title: Why the DNA self-depurination mechanism operates in HB-β but not in β-globin paralogs HB-δ, HB-ɛ1, HB-γ1 and HB-γ2.
abstract: The human β-globin, δ-globin and ɛ-globin genes contain almost identical coding strand sequences centered about codon 6 having potential to form a stem-loop with a 5'GAGG loop. Provided with a sufficiently stable stem, such a structure can self-catalyze depurination of the loop 5'G residue, leading to a potential mutation hotspot. Previously, we showed that such a hotspot exists about codon 6 of β-globin, with by far the highest incidence of mutations across the gene, including those responsible for 6 anemias (notably Sickle Cell Anemia) and β-thalassemias. In contrast, we show here that despite identical loop sequences, there is no mutational hotspot in the δ- or ɛ1-globin potential self-depurination sites, which differ by only one or two base pairs in the stem region from that of the β-globin gene. These differences result in either one or two additional mismatches in the potential 7-base pair-forming stem region, thereby weakening its stability, so that either DNA cruciform extrusion from the duplex is rendered ineffective or the lifetime of the stem-loop becomes too short to permit self-catalysis to occur. Having that same loop sequence, paralogs HB-γ1 and HB-γ2 totally lack stem-forming potential. Hence the absence in δ- and ɛ1-globin genes of a mutational hotspot in what must now be viewed as non-functional homologs of the self-depurination site in β-globin. Such stem-destabilizing variants appeared early among vertebrates and remained conserved among mammals and primates. Thus, this study has revealed conserved sequence determinants of self-catalytic DNA depurination associated with variability of mutation incidence among human β-globin paralogs.
authors.affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Electronic address: amosova@princeton.edu.
authors.forename: Olga
authors.initials: O
authors.lastname: Amosova
authors.affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Electronic address: jalvarez@wi.mit.edu.
authors.forename: Juan R
authors.initials: JR
authors.lastname: Alvarez-Dominguez
authors.affiliation: Department of Molecular Biology, Princeton University, Princeton, NJ 08544, USA. Electronic address: jrfresco@princeton.edu.
authors.forename: Jacques R
authors.initials: JR
authors.lastname: Fresco
mesh_terms: D000818:Animals; D020137:Base Pair Mismatch; D001483:Base Sequence; D002384:Catalysis; D003062:Codon / Q000235:genetics; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D019143:Evolution, Molecular; D006147:Guanine / Q000378:metabolism*; D006453:Hemoglobinopathies / Q000235:genetics; D006801:Humans; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D017354:Point Mutation; D016415:Sequence Alignment; D012689:Sequence Homology, Nucleic Acid; D013045:Species Specificity; D014714:Vertebrates / Q000235:genetics; D055544:beta-Globins / Q000737:chemistry / Q000235:genetics*; D055546:delta-Globins / Q000737:chemistry / Q000235:genetics*; D055545:gamma-Globins / Q000737:chemistry / Q000235:genetics*
chemical_list: D003062:Codon; D055544:beta-Globins; D055546:delta-Globins; D055545:gamma-Globins; D006147:Guanine; D004247:DNA
keywords: DNA self-catalyzed depurination; DNA self-depurination mechanism; DNA stem-loop structures; HB β, δ, ɛ1, γ1, γ2 genes; Human β-globin gene paralogs