Immunology Somatic Recombination

B cell maturation location

B cell maturation takes place in the bone marrow.

Chromosome where heavy chain genes are located

Heavy chain genes for B cell receptor (BCR) are located on chromosome 14.

Allelic exclusion

Only one allele (either maternal or paternal) of the heavy chain gene and light chain gene is expressed in a B cell, ensuring one receptor specificity.

Somatic recombination

Process of rearranging V (variable), D (diversity), and J (joining) gene segments to form a functional gene coding for the variable region of the antibody or BCR.

Gene segments in heavy chain variable region

Heavy chain variable region is formed from V, D, and J gene segments.

Gene segments in light chain variable region

Light chain variable region is formed from V and J gene segments only (no D segments).

Germline configuration

The original, unrearranged configuration of V, D, and J gene segments in all nucleated cells except developing B and T cells.

Cells undergoing somatic recombination

Only developing B cells (for BCR) and T cells (for TCR) undergo somatic recombination.

Order of heavy chain gene rearrangement

D gene segments first join to J segments, then a V segment joins to the DJ complex.

Number of gene segments approximately in heavy chain locus

About 40 V segments, 23 D segments, and 6 J segments exist at the heavy chain locus.

Intervening DNA during recombination

The DNA between chosen gene segments is cut out and permanently deleted.

Enzymes involved in somatic recombination

RAG1, RAG2, Terminal deoxynucleotidyl transferase (TDT), Artemis, DNA ligase, and other proteins in non-homologous end joining.

RAG1 and RAG2 expression

Expressed only in developing B and T lymphocytes during receptor gene rearrangement.

Function of RAG1 and RAG2

Bind recombination signal sequences (RSS) and introduce double-stranded DNA breaks to initiate rearrangement.

Terminal deoxynucleotidyl transferase (TDT) function

Adds random, non-templated nucleotides (N nucleotides) at junctions during recombination to increase diversity.

Recombination Signal Sequences (RSS)

Conserved heptamer and nonamer sequences flanking V, D, and J segments with 12 or 23 base pair spacers; guide RAG complex to correct cut sites.

Junctional diversity

Created by palindromic (P) nucleotide addition and non-templated (N) nucleotide addition at coding joints during recombination, increasing receptor diversity.

Palindromic nucleotide (P nucleotide) addition

Single-strand nicks create hairpin loops, which after cleavage leave palindromic sequences at coding ends.

Non-templated nucleotide (N nucleotide) addition

Random nucleotides added by TDT not present in the germline DNA, contributing to junctional diversity.

CDR (Complementarity Determining Region) 3

Encoded mainly by junctional diversity at the V-D-J junctions; most variable and critical for antigen specificity.

CDR1 and CDR2

Encoded by the chosen V gene segment.

Number of CDRs per variable domain

Three CDRs per variable domain: CDR1, CDR2, and CDR3.

Light chain recombination attempts

Multiple attempts possible on the light chain loci because rearrangement involves only V and J segments, and unrearranged segments remain for retries.

Heavy chain recombination attempts

Only two attempts possible (one per allele) because D segments are deleted after rearrangement, preventing retries on the same chromosome.

Nonproductive rearrangement

A rearrangement that does not produce a functional protein (e.g., due to frame shifts or stop codons).

Difference in recombination between BCR and TCR

Both use V(D)J recombination, but TCR alpha chains rearrange V and J segments only; beta chains rearrange V, D, and J segments.

Non-homologous end joining mechanism

DNA repair process that joins broken coding ends during recombination.

Permanent change in B/T cell DNA

DNA at the receptor loci is permanently altered during somatic recombination from the inherited germline sequence.

Importance of somatic recombination

Generates enormous diversity of antigen receptors essential for adaptive immunity.

Role of stromal cells in B cell maturation

Provide signals in the bone marrow to instruct lymphoid precursors to become B cells and undergo receptor rearrangement.

Four domains of heavy chain

Heavy chain variable domain has four domains total, including the variable and constant domains.

Two domains of light chain

Light chain has two domains: variable and constant.

Function of constant domains

Constant domains of heavy and light chains determine antibody isotype and effector function; coded downstream of VDJ segments.

RAG complex composition

The RAG1 and RAG2 proteins form a complex known as V(D)J recombinase.

RAG complex binding sites

Bind specifically to recombination signal sequences (RSS) adjacent to V, D, and J segments.

Molecular detail of recombination

Recombination involves double-strand breaks, hairpin formation, nicking for sticky ends, nucleotide additions, and ligation.

Function of Artemis

An endonuclease that opens hairpin coding ends during recombination to allow nucleotide addition and joining.

Junctional diversity coding

Codes for the CDR3 region, critical for antigen specificity.

Palindromic and non-templated nucleotide addition effect

Increase variability beyond germline-encoded sequences, enhancing the antibody repertoire.

Multiple attempts at light chain rearrangement

Allowed due to the presence of multiple V and J segments and retention of unrearranged segments.

Restriction of heavy chain rearrangement attempts

Limited because D segments and intervening DNA are deleted after rearrangement.