9.9: Genome dynamics
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Up to now, aside from the insertion of “external” DNA and the recombination events of meiosis, we have considered the genome, once inherited by a cell, to be static, but it has become increasingly apparent that genomes are more dynamic than previously thought. For example, consider the number of new mutations (SNPs and such) that arise in each generation. This can be estimated based on the number of times a DNA molecule is replicated between the formation of a new organism (the fusion of haploid cells during fertilization) and the ability of that organism to form new haploid cells (about 400 replication events in a human male, fewer in a female) and the error rate of DNA replication (~1 x 10–10 per nucleotide per division.) Since each diploid cell contains ~6 x 109 nucleotides, one can expect about 1 new mutation for every two rounds of DNA replication. It has been estimated that, compared with the chromosomes our parents supplied us, we each have between 60 to 100 new mutations in our chromosomes. Given that less than ~5% of our DNA encodes gene products, only of few of these new mutations are likely to influence a gene coding region or its expression. Even when they occur in a gene’s coding region, the redundancy of codons means that many SNPs will not lead to functionally significant alterations in the gene products. That said, even apparently “neutral” mutations can lead to changes in genotype that can have effects on phenotype, and so evolutionary impacts. As we have already discussed, in small populations genetic drift can influence whether new alleles (with non-lethal effects) are retained in the population..
In addition to the point mutations that arise from mistakes in DNA replication, a whole other type of genomic variation has been uncovered in the course of genome sequencing studies. These are known as “structural variants.” They include flipping of the orientation of a DNA region (inversion) and sequence insertions or deletions, known as copy number variations)..272
As noted previously~50% of the human genome, and similar levels in other eukaryotic genomes, is composed of various virus-like sequences. Most of these have been degraded by mutation, but some remain active. For example, there are ~100 potentially active L1 type transposons (known as LINE elements) in the human (your) genome273. These 6000 base pair long DNA regions contain genes that encode proteins involved in making and moving a copy of themselves to another position in the genome. Some genomic variants have no direct phenotypic effects. For example a region of a chromosome can be “flipped” around; as long as no regulatory or coding sequences are disrupted, there may be no obvious effect on phenotype. That said, large flips or the movements of regions of DNA molecules between chromosomes can have effects on chromosome pairing during meiosis. It has been estimated that each person contains about 2000 “structural variants”274.
An important point with all types of new variants is that if they occur in the soma, that is in cells that do not give rise to the haploid cells (gametes) involved in reproduction, they will be lost when the host organism dies. At this point, there is no evidence of horizontal gene transfer between somatic cells. Moreover, if a mutation disrupts an essential function, the affected cell will die, to be replaced by surrounding normal cells. Finally, as we have discussed before and will discuss later on, multicellular organisms are social systems. Mutations, such as those that give rise to cancer, can be seen as cheating the evolutionary (cooperative) bargain that multicellular organisms are based on. It is often the case that organisms have both internal and social policing systems. Mutant cells often actively kill themselves (through apoptosis) or, particularly in organisms with an immune system, theycan be actively identified and killed.
Contributors and Attributions
Michael W. Klymkowsky (University of Colorado Boulder) and Melanie M. Cooper (Michigan State University) with significant contributions by Emina Begovic & some editorial assistance of Rebecca Klymkowsky.