Recombination Vocabulary

Site-specific recombination involves specific DNA sequences.
Somatic recombination:
- Occurs in non-germ cells (i.e., not during meiosis).
- Most commonly refers to recombination in the immune system.
Recombination systems have been adapted for experimental use.
Figure 13.2: Site-specific recombination occurs between circular and linear DNAs at the boxed region.

Chromosomes must synapse (pair) for chiasmata to form, where crossing over occurs.
The stages of meiosis correlate with molecular events at the DNA level.
Figure 13.3: Recombination occurs during the first meiotic prophase.
Sister chromatid: Each of two identical copies of a replicated chromosome, linked at the centromere.
Sister chromatids separate during anaphase in mitosis or anaphase II in meiosis.
Bivalent: The structure containing all four chromatids (two representing each homolog) at the start of meiosis.
Synaptonemal complex: The morphological structure of synapsed chromosomes.
Joint molecule: A pair of DNA duplexes connected through a reciprocal exchange of genetic material.

The double-strand break repair (DSBR) model of recombination is initiated by making a double-strand break in one (recipient) DNA duplex and involves meiotic and mitotic homologous recombination.
In 5' end resection, exonuclease action generates 3'-single-stranded ends that invade the other (donor) duplex.
Single-strand invasion: When a single strand from one duplex displaces its counterpart in the other duplex, creating a branched structure called a D-loop.
Strand exchange generates a stretch of heteroduplex DNA consisting of one strand from each parent.
Figure 13.4: The double-strand break repair (DSBR) model of homologous recombination.
New DNA synthesis replaces the degraded material.
Branch migration: The ability of a DNA strand partially paired with its complement in a duplex to extend its pairing by displacing the resident strand.
Figure 13.6: Branch migration can occur in either direction when an unpaired single strand displaces a paired strand.
Capture of the second double-strand break end by annealing generates a recombinant joint molecule in which the two DNA duplexes are connected by heteroduplex DNA and two Holliday junctions.
The joint molecule is resolved into two separate duplex molecules by nicking two of the connecting strands.
Recombinants are formed depending on which strands are nicked during resolution.

Heteroduplex DNA created by recombination can have mismatched sequences where the recombining alleles are not identical.
Repair systems may remove mismatches by changing one of the strands to be complementary to the other.
Mismatch (gap) repair of heteroduplex DNA generates nonreciprocal recombinant products called gene conversions.
Figure 13.7: Spore formation in ascomycetes allows determination of the genetic constitution of each of the DNA strands involved in meiosis.

Break-induced replication (BIR) is initiated by a one-ended double-strand break.
BIR at repeated sequences can result in translocations.
Figure 13.10: Break-induced replication can result in nonreciprocal translocations.

During the early part of meiosis, homologous chromosomes are paired in the synaptonemal complex.
The mass of chromatin of each homolog is separated from the other by a proteinaceous complex.
Figure 13.13: Each pair of sister chromatids has an axis made of cohesins.
Axial element: A proteinaceous structure around which the chromosomes condense at the start of synapsis.
Lateral element: A structure in the synaptonemal complex that forms when a pair of sister chromatids condenses onto an axial element.
Central element: A structure that lies in the middle of the synaptonemal complex, along which the lateral elements of homologous chromosomes align; it is formed from Zip proteins.
Recombination nodules (nodes): Dense objects present on the synaptonemal complex; they may represent protein complexes involved in crossing over.

Specialized recombination involves reaction between specific sites that are not necessarily homologous.
Recombinase: Enzyme that catalyzes site-specific recombination.
Phage lambda integrates into the bacterial chromosome by recombination between the attP site on the phage and the attB site on the E. coli chromosome.
Figure 13.24: Circular phage DNA is converted to an integrated prophage by a reciprocal recombination between attP and attB.
Core sequence: The segment of DNA common to the attachment sites on both the phage lambda and bacterial genomes; it is the location of the recombination event that allows phage lambda to integrate.
The phage is excised from the chromosome by recombination between the sites at the end of the linear prophage.
Phage lambda int encodes an integrase that catalyzes the integration reaction.

Integrases are related to topoisomerases, and the recombination reaction resembles topoisomerase action, except that nicked strands from different duplexes are sealed together.
Figure 13.27: Integrases catalyze recombination by a mechanism similar to that of topoisomerases.

Mitotic homologous recombination allows for targeted transformation.
The Cre/lox and Flp/FRT systems allow for targeted recombination and gene knockout construction.