structure databases in the analysis.
The Human Genome Project, completed in 2003, was a 13‐year international effort that was described at the time as the biological equivalent of putting a man on the moon. As more and more genomes were sequenced, the technology became quicker and, more importantly, cheaper. Using Next Generation Sequencing (NGS) technologies, it is currently possible to have our genomes sequenced at a cost that ranges between a few hundred and a thousand dollars per person. As an increasing number of us have our genomes sequenced, this inexpensive but informative resource is bringing personalized medicine closer to our everyday lives. Soon, clinicians will routinely tailor treatment for a wide range of diseases to our own unique genetic makeup.
In 2012 the 100 000 genomes project was set in motion through a collaboration between scientists and the government of the United Kingdom. Under the direction of Genomics England, the remit was to sequence 100 000 complete genomes from NHS (National Health Service) patients. The aim of this large‐scale project was to analyze DNA from patients with cancer or who had a rare disorder to try to provide an understanding of the causes of a condition and inform best treatments. In a cancer patient the genome sequence from both tumor and normal tissue was compared. For patients with a rare disease, the genomes of two relatives were also sequenced. In December 2018 the project met its target of sequencing 100 000 genomes, a remarkable achievement of progress in DNA sequence technology and analysis. To date, the project has generated over 21 petabytes of genome data and is already delivering valuable insights into how DNA sequences inform an individual's medical condition. In response to the COVID‐19 pandemic, genome sequencing of both patients and SARS‐CoV‐2 samples has provided us with information on both the way in which an individual's genome influences their susceptibility to COVID‐19 infection and on the spread of new variants through the population.
Answer to thought question: Guanine cannot base pair with uracil, so there is certainly a mismatch in the DNA. However, mismatch repair cannot correct the error, because the mutation has occurred in a mature chromosome in which both DNA strands are methylated.
When the bacterium replicates its DNA, the strands will separate and each will act as a template for the synthesis of a new strand. The unmodified strand, 5′ TGAA 3′ will have the matching strand 3′ ACTT 5′ synthesized on it, and the resulting newly synthesized strand will be unmutated, as will its own daughter strands.
However, the modified strand 3′ AUTT 5′ will have the matching strand 5′ TAAA 3′ synthesized on it, since adenine base pairs with uracil. The daughter cell that inherits this chromosome, assuming that it is still infected with PBS2 and therefore allows the uracil to remain, will now have a chromosome with the structure
with each base pair now nicely hydrogen bonded to its partner. Only the presence of uracil in the DNA molecule betrays the fact that a deamination event has occurred.
When this cell replicates its DNA the strands will separate and each will act as a template for the synthesis of a new strand. The lower strand, 3′ AUTT 5′ will as before have the matching strand 5′ TAAA 3′ synthesized on it. The upper strand 5′ TAAA 3′ will generate a chromosome with the structure
and the daughter cell that inherits this, and all its daughters in turn, will have a mutation that can no longer be easily identified as arising from a deamination.
This answer neglects the fact that a bacterium infected by a bacteriophage will likely die without generating any daughters.
Elizabeth Blackburn, Carol Greider, and Jack Szostak.
Source: Nobel organization website.
Maintaining the information encoded within DNA is essential for the health of cells and organisms, and since the 1930s it had been speculated that the ends of chromosomes, called the telomeres, must be highly specialized to protect DNA strands from being degraded. In the late 1970s Elizabeth Blackburn, studying the model organism tetrahymena, discovered that the ends of chromosomes contain repeats of the sequence CCCCAA. Together with colleague Jack Szostak she also found that a minichromosome injected into cells would be rapidly degraded, unless this CCCCAA sequence was located at its ends – in which case the minichromosome was protected. Later, a PhD student named Carol Greider working in Blackburn's lab discovered the enzyme telomerase, which is responsible for depositing the CCCCAA repeats at chromosome ends. It is now understood that loss of telomeres contributes to the loss of cells' ability to divide and, conversely, that the unwanted ability of many cancer cells to over‐proliferate is linked to the overactivity of telomerase. Blackburn, Szostak, and Greider together won the Nobel Prize in Physiology and Medicine in 2009 for explaining “how chromosomes are protected by telomeres and the enzyme telomerase.”
SUMMARY
1 During replication each parent DNA strand acts as the template for the synthesis of a new daughter strand. The base sequence of the newly synthesized strand is complementary to that of the template strand.
2 Replication starts at specific sequences called origins of replication. The two strands untwist and form the replication fork. Helicase enzymes unwind the double helix, and single‐stranded DNA‐binding proteins keep it unwound during replication. In prokaryotes, DNA polymerase III synthesizes the leading strand continuously in the 5′ to 3′ direction. The lagging strand is made discontinuously in short pieces in the 5′ to 3′ direction. These are joined together by DNA ligase. DNA polymerase is a self‐correcting enzyme. It can remove an incorrect base using its 3′‐ to 5′‐exonuclease activity and then replace it with the correct base.
3 DNA repair enzymes can correct mutations. Uracil in DNA, resulting from the spontaneous deamination of cytosine, is removed by uracil – DNA glycosidase. The depyrimidinated sugar is cleaved from the sugar‐phosphate backbone by AP endonuclease, and DNA polymerase then inserts the correct nucleotide. The phosphodiester bond is reformed by DNA ligase.
4 In eukaryotes protein‐coding genes are split into exons and introns. Only exons code for protein. The human genome has a large amount of DNA whose function is not obvious. This includes much repetitious DNA, whose sequence is multiplied many times.
5 Protein‐coding genes may be found in repeated groups of slightly diverging structure called gene families, either close together or scattered over the genome. Some of the family members have lost the ability to operate – they are pseudogenes.
FURTHER READING
1 Brenner, S., Elgar, G., Sandford, R. et al. (1993). Characterization of the pufferfish (Fugu) genome as a compact model vertebrate genome. Nature 366: 265–268.
2 Chatterjee, N. and Walker, G.C. (2017). Mechanisms of DNA damage, repair, and mutagenesis. Environmental and Molecular Mutagenesis 58: 235–263.
3 O'Donnell, M., Langston, L., and Stillman, B. (2013). Principles and concepts of DNA replication in bacteria, archaea, and eukarya. Cold Spring Harbor Perspectives in Biology 5 (7): a010108.
4 Radman, M. and Wagner, R. (1988). The high fidelity of DNA duplication. Scientific American 259 (2): 40–46.
5 Venter, J.C. et al. (2001). The sequence of the human genome. Science 291: 1304–1351.