Why can human antibodies deal with various pathogens? Two studies of nature reveal that V (d) J recombination and antibody class conversion recombination are caused by chromatin ring extrusion

November 17, 2019 / BIOON / - -- our ability to fight against many potential pathogenic factors we encounter depends on a process called recombination, which can occur in different ways, such as V (d) J recombination and antibody class switch recombination (CSR) These recombination processes manipulate DNA sequences, enabling our bodies to produce a wide variety of immune system recognition components: antibodies and T cell receptors (TCRs) Today, Frederick W ALT of Boston Children's Hospital and his team published two papers in the journal Nature, revealing unexpected similarities in the way these types of restructuring events occur In developing immune system cells, a process called V (d) J recombination uses three kinds of gene fragments called V, D and j to rearrange DNA sequences, thus assembling genes that will encode antibodies or TCRs The two sides of these gene fragments are evolutionarily conserved DNA sequences called recombinant signal sequences (RSS), which indicate that rag connects a V segment with a j segment, sometimes including a D segment in an astonishingly diverse combination The DNA between these linked gene segments is usually deleted, but in rare cases, when two gene segments are linked together, it reverses and remains This recombination process enables antibodies and TCRs to have diverse protein domains called variable domains, which recognize protein fragments called antigens It is the diversity of these variable regions that make the immune system be able to deal with various pathogenic factors effectively These genes encoding antibodies sometimes undergo further modifications to alter the single DNA nucleoside base (which produces so-called somatic point mutations) to enhance the antibody's ability to recognize antigens The DNA in these genes can also undergo a series of DNA changes called CSR recombination, which do not affect antigen recognition Instead, they give antibodies multiple effects, such as the ability to bind to the mucosal surface, or help other immune cells cope with infection The recombination of V (d) J is initiated by rag, while the somatic point mutation and CSR recombination in the antibody coding sequence are initiated by a DNA mutant enzyme called aid The potential ability of rag and aid to cause wide-ranging changes in genome is dangerous, so their role must be limited to the target sequences that can be used for host defense As a kind of DNA protein complex, chromatin is tightly packed in human nucleus, forming thousands of rings of different sizes These rings (or DNA rings) are anchored on their bottom through a ring structure called cohesin protein complex When the molecular motor components of adhesin actively squeeze chromatin through the annular structure of adhesin until chromatin encounters "barrier", these chromatin rings will be formed This may be formed before or at the time when chromatin enters the annexin ring structure, usually when DNA binds to CTCF protein Binding protein dependent squeezing of larger chromatin rings divides chromatin into discrete regions called topologically associated domains, while smaller chromatin rings enable DNA regulatory sequences (such as enhancers and promoters located far away in linear DNA sequences) to be placed adjacent to each other, thus driving gene expression These two papers of ALT team show that chromatin loop extrusion is also the basis of controlling V (d) J recombination and CSR recombination (Figure 1) Figure 1 DNA ring extrusion leads to antibody class conversion and recombination Picture from nature, 2019, DOI: 10.1038/d41586-019-03200-4 During the recombination of V (d) J, rag was recruited to the modified DNA binding histones, which were accumulated in a chromosomal region containing antibody or TCR coding J gene at a high level This will produce a VDJ recombination center, where rag binds to RSS motifs located on both sides of the J gene fragment Rag then scans the rest of the chromosomes in a linear fashion to find the RSS motif of another gene fragment that is far away Once two compatible RSS are aligned, rag induces DNA fragmentation to initiate recombination between the two RSS Rag is anchored in the VDJ recombination center, which leads to the problem of how DNA moves during this scanning process In the first paper, the ALT team realized that chromatin ring squeezing might explain this DNA movement In this model, after the binding protein and the rag binding RSS are assembled in the VDJ recombination center, the binding protein "twines" on the DNA through its ring structure, so that the RSS in the chromatin ring may find a compatible RSS binding rag for recombination This model is supported by experiments carried out by the ALT team, for example, they have confirmed that blocking DNA movement by binding protein ring structure will bias the recombination event, which is conducive to the recombination of RSS near the site where DNA movement is blocked Importantly, the directed DNA scanning mechanism in this model also explains the overwhelming advantage of deletion rather than inversion in the process of V (d) J recombination, which has long been an unexplained problem In view of the fact that these experiments, together with earlier studies, have confirmed that the binding elements of adhesins (DNA motifs located near some antibody V gene segments) are the main determinants of DNA rearrangement patterns and the resulting antibody library, a convincing model has emerged that chromatin cycloextrusion contributes to V (d) J recombination Although there are differences in Enzymology between CSR and V (d) J recombination, they are similar in concept In the second paper, the ALT team looked at whether annexin driven DNA ring extrusion also forms the basis for CSR recombination During the recombination of CSR, aid introduced a multipoint mutation of DNA nucleotide base in the specific "switch region" of antibody coding gene, which eventually led to DNA breakage Unlike V (d) J recombination - rag mediated DNA cleavage relies on the assembly of a pair of compatible RSS - aid causes mutations at a single DNA site that can cause DNA to break before or after the alignment of the transition regions, which are then joined together The ALT team proposed that, similar to what happened in the VDJ recombination center, the CSR recombination center was formed on a specific conversion region (called s μ) in the antibody coding gene Previous studies have supported diffusion as a mechanism for DNA alignment during antibody class switching, while ALT team's work supports the idea that chromatin ring Extrusion Based on binding proteins aligns the two conversion regions so that they can be recombined (Figure 1) Therefore, the first mock exam of the two papers provides convincing evidence for the reunification of V (D) J and CSR recombination They also associate these processes with gene expression regulation based on the dynamic regulation of chromatin structure This model provides testable predictions and raises many questions For example, how to recruit adhesins into VDJ recombination center and CSR recombination center? The removal of adhesins from specific cell lineages leads to defective recombination of V (d) J, while the deletion of adhesins eliminates all chromatin rings on the whole chromosome However, the impact of these changes on CSR restructuring remains to be determined The compression of chromatin ring produces torsional stress in DNA, which can be relieved by the transient DNA rupture caused by topoisomerase IIB As a result, binding proteins around DNA to regulate gene expression or achieve immune diversity based on recombination may drive a chromosomal abnormality called chromosomal translocation, which may lead to cancer Like the DNA loop itself, these new insights into the role of chromosomal structure may help reveal the links that existed between previously thought independent domains (bio Com) reference: 1 Yu Zhang et al The fundamental role of chromium loop extension in physical V (d) J recommendation Nature, 2019, DOI: 10.1038/s41586-019-1547-y 2 Xuefei Zhang et al Fundamental roles of chromium loop extension in antibiosis class switching Nature, 2019, DOI: 10.1038/s41586-019-1723-0.3 Livak et al One ring to rule them all Nature, 2019, doi:10.1038/d41586-019-03200-4.