Nonamer dependent RAG cleavage at CpGs can explain mechanism of chromosomal translocations associated to lymphoid cancers

Abstract

Chromosomal translocations are considered as one of the major causes of lymphoid cancers. RAG complex, which is responsible for V(D)J recombination, can also cleave non-B DNA structures and cryptic RSSs in the genome leading to chromosomal translocations. The mechanism and factors regulating the illegitimate function of RAGs resulting in oncogenesis are largely unknown. Upon in silico analysis of 3760 chromosomal translocations from lymphoid cancer patients, we find that 93% of the translocation breakpoints possess adjacent cryptic nonamers (RAG binding sequences), of which 77% had CpGs at proximity. As a proof of principle, we show that RAGs can efficiently bind to cryptic nonamers present at multiple fragile regions and cleave at adjacent mismatches generated to mimic the deamination of CpGs. ChIP studies reveal that RAGs can indeed recognize these fragile sites on a chromatin context inside the cell. Finally, we show that AID, the cytidine deaminase, plays a significant role during the generation of mismatches at CpGs and reconstitute the process of RAG-dependent generation of DNA breaks both in vitro and inside the cells. Thus, we propose a novel mechanism for generation of chromosomal translocation, where RAGs bind to the cryptic nonamer sequences and direct cleavage at adjacent mismatch generated due to deamination of meCpGs or cytosines.

Role of the mechanisms for antibody repertoire diversification in monoclonal light chain deposition disorders: when a friend becomes foe

“…These molecular events imply a latent risk of genome instability and the development of malignant diseases, such as leukemias and lymphomas, if they occur uncontrolled. (55)(56)(57)(58)(59)(60)(61). Thus, V(D)J gene recombination is tightly regulated by several mechanisms operating at various levels, to ensure that it occurs at the appropriate cell lineage and stage of development.…”

Molecular Mechanisms of DNA Sequence Selectivity in V(D)J Recombination

“…It is also possible that the cRSSs that do not contain discernible heptamers or nonamers are able to be cleaved due to other mechanisms that lead to unpaired bases, thus bypassing the necessity for heptamer-related base unpairing prior to DNA cleavage. 23 Because SARP-seq analyzed the complete V(D)J recombination reaction, in vitro biochemical studies on RAG1/2 nicking specificity will help determine whether some RSS motifs inhibit specific steps, such as nicking or hairpin formation. Future studies using this method, as well as additional structural studies and sm studies, will be important to fully understand the molecular basis for RAG activity in variant RSSs.…”

“…RSS heptamers that do not contain the preferred YpR motif at base positions 6–7 would have a decreased ability to facilitate the base unpairing conformational change, and as mentioned above, these substrates may be misaligned such that the scissile bond is not stably positioned in the active site. It is also possible that the cRSSs that do not contain discernible heptamers or nonamers are able to be cleaved due to other mechanisms that lead to unpaired bases, thus bypassing the necessity for heptamer-related base unpairing prior to DNA cleavage …”

“…It is also possible that the cRSSs that do not contain discernible heptamers or nonamers are able to be cleaved due to other mechanisms that lead to unpaired bases, thus bypassing the necessity for heptamer-related base unpairing prior to DNA cleavage. 23 …”

TREC mediated oncogenesis in human immature T lymphoid malignancies preferentially involves ZFP36L2

“…Besides its essential role to provide a large antigen receptor repertoire in T and B cells, the V(D)J recombination machinery is also a threat to genomic stability, given its ability to induce DSB followed by erroneous repair of breaks in non-antigen receptor loci during the recombination process [ 4 , 5 ]. Such aberrant recombination is involved in lymphoid oncogenesis, giving rise to translocations inducing activation of oncogenes as t(14;18)/ IGH-BCL2 in follicular lymphoma and t(11;14)/ IGH-CCND1 in mantle cell lymphoma or deletion of tumor suppressor genes such as IKZF1 and CDKN2A/B in B and T-cell acute lymphoblastic leukemia (T-ALL) [ 6 , 7 ].…”