1. Site-specific recombination
Site-specific recombination alters gene order, which would not happen during general recombination.

2. Site-specific recombination
Site-specific recombination moves specialized nucleotide sequences (mobile genetic elements) between nonhomologous sites within a genome.
All types of mobile genetic elements occasionally move or rearrange neighboring DNA sequences of the host cell genome.

3. Site-specific recombination
The relics of site-specific recombination (repeated DNA sequences) can be found in many vertebrate chromosomes (45% in human).
The translocation of mobile genetic elements gives rise to spontaneous mutations in organisms.

4. Site-specific recombination
Site-specific recombination is guided by recombination enzymes that recognize short, specific nucleotide sequences present on one or both of the recombining DNA molecules.

5. There are two types of site-specific recombination
Transpositional site-specific recombination does not involve the formation of heteroduplex DNA between mobile DNA segments and its host, so a short homologous sequence is not required.
Conservative site-specific recombination requires the formation of heteroduplex DNA so a short homologous sequence is required.

6. Transpositional site-specific recombination
Most transposons move only very rarely (10-5)

7. Three types of transposons

8. DNA-only transposon
DNA-only transposons exist as DNA throughout its life cycle. The translocating DNA segment is directly cut out of the donor DNA and joined to the target site by a transposase.

9. DNA-only transposons : cut-and-paste transposition
(dimer)
NHEJ or HEJ
Because staggered breaks were generated during insertion

10. Some DNA-only transposons use replicative transposition, a variation of the cut-and-paste mechanism

11. Retroviral-like retrotransposons
Retrovirus and retroviral-like retrotransposons use the same mechanism to move themselves.

12. The propagation of retroviral-like retrotransposons
transcription

13. Integrase made the integration of retroviral-like retrotransposons

14. Nonretroviral retrotransposons
The RNA and reverse transcriptase have a much direct role in the recombination event for nonretroviral retrotransposons.

15. Nonretroviral retrotransposons
Nonretroviral retrotransposons left large number of repeated sequences in human genome. These repeats are mostly mutated and truncated so they cannot transpose anymore.
L1 element (LINE, long interspersed nuclear element) belongs to this group. It carries its own reverse transcriptase and endonuclease.

16. The transposition of nonretroviral retrotransposons
(this part is not fully understood yet)

17. Nonretroviral retrotransposons
Other nonretroviral retrotransposons like Alu element lacks reverse transcriptase or endonuclease can still propagate themselves by using those enzymes from host or other nonretroviral retrotransposons.

19. Genomes of eukaryotic organisms are littered with relics of transposons

20. Genomes of eukaryotic organisms are littered with relics of transposons
In human, DNA-only and retroviral-like transposons have been inactive in the human lineage since very long ago. In contrast, some of the nonretroviral retrotransposons are still moving (2%).
In mouse, both types of retrotransposons are still moving and are responsible for 10 percent of new mutations.

21. Conservative site-specific recombination
The best example of the conservative site-specific recombination is bacteriophage lambda.

23. Because integrase remained bound with DNA just like topoisomerase, the action of lambda integrase does not require ATP.

25. excisionase