Evaluation of potential role of R-loop and G-quadruplex DNA in the fragility of c-MYC during chromosomal translocation associated with Burkitt’s lymphoma

• Published in: The Journal of biological chemistry Vol. 299; no. 12; p. 105431
• Main Authors: Kumari, Nitu, Das, Kohal, Sharma, Shivangi, Dahal, Sumedha, Desai, Sagar Sanjiv, Roy, Urbi, Sharma, Anju, Manjunath, Meghana, Gopalakrishnan, Vidya, Retheesh, S.T., Javadekar, Saniya M., Choudhary, Bibha, Raghavan, Sathees C.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 01.12.2023
• Subjects: AID; Burkitt Lymphoma - genetics; Burkitt Lymphoma - pathology; chromosomal aberration; cytidine deaminase; DNA; DNA double-strand break; G-Quadruplexes; G-quartets; Genes, myc; genomic instability; Humans; R-loop; R-Loop Structures; RNA-DNA hybrid; RNase H; t(8;14) translocation; Translocation, Genetic; DSBs; ALL; TAM; CML; CSR; R-loop; RNA-DNA hybrid; chromosomal aberration; BL; ChIP; G-quartets; DNA double-strand break; BER; eBL; t(8;14) translocation; APE; RNase H; cytidine deaminase; AID; genomic instability; sBL; RAGs
• ISSN: 0021-9258; 1083-351X; 1083-351X
• DOI: 10.1016/j.jbc.2023.105431

t(8;14) translocation is the hallmark of Burkitt’s lymphoma and results in c-MYC deregulation. During the translocation, c-MYC gene on chromosome 8 gets juxtaposed to the Ig switch regions on chromosome 14. Although the promoter of c-MYC has been investigated for its mechanism of fragility, little is known about other c-MYC breakpoint regions. We have analyzed the translocation break points at the exon 1/intron 1 of c-MYC locus from patients with Burkitt’s lymphoma. Results showed that the breakpoint region, when present on a plasmid, could fold into an R-loop confirmation in a transcription-dependent manner. Sodium bisulfite modification assay revealed significant single-strandedness on chromosomal DNA of Burkitt’s lymphoma cell line, Raji, and normal lymphocytes, revealing distinct R-loops covering up to 100 bp region. Besides, ChIP-DRIP analysis reveals that the R-loop antibody can bind to the breakpoint region. Further, we show the formation of stable parallel intramolecular G-quadruplex on non-template strand of the genome. Finally, incubation of purified AID in vitro or overexpression of AID within the cells led to enhanced mutation frequency at the c-MYC breakpoint region. Interestingly, anti-γH2AX can bind to DSBs generated at the c-MYC breakpoint region within the cells. The formation of R-loop and G-quadruplex was found to be mutually exclusive. Therefore, our results suggest that AID can bind to the single-stranded region of the R-loop and G4 DNA, leading to the deamination of cytosines to uracil and induction of DNA breaks in one of the DNA strands, leading to double-strand break, which could culminate in t(8;14) chromosomal translocation.