortium estimates that the human genome may contain as few as 40,000 genes. However, this is based on complete sequences for just 2% of the human genome, and could be low for a variety of reasons. For example, other human chromosomes may be more gene-rich. The major histocompatibility complex (MHC) region on chromosome 6 — a region essential to the immune system — spans only 3.6 Mb, but contains 128 genes and 96 pseudogenes5.

Another measure of gene richness is provided by the number of ‘CpG islands’ on the long arms of chromosomes 21 and 22. These islands are DNA sequences of a few hundred base pairs that have a high amount (more than 55%) of cytosine and guanine nucleotides. They are associated with about 60% of known human genes, and might be useful in gene identification. The two sequencing consortia1,2 again applied different criteria to count CpG islands (Box 1), and these differences probably produce a total that is higher — by an unknown amount — for chromosome 22's long arm. Even so, chromosome 21 appears to be even poorer in CpG islands than in genes when compared with chromosome 22.

The chromosome 22 sequencing consortium suggested that its identification of 545 genes on the long arm was low — a conclusion based in part on the fact that 271 of the 553 identified CpG islands have not yet been associated with genes. In fact, nearly all of the 115 conservatively predicted CpG islands on chromosome 21's long arm are associated with genes. Analysis of both chromosomes using the same methods will help to determine the accuracy of identifying genes by counting CpG islands.

The chromosome 21 sequencing consortium also compared the chromosome 21 sequence with data in the available mouse genome database. No new conserved syntenies — regions where the same genes are ‘linked’ on chromosomes in different species — were identified. The previously known conserved syntenies are with mouse chromosomes 10, 16 and 17. The chromosome 21 consortium suggests that discrepancies in the gene order predicted by comparing the sequence to mouse gene-linkage maps may result from the differing resolution of these maps. In fact, the higher-resolution physical map6 of mouse chromosome 10 shows that all 24 genes known to be shared between mouse chromosome 10 and human chromosome 21 occur in the same order. The high degree of conservation between human and mouse is important, because comparing the two sequences — as more of the mouse sequence becomes available — is likely to increase our ability to pick out genes and other significant features from the welter of sequence information.

The availability of the chromosome 21 sequence will have an immediate impacton the study of human single-gene disorders. For example, the genes responsible for five of those monogenic disorders that map to chromosome 21 — including two forms of deafness, Usher and Knobloch's syndromes — have not yet been identified. But having the complete sequence will obviate the labour-intensive step of identifying candidate genes. The genes responsible for these disorders are likely to be found rapidly.

But the greatest impact of the chromosome 21 gene catalogue will be in assessing the contributions of specific genes to traits seen in Down syndrome. The small number of genes on chromosome 21 is likely to be part of the reason why the presence of three copies of this chromosome — unlike so many chromosome defects — is not fatal at a very young age, or even before birth. Yet there are varying ideas about which genes are associated with particular features of Down syndrome, and the mechanisms by which an imbalance in the number of genes might produce the more than 80 physical andmental disorders that can be seen in this trisomy. Obtaining a comprehensive catalogue of the genes on chromosome 21 has been a goal of Down syndrome researchers for many years, and is realized in this landmark contribution.