Probing the Potential Role of Non-B DNA Structures at Yeast Meiosis-Specific DNA Double-Strand Breaks

Abstract

A plethora of evidence suggests that different types of DNA quadruplexes are widely present in the genome of all organisms. The existence of a growing number of proteins that selectively bind and/or process these structures underscores their biological relevance. Moreover, G-quadruplex DNA has been implicated in the alignment of four sister chromatids by forming parallel guanine quadruplexes during meiosis; however, the underlying mechanism is not well defined. Here we show that a G/C-rich motif associated with a meiosis-specific DNA double-strand break (DSB) in Saccharomyces cerevisiae folds into G-quadruplex, and the C-rich sequence complementary to the G-rich sequence forms an i-motif. The presence of G-quadruplex or i-motif structures upstream of the green fluorescent protein-coding sequence markedly reduces the levels of gfp mRNA expression in S. cerevisiae cells, with a concomitant decrease in green fluorescent protein abundance, and blocks primer extension by DNA polymerase, thereby demonstrating the functional significance of these structures. Surprisingly, although S. cerevisiae Hop1, a component of synaptonemal complex axial/lateral elements, exhibits strong affinity to G-quadruplex DNA, it displays a much weaker affinity for the i-motif structure. However, the Hop1 C-terminal but not the N-terminal domain possesses strong i-motif binding activity, implying that the C-terminal domain has a distinct substrate specificity. Additionally, we found that Hop1 promotes intermolecular pairing between G/C-rich DNA segments associated with a meiosis-specific DSB site. Our results support the idea that the G/C-rich motifs associated with meiosis-specific DSBs fold into intramolecular G-quadruplex and i-motif structures, both in vitro and in vivo, thus revealing an important link between non-B form DNA structures and Hop1 in meiotic chromosome synapsis and recombination.

Extreme clustering of type-1 NF1 deletion breakpoints co-locating with G-quadruplex forming sequences

“…A role for GQs during meiotic AHR is also supported by the finding that Hop1, a protein that is critical for the synapsis of homologous chromosomes during meiosis, binds to G-quadruplex forming DNA sequence structures in vitro (Muniyappa et al, 2000;Anuradha and Muniyappa, 2004). Hop1 promotes intermolecular pairing between GQs at sites of meiosis-specific DNA double strand breaks suggesting that GQs could mediate the pairing between homologous chromosomes during meiotic prophase I (Kshirsagar et al, 2017). Since meiotic AHR and NAHR events are assumed to be mechanistically similar processes (Lupski et al, 2004;Liu et al, 2011), GQs are likely to play an important role during NAHR as well as AHR.…”

Polymorphism of G4 associates: from stacks to wires via interlocks

“…Our major goal was to identify the basic features of the G4 motif that predetermine association, and we focused on the roles of loops and general topologies (parallel, antiparallel or hybrid). We used motifs that are ubiquitous in the human genome, because the association of such fragments might occur in vivo and could account for the packaging of G-rich microsatellites ( 18 , 27–29 ) and G4-driven juxtaposition or for the specific alignment of the nucleic acid strands ( 16 , 30 ). The general regularities of G4 multimerization discussed in this study can also be useful for guided assembly of supramolecular DNA structures for nanotechnological applications.…”

Two pathways drive meiotic chromosome axis assembly in Saccharomyces cerevisiae

“…It is possible that other chromatin marks or even inherent nucleosomal features, such as unmodified histone surfaces or the associated DNA conformations, could create a broad signal that modulates binding of axis proteins, but this question requires further investigation. Intriguingly, the axis factor Hop1, which is required for Red1 recruitment to cluster regions ( [7] and this study), binds structured DNA in vitro [41,42]. Thus, a better understanding of Hop1 in vivo chromatin binding activities may help identify the chromatin features differentiating clusters from deserts.…”