Related Experiment Video
Updated: Aug 8, 2026
VDJ-Seq: Deep Sequencing Analysis of Rearranged Immunoglobulin Heavy Chain Gene to Reveal Clonal Evolution Patterns of B Cell Lymphoma
Published on: December 28, 2015
The cleavage efficiency of the human immunoglobulin heavy chain VH elements by the RAG complex: implications for the
Kefei Yu1, Alex Taghva, Michael R Lieber
1Norris Comprehensive Cancer Center, Department of Pathology, , University of Southern California, Keck School of Medicine, Los Angeles, California 90089-9176, USA.
Insights
Researchers studied how RAG proteins cleave human V(H) elements, finding significant efficiency variations. These cleavage efficiencies correlate with V(H) family usage in adult B cells, suggesting a key role in immune repertoire generation.
Area of Science:
- Immunology
- Molecular Biology
- Genetics
Background:
- The human immunoglobulin heavy chain locus comprises 39 functional V(H) elements.
- Understanding V(H) element utilization is crucial for immune repertoire generation.
Purpose of the Study:
- To quantify the site-specific cleavage efficiencies of all 39 human V(H) elements by core RAG1, RAG2, and HMG1 proteins.
- To investigate the relationship between V(H) cleavage efficiencies and their usage in the peripheral B cell repertoire.
Main Methods:
- A 12/23-coupled cleavage reaction was employed to test V(H) elements.
- Nicking and hairpin formation were measured to assess cleavage efficiency.
- Cleavage efficiencies were summed for each V(H) family.
Main Results:
- Individual V(H) element cleavage efficiencies exhibited a nearly 30-fold range.
- Summed V(H) family cleavage efficiencies closely matched the observed usage profile of V(H) families in normal adult peripheral B cells.
Conclusions:
- RAG-mediated cleavage efficiency of V(H) elements is a significant factor influencing their utilization in the human immunoglobulin repertoire.
- This finding provides insights into the mechanisms shaping immune diversity in adult humans.
Abstract:
The human immunoglobulin heavy chain locus contains 39 functional human V(H) elements. All 39 V(H) elements (with their adjacent heptamer/nonamer signal) were tested for site-specific cleavage with purified human core RAG1 and RAG2, and HMG1 proteins in a 12/23-coupled cleavage reaction. Both nicking and hairpin formation were measured. The individual V(H) cleavage efficiencies vary over nearly a 30-fold range. These measurements will be useful in considering the factors affecting the generation of the immunoglobulin and T-cell receptor repertoires in the adult humans. Interestingly, when these cleavage efficiencies are summed for each of the V(H) families, the six V(H) family efficiencies correspond closely to the observed profile of unselected V(H) family usage in the peripheral B cells of normal adult humans. This correspondence raises the possibility that the dominant factor determining V(H) element utilization within the 1-megabase human genomic V(H) array is simply the individual RAG cleavage efficiencies.
Related Concept Videos
01:10Antibody Structure
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
01:10Antibody Structure
Antibodies, also known as immunoglobulins (Ig), are essential players of the adaptive immune system. These antigen-binding proteins are produced by B cells and make up 20 percent of the total blood plasma by weight. In mammals, antibodies fall into five different classes, which each elicits a different biological response upon antigen binding.
The Y-Shaped Structure of Antibodies Consists of Four Polypeptide Chains
Antibodies consist of four polypeptide chains: two identical heavy...
01:31Immunoglobulin-like Cell Adhesion Molecules
Ig-CAMs exhibit either homophilic binding (to other Ig-CAMs) or heterophilic binding (to other ligands such as integrins). While most Ig-CAMs...
01:26Antigens Involved in Adaptive Immunity
Complete Antigens
Complete antigens possess both immunogenicity and reactivity.
01:28Diversity of Antigen Receptors
Before encountering any antigen, lymphocytes express these receptors. On B cells, the antigen receptor is a membrane-bound antibody molecule called BCR; on T cells, it is a T cell receptor or TCR. B and T cell receptors are composed of two...
01:25Antibody Structure and Classes
The basic structure of an antibody consists of four protein chains: two identical heavy chains and two identical light chains. These chains are held together by disulfide bonds and other non-covalent interactions, forming a Y-shaped structure.