VDJ Gene Recombination

Immunoglobulin Gene Somatic Recombination

A DNA rearrangement process occurring in B lymphocytes that assembles separate gene segments into a functional immunoglobulin (antibody) gene. This creates a vast diversity of antibodies from a limited amount of genetic material.

Immunoglobulin Gene Segments (Heavy Chain)

Composed of three types of gene segments: Variable (V), Diversity (D), and Joining (J). These segments are physically separated in the genome of germline and progenitor cells and are joined to form a contiguous V-D-J exon.

Immunoglobulin Gene Segments (Light Chain)

Composed of only two types of gene segments: Variable (V) and Joining (J). The lack of a D segment is a key structural difference from the heavy chain.

Recombination Signal Sequence (RSS)

A specific DNA sequence motif flanking each V, D, and J gene segment.

It serves as the binding site for the RAG protein complex and

directs the recombination machinery to the correct location.

RAG Complex (RAG-1 and RAG-2)

The protein complex composed of Recombination Activating Gene 1 and 2 products.

It initiates somatic recombination by specifically binding to the RSS motifs flanking two gene segments and

cleaving the DNA.

RAG-Mediated DNA Cleavage, where does it happen

The enzymatic step where the RAG complex makes double-stranded breaks.

It cleaves precisely at the junction between the coding gene segment (V, D, or J) and its adjoining RSS motif.

DNA Hairpin Formation

The result of RAG cleavage at the coding segments. The ends of the V, D, or J gene segments are sealed to form a hairpin structure, a crucial intermediate for generating diversity.

Signal Joint Formation

The ligation of the two RSS ends after they are cleaved by the RAG complex. This creates a closed circular DNA molecule that is excised from the genome and plays no further role.

DNA-PK, Artemis, and Ligase/XRCC4 Complex

Additional enzymes recruited to the complex after RAG cleavage.

DNA-PK is a kinase that activates Artemis, an endonuclease that opens the DNA hairpins.

The DNA Ligase IV/XRCC4 dimer then ligates the DNA ends.

Hairpin Cleavage by Artemis

The process where the endonuclease Artemis cleaves the hairpin structures at the ends of the gene segments. This cleavage is not always even, creating single-stranded overhangs that contribute to junctional diversity.

Terminal Deoxynucleotidyl Transferase (TDT)

A specialized enzyme recruited to the complex that adds random nucleotides (non-templated) to the single-stranded ends of the cleaved hairpins. This process, called N-nucleotide addition, greatly increases sequence diversity at the junctions (e.g., V-D and D-J joints).

Junctional Diversity

The immense sequence variation generated at the junctions where gene segments join. It is caused by the imprecise joining of segments, P- and N-nucleotide addition, and exonuclease trimming, and is a primary source of antibody diversity.

Overall Process Summary

1) RAG binds RSS. 2) Cleaves DNA, creating hairpins (coding ends) and blunt breaks (RSS ends). 3) Signal joint forms from RSS ends. 4) Hairpins are cleaved by Artemis. 5) TDT adds N-nucleotides. 6) DNA Ligase IV/XRCC4 ligates the coding ends together.