Question

Describe the V(D)J and VJ arrangements that occur to generate the variable region of the heavy and light chains of an antibody. Be sure to list the arrangements in the order in which they occur for each chain. Be sure to include discussion of the following: RAG-1/RAG-2, RSS, Ku, Artemis, DNA Dependent protein kinase, DNA ligase/XRCC4, and terminal deoxynucleotidyl transferase (TdT) and the signal joint.

Please help, i don’t understand that at all:(

Answer 1

V(D)J rearrangement means a rearrangement of variable (V), joining (J), and in some cases, diversity (D) gene segments in random fashion. This rearrangement occurs in primary lymphoid organs i.e., bone marrow for B cells and thymus for T cells and results in and results in the highly diverse range of antibodies that are found on B cells and T cell receptors (TCRs) that are present on T cells.

V(D)J recombination process is carried by group of enzymes collectively termed as VDJ recombinase. The enzymes that are involved in this recombination process include recombination activating genes 1 and 2 (RAG1 and RAG 2), terminal deoxynucleotidyl transferase (TdT), Artemis nuclease, DNA-dependent protein kinase (DNA-PK), X-ray repair cross-complementing protein 4 (XRCC4), DNA ligase IV, non-homologous end-joining factor 1 and DNA polymerases.

The recombination starts by binding of V(D)J recombinase i.e., RAG 1 with a V, D or J gene segment , flanked by recombination signal sequencing (RSS). This leads to formation of two DNA ends: a hairpin (stem-loop) on the coding segment and a blunt end on the signal segment. This process involves other recombinase enzymes as well. The DNA nicking and hairpin formation occurs on both strands simultaneously in a complex known as a recombination center.

The blunt signal ends ligate together to form a circular piece of DNA containing all of the intervening sequences between the coding segments known as a signal joint. Junctional diversity occurs due to the processing of coding ends prior to their ligation. The processing starts with binding of DNA-PK each broken DNA end. This then recruits several other proteins including Artemis, XRCC4, DNA ligase IV, Cernunnos, and several DNA polymerases.

DNA-PK leads to autophosphorylation through complex formation. This complex in turn activates Artemis. The process of hairpin opening by Artemis occurs and is a crucial step of V(D)J recombination. Further, XRCC4, Cernunnos, and DNA-PK along with terminal deoxynucleotidyl transferase (TdT), carry ot addition of non-templated nucleotides to the coding end. After the completion of addition process, exonucleases remove unwanted bases from the coding ends and DNA polymerases insert additional nucleotides as needed to make the two ends compatible for joining. Final ligation of the processed coding ends is carried out by DNA ligase IV.

Thus, the process of V(D)J recombination is completed with the help of many enzymes.