Somatic recombination

Somatic recombination occurs during D → J gene rearrangements and V → DJ gene rearrangements.

RAG-1/2 bind either side of the selected gene segment and recruit other DNA repair enzymes
Recombination signal sequences (RSS) that flank V, D and J segments are recognized by enzymes (RAG-1/2) involved in cutting and rejoining the gene segments. An RSS contains a conserved nonamer sequence and heptamer sequence separated by a spacer sequence either of either 12 bp or 23 bp. To ensure that segments are brought together in the correct order, an RSS with a 12-bp spacer is always paired with one with a 23-bp spacer (12/23 rule).

2 RSSs are aligned
Pairs heptamers together and nonamers together.

DNA is cleaved at random sites, forming a hairpin on each end
Splicing is imprecise.

Intervening DNA is cut out. Its ends are joined, forming a signal joint, then it is sent to be degraded.

Chromosomal DNA is ligated by DNA repair enzymes, forming a coding joint.

Generation of junctional diversity
Palindromic (P) nucleotides are added depending where the enzyme cuts into the hairpin.

TdT adds non-templated (N) nucleotides, generating diversity although frameshift mutations and/or stop codons may be introduced.

Ends are ligated together
The exonuclease of DNA repair enzymes removes nucleotides that do not complementary base pair.

Gaps are filled in by DNA synthase and DNA ligase seals gaps.