Site-specific recombination

Site-specific recombination alters gene order, which would not happen

during general recombination.

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.

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.

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.

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.

Transpositional site-specific recombination

Most transposons move only very rarely (10-5)

Three types of transposons

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.

DNA-only transposons : cut-and-paste transposition

(dimer)

Because staggered breaks were generated during insertion

NHEJ or HEJ

Some DNA-only transposons use replicative transposition, a variation of t

he cut-and-paste mechanism

Retroviral-like retrotransposons

Retrovirus and retroviral-like retrotransposons use the same mechanism to

move themselves.

transcription

The propagation of retroviral-like retrotr

ansposons

Integrase made the integration of retroviral-like retrotransposons

Nonretroviral retrotransposons

The RNA and reverse transcriptase have a much direct role in the recombination event for nonretroviral retrotran

sposons.

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.

(this part is not fully understood yet)

The transposition of nonretroviral retrotransposons

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.

Genomes of eukaryotic organisms are littered with relics of transp

osons

Genomes of eukaryotic organisms are littered with relics of transp

osons• In human, DNA-only and retroviral-like tra

nsposons 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.

Conservative site-specific recombination

The best example of the conservative site-specific recombination is bacteri

ophage lambda.

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

excisionase