Preliminary Findings of The Human Genome Projects

Shortly after their press conferences, the two groups that had been striving for several years to map the human genome published their findings:

• the International Human Genome Sequencing Consortium (IHGSC) in the 15 February 2001 issue of Nature;
• Celera Genomics, a company in Rockville, Maryland, in the 16 February issue of Science.

What was not found

• Neither group had determined the complete sequence of the human genome.

  Each of our chromosomes is a single molecule of DNA. Some day the sequence of base pairs in each will be known from one end to the other. But in 2001, thousands of gaps remained to be filled.

  What they had done was present a series of draft sequences that represented about 90% (probably the most interesting 90%) of the genome.

• Even taken together, the results did not provide an accurate count of the number of protein-encoding genes in our genome (in contrast to such genomes as those of
  • mitochondrial DNA;
  • the Epstein-Barr virus;
  • many of the bacterial genomes.)
  One reason: the
  • large number and
  • large size
  of the introns that split these genes make it difficult to recognize the open reading frames (ORFs) that encode proteins.

What was found

1. The number of genes turned out to be much smaller than once predicted.

• only two to three times larger than the genomes of
  • Drosophila (~13,500 genes)
  • C. elegans (~19,000 genes)
• and representing only 1– 2% of the total DNA in the cell;
• and a third of the 100,000 genes that many had predicted would be found.
• (By the end of 2004, the number had been reduced to some 20,000–25,000.)

Are we only twice as complex as the tiny roundworm and fruit fly?

But,

• many of our protein-encoding genes produce more than one protein product (e.g., by alternative splicing of the primary transcript of the gene). On average, each of our ORFs produces 2 to 3 different proteins.

  So the human "proteome" (our total number of proteins) may be 10 or more times larger than that of the fruit fly and roundworm.

• A larger proportion of our genome
  • encodes transcription factors
  • is dedicated to control elements (e.g., enhancers) to which these transcription factors bind.
  The combinatorial use of these elements probably provides much greater flexibility of gene expression than is found in Drosophila and C. elegans.

2. Gene diversity and density.

• dystrophin with its 79 exons spread over 2.4 million base pairs of DNA;
• titin whose exons (Celera identified 234; IHGSC only 178) encode a single polypeptide of ~27,000 amino acids;

The density of genes on the different chromosomes varies from

• 23 genes per million base pairs on chromosome 19 (for a total of 1,400 genes) to
• only 5 genes per million base pairs on chromosome 13.

3. Humans have many genes not found in invertebrates.

These include genes encoding

• antibodies and T cell receptors for antigen (TCRs) [Discussion]
• the transplantation antigens of the major histocompatibility complex (HLA, the MHC of humans) [Link]
• cell-signaling molecules including the many types of cytokines
• the molecules that participate in blood clotting. [Link]
• mediators of apoptosis. Although these proteins occur in Drosophila and C. elegans, we have a much richer assortment of them.

4. Gene Duplication.

• the genes (several hundred) for olfactory receptors
• the various globin genes.

5. Repetitive DNA.

• LINES (long interspersed elements) [Discussion]
  • 16–19% of our genome
• SINES (short interspersed elements) including Alu elements [Discussion]
  • about 12%
• Retrotransposons
  • 5 to 8%
• DNA transposons
  • about 3%

What remains to be done?

• Fill in the gaps.

  This will make the human genome truly complete. On October 21, 2004, the IHGSC announced that they had pretty much (99%) completed the job with only 341 gaps remaining. However, they still could not determine the exact number of our genes (probably 20,000–25,000 of them).

• Determine the human proteome; that is, the total complement of proteins we synthesize.
• Analyze how clusters of genes are coordinately expressed
  • in various types of cells
  • at different times in the life of a cell.
  Such analysis will benefit greatly from the availability to gene chip technology and will also help us to understand how such a modest increase in gene number from Drosophila to humans could produce such a different outcome!
• Determine the genomes of other vertebrates, e.g., mouse and the chimpanzee.

  This will not only help us recognize more human genes but will give us insight into what makes us unique.

  Already we know that large sections of our genome have closely-related homologs in the mouse.

  Examples:
  • The collection of genes — and even their order — on human chromosome 17 matches closely those of mouse chromosome 11. The same is true of human chromosome 20 and mouse chromosome 2.
  • Humans and mice (also rats) share several hundred absolutely identical stretches of DNA extending for 200–800 base pairs.
    • Some are present in the exons of genes, especially genes involved in RNA processing.
    • Some are found in or near the introns of genes, especially genes encoding proteins involved in DNA transcription.
    • Some are found between genes — especially those, like Pax-6, essential to embryonic development — and may serve as enhancers.
    To have avoided any mutations for 60 million years since humans and rodents went their separate evolutionary ways suggest that these regions perform functions absolutely essential to mammalian life.