Formation of a G-quadruplex at the BCL2 major breakpoint region of the t(14;18) translocation in follicular lymphoma

Abstract

The t(14;18) translocation in follicular lymphoma is one of the most common chromosomal translocations. Most breaks on chromosome 18 are located at the 3′-UTR of the BCL2 gene and are mainly clustered in the major breakpoint region (MBR). Recently, we found that the BCL2 MBR has a non-B DNA character in genomic DNA. Here, we show that single-stranded DNA modeled from the template strand of the BCL2 MBR, forms secondary structures that migrate faster on native PAGE in the presence of potassium, due to the formation of intramolecular G-quadruplexes. Circular dichroism shows evidence for a parallel orientation for G-quadruplex structures in the template strand of the BCL2 MBR. Mutagenesis and the DMS modification assay confirm the presence of three guanine tetrads in the structure. 1H nuclear magnetic resonance studies further confirm the formation of an intramolecular G-quadruplex and a representative model has been built based on all of the experimental evidence. We also provide data consistent with the possible formation of a G-quadruplex structure at the BCL2 MBR within mammalian cells. In summary, these important features could contribute to the single-stranded character at the BCL2 MBR, thereby contributing to chromosomal fragility.

G quadruplex RNA structures in PSD-95 mRNA: potential regulators of miR-125a seed binding site accessibility

“…2B), even in the absence of KCl (bottom spectra). Imino proton resonances in the region 10-12 ppm have been assigned to guanine imino protons engaged in Hoogsteen base pairs within individual G quartets and are considered signatures of G quadruplex structure formation (Fürtig et al 2003;Menon et al 2008;Nambiar et al 2011). While DNA G quadruplexes require the presence of potassium ions for folding, RNA G quadruplexes of identical sequence can fold even in the absence of these ions, but have low stability (Joachimi et al 2009).…”

G-Quadruplex Structures Formed at the HOX11 Breakpoint Region Contribute to Its Fragility during t(10;14) Translocation in T-Cell Leukemia

“…One of the major causes of genomic instability being actively investigated is the occurrence of non-B DNA in the genome (15)(16)(17)(18)(19)(20)(21)(22)(23)(24)(25). Bioinformatic analyses have revealed the presence of several such non-B DNA structures throughout the genome (26,27).…”

“…Gquadruplexes, which are four-stranded DNA molecules, are suggested to be present in the promoters of many genes and at the telomeres, thereby performing functions like gene regulation and chromosomal end protection (28)(29)(30)(31)(32)(33). Recent studies have also shown that altered DNA structures like cruciform and G-quadruplexes could play a significant role in the generation of chromosomal translocations in certain leukemias and lymphomas (15,18,20,(34)(35)(36)(37).…”

“…Taq polymerase stop assay was performed as described previously (18 (18), and the HIF1␣ promoter region (MN118) (18) were heat denatured and slowly reannealed in the presence of 100 mM KCl or LiCl (for titration experiments, 50,100, 150, and 200 mM) with radiolabeled MN96 or MN119 (for HIF1␣). Products were resolved on a 12% denaturing PAGE gel and visualized.…”

Methylation of CpG sites in BCL2 major breakpoint region and the increase of BCL2/JH translocation with aging

“…Recent studies point out that BCL2 MBR adopts a non-B DNA structure in genomic DNA (Gquadruplex), which contributes to chromosomal fragility due to the single-stranded character at the region (Nambiar et al 2011;Zhao et al 2010). Moreover, the analysis of breakpoint junctions in lymphoma patients displayed that MBR breaks focused on three CpG peaks (Tsai et al 2008), suggesting that CpG sites are hotspot for breaks in MBR.…”