Illegitimate recombination, or nonhomologous recombination, is the process by which two unrelated double stranded segments of DNA are joined. This insertion of genetic material which is not meant to be adjacent tends to lead to genes being broken causing the protein which they encode to not be properly expressed. One of the primary pathways by which this will occur is the repair mechanism known as non-homologous end joining (NHEJ). Discovery Illegitimate recombination is a natural process which was first found to be present within E. coli. A 700-1400 base pair segment of DNA was found to have inserted itself into the gal and lac operons resulting in a strong polar mutation. This mechanism was then found to have the ability to insert other short genetic sequences into other locations within the bacterial genome often leading to a change in the expression of neighboring genes. Oftentimes it leads to the neighboring genes to simply shut off. However some of these segments also had strong start and stop signals which changed the regulation of neighboring genes leading in changes in the amount of transcription. What differentiated this form of genetic recombination from those dependent of genetic homology was that the process observed as illegitimate did not require the use of homologous segments of DNA. While not being entirely understood at the time, it was recognized to hold potential in generating changes in the chromosomal evolution. Mechanism In prokaryotes In prokaryotes, illegitimate recombination results in a mutation of the genetic sequence of the prokaryote. This process takes different forms in eukaryotes one of which is deletions. In a deletion mutation the prokaryotic organism undergoes illegitimate recombination resulting in the removal of a continuous segment of genetic code. However this form of mutation occurs infrequently among mutants of natural origin rather than those that have been induced. Another form of illegitimate recombination in prokaryotes is that of a duplication mutations of a genome. In this case a portion of the parental genome is inserted multiple times into the genome. This duplication either inserts the genetic material in the same orientation or opposite of the original parental segments as it is non-homology driven. In eukaryotes The mechanism of Illegitimate recombination is that of non-homologous end joining in which two strands of DNA not sharing homology will be joined together by the gene repair machinery. Upon recognition of a double strand break a protein complex will