The Schizosaccharomyces pombe imprint — nick or ribonucleotide(s)?

(2004). The motion-induced position shift depends on the perceived direction of bistable quartet motion. influence of test patterns on the perception of motion aftereffect and position. (2004). Asymmetry in visual cortical circuits underlying motion-induced perceptual mislocalization. The nature of the Schizosaccharomyces pombe mat1 imprint, which acts to initiate mating-type switching, has been a subject of dispute. The imprint was proposed to be a site-and strand-specific nick [1]. Meanwhile, our work has shown i) that imprinted DNA can be purified such that both mat1 strands are intact, ii) that imprinted mat1 DNA can be broken by alkali or RNase treatment, and iii) that two populations of imprints exist, where either one or two ribonucleotides have been incorporated into the mat1 DNA, creating a DNA–RNA–DNA hybrid strand [2,3]. A recent paper by A. Kaykov and B. Arcangioli presents data that the authors claim 'are in disagreement with the RNA model and strongly indicate that the imprint is a nick' [4]. However, our analysis suggests that Kaykov and Arcangioli's data are fully compatible with the imprint being RNA in nature. It has long been known that the S. pombe mat1 imprint is labile during purification. Are the data presented by Kaykov and Arcangioli consistent with a nick being formed during purification due to hydrolysis of a ribonucleotide imprint? In the presented paper, it is assumed that the hydrolysis of an RNA imprint always leaves a gap [4]. However, when a DNA–RNA–DNA hybrid molecule, consisting of only one ribonucleotide incorporated into a DNA strand, is hydrolysed at the ribose residue, the ribonucleotide will stay attached to the 3′ ′ end of the 5′ ′ fragment and a nick will be present. Only if the hybrid molecule contains two or more consecutive ribonucleotides will a gap be formed by the hydrolysis (see below). Kaykov and Arcangioli detect the nick in mat1 DNA using different enzymatic activities and assays, but do not address whether their results are compatible with the RNA nature of the imprint. The enzymes used in their study (Escherichia coli DNA ligase, PstI restriction endonuclease and Taq DNA polymerase) are assumed to act specifically on DNA. However, the activities of these enzymes on substrates resembling either an intact or hydrolysed ribonucleotide imprint are not tested. Our unpublished characterization of these enzymes shows that they are able to utilize such substrates. In particular, Taq DNA polymerase can efficiently elongate across up to three ribonucleotides; …