Genetic recombination occurs when a molecule of nucleic acid is broken then joined to a different one. Recombination may occur between similar (homologous) or dissimilar molecules, either DNA or RNA.
In homologous recombination (HR) nucleotide sequences are exchanged between similar genes. HR is most widely used by cells trying to repair ruptured DNA sequences after the double-strand breaks.
Non-homologous end joining (NHEJ) repairs breaks when no homologous copy exists. Non-homologous recombination helps immune cells in an adaptive immune system rapidly diversify to recognize and adapt to new pathogens. NHEJ may have evolved to allow bacteria to survive desiccation: being able to repair breaks without a template to gain a soluble rebound.
Recombination is a common technique for both microbes and eukaryotes for various purposes. During meiosis, in which eukaryotes make gamete cells (e.g., sperm and egg cells in animals), a dash of recombination puts some spice in the genome potential for offspring. Chromosomal crossover – exchange of genetic material between homologous chromosomes – is how offspring become a blend of parental genomes.
Transposable elements (TE) are a genetic wildcard: DNA sequences able to self-transpose. These Tinkertoy genes may decide to change relative position with a cell’s genome. Such mobile elements provide powerful pathways to genetic recombination and are mutagens of the highest order.
TEs are ubiquitous among prokaryotes and eukaryotes. There are 2 classes of transposable element: transposons and retrotransposons.
Retrotransposons (aka retroelements) are DNA genetic amplifiers: mobile “copy and paste” elements via an RNA assist. The copy comes in 2 stages: 1) DNA to RNA by transcription; 2) from RNA back to DNA via reverse transcription. The DNA copy is inserted into a different position in the genome.
Large swaths of the genomes of eukaryotes are taken up by retroelements. Retrotransposons are especially abundant in plants: often comprising the principal component of nuclear DNA. 42% of the human genome are retroelements.
Retroviruses, such as HIV, do their business along the retroelement road, hijacking host machinery for production. The disorderly nature of genetic insertion by retroviruses can activate oncogenes: errant DNA with the potential to cause cancer.
Transposons are a “cut and paste” TEs, able to work their magic without an RNA intermediate. Transposons are also able to adopt external DNA sequences as their own.