Site-specific recombination

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Site-specific recombination

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

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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.

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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.

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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.

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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.

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Transpositional site-specific recombination

• Most transposons move only very rarely (10-5)

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Three types of transposons
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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.

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DNA-only transposons cut-and-paste transposition
(dimer)
NHEJ or HEJ
Because staggered breaks were generated during
insertion
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Some DNA-only transposons use replicative
transposition, a variation of the cut-and-paste
mechanism
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Retroviral-like retrotransposons

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

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The propagation of retroviral-like
retrotransposons
transcription
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Integrase made the integration of retroviral-like
retrotransposons
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Nonretroviral retrotransposons

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

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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.

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

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Genomes of eukaryotic organisms are littered with
relics of transposons
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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.

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Conservative site-specific recombination

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

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