title: Structure-specific nuclease activity of RAGs is modulated by sequence, length and phase position of flanking double-stranded DNA.
abstract: RAGs (recombination activating genes) are responsible for the generation of antigen receptor diversity through the process of combinatorial joining of different V (variable), D (diversity) and J (joining) gene segments. In addition to its physiological property, wherein RAG functions as a sequence-specific nuclease, it can also act as a structure-specific nuclease leading to genomic instability and cancer. In the present study, we investigate the factors that regulate RAG cleavage on non-B DNA structures. We find that RAG binding and cleavage on heteroduplex DNA is dependent on the length of the double-stranded flanking region. Besides, the immediate flanking double-stranded region regulates RAG activity in a sequence-dependent manner. Interestingly, the cleavage efficiency of RAGs at the heteroduplex region is influenced by the phasing of DNA. Thus, our results suggest that sequence, length and phase positions of the DNA can affect the efficiency of RAG cleavage when it acts as a structure-specific nuclease. These findings provide novel insights on the regulation of the pathological functions of RAGs.
authors.affiliation: Department of Biochemistry, Indian Institute of Science, Bangalore, India.
authors.forename: Rupa
authors.initials: R
authors.lastname: Kumari
authors.forename: Sathees C
authors.initials: SC
authors.lastname: Raghavan
mesh_terms: D024506:5' Flanking Region; D001483:Base Sequence; D001665:Binding Sites; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D003851:Deoxyribonucleases / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D016654:Genes, RAG-1; D057809:HEK293 Cells; D018398:Homeodomain Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D006801:Humans; D009687:Nuclear Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D060152:V(D)J Recombination
chemical_list: D004268:DNA-Binding Proteins; D018398:Homeodomain Proteins; D009687:Nuclear Proteins; D009692:Nucleic Acid Heteroduplexes; C499311:RAG2 protein, human; D011994:Recombinant Proteins; C064658:RAG-1 protein; D003851:Deoxyribonucleases
keywords: RAG cleavage; chromosomal translocation; double-strand break repair; genomic instability; heteroduplex DNA; non-B DNA structure