Mechanistic basis for chromosomal translocations at the E2A gene and its broader relevance to human B cell malignancies
Di Liu,
Yong-Hwee Eddie Loh,
Chih-Lin Hsieh,
Michael R. Lieber
Affiliations
Di Liu
Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
Yong-Hwee Eddie Loh
USC Libraries Bioinformatics Services, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
Chih-Lin Hsieh
Department of Urology, USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA
Michael R. Lieber
Departments of Pathology, Biochemistry & Molecular Biology, and Molecular Microbiology & Immunology, and Section of Molecular & Computational Biology (Department of Biological Sciences), USC Norris Comprehensive Cancer Center, University of Southern California and USC Keck School of Medicine, Los Angeles, CA, USA; Corresponding author
Summary: Analysis of translocation breakpoints in human B cell malignancies reveals that DNA double-strand breaks at oncogenes most frequently occur at CpG sites located within 20–600 bp fragile zones and depend on activation-induced deaminase (AID). AID requires single-stranded DNA (ssDNA) to act, but it has been unclear why or how this region transiently acquires a ssDNA state. Here, we demonstrate the ssDNA state in the 23 bp E2A fragile zone using several methods, including native bisulfite DNA structural analysis in live human pre-B cells. AID deamination within the E2A fragile zone does not require but is increased upon transcription. High C-string density, nascent RNA tails, and direct DNA sequence repeats prolong the ssDNA state of the E2A fragile zone and increase AID deamination at overlapping AID hotspots that contain the CpG sites at which breaks occur in patients. These features provide key insights into lymphoid fragile zones generally.
