PMID:28369605

Citation	Lopez, CR, Singh, S, Hambarde, S, Griffin, WC, Gao, J, Chib, S, Yu, Y, Ira, G, Raney, KD and Kim, N' (2017) Yeast Sub1 and human PC4 are G-quadruplex binding proteins that suppress genome instability at co-transcriptionally formed G4 DNA. Nucleic Acids Res. '
Abstract	G-quadruplex or G4 DNA is a non-B secondary DNA structure consisting of a stacked array of guanine-quartets that can disrupt critical cellular functions such as replication and transcription. When sequences that can adopt Non-B structures including G4 DNA are located within actively transcribed genes, the reshaping of DNA topology necessary for transcription process stimulates secondary structure-formation thereby amplifying the potential for genome instability. Using a reporter assay designed to study G4-induced recombination in the context of an actively transcribed locus in Saccharomyces cerevisiae, we tested whether co-transcriptional activator Sub1, recently identified as a G4-binding factor, contributes to genome maintenance at G4-forming sequences. Our data indicate that, upon Sub1-disruption, genome instability linked to co-transcriptionally formed G4 DNA in Top1-deficient cells is significantly augmented and that its highly conserved DNA binding domain or the human homolog PC4 is sufficient to suppress G4-associated genome instability. We also show that Sub1 interacts specifically with co-transcriptionally formed G4 DNA in vivo and that yeast cells become highly sensitivity to G4-stabilizing chemical ligands by the loss of Sub1. Finally, we demonstrate the physical and genetic interaction of Sub1 with the G4-resolving helicase Pif1, suggesting a possible mechanism by which Sub1 suppresses instability at G4 DNA.
Links	PubMed Online version:10.1093/nar/gkx201
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Annotations

Gene product	Qualifier	GO Term	Evidence Code	with/from	Aspect	Extension	Notes	Status
YEAST:SUB1		GO:0051053: negative regulation of DNA metabolic process	ECO:0000315:		P		Paper’s Protein Name: Co-transcriptional activator Sub1. UniProt’s Protein Name: RNA polymerase II transcriptional coactivator SUB1. Organism: Saccharomyces cerevisiae (“all strains derived from YPH45”). Notes: Figure 1B is used. According to the paper “When highly transcribed, the rate of recombination for the pTET-lys2-GTOP was elevated by ∼7-fold in top1Δ sub1Δ strain compared to top1Δ (Figure 1B).” The chart indeed shows exactly this, although it doesn’t use the delta symbols on its labels. If recombination is elevated in Sub1’s absence, this implies that Sub1 negatively regulates DNA recombination.	complete CACAO 12407
HUMAN:TCP4		GO:0051053: negative regulation of DNA metabolic process	ECO:0000314:		P		Paper’s Protein Name: “Human homolog of Sub1, variously referred to as hSub1, p15 or PC4.” PC4 is primarily used. Uniprot’s Protein Name: Activated RNA polymerase II transcriptional coactivator p15. Organism: Homo sapiens. Notes: Figures 2B-E are all applicable, but I will primarily use 2B. The paper states that “the ectopic expression of Sub1 or PC4 reduced the rate of recombination for the pTET-lys2-GTOP construct by 9.6- and 10.3-fold, respectively, thereby resulting in the rates of recombination that are significantly lower than in top1Δ single deletion strains (Figure 2B).” Thus, PC4 seems to be linked to down-regulation of DNA recombination. The procedures of this experiment involve transforming yeast strains with a “PC4 expression vector,” so the evidence code should be IDA.	complete CACAO 12427
YEAST:TOP1		GO:0045910: negative regulation of DNA recombination	ECO:0000315:		P		Paper’s Protein Name: Top1. UniProt.’s Protein Name: DNA topoisomerase 1. Organism: Saccharomyces cerevisiae (“all strains derived from YPH45”). Notes: This paper actually implies that Top1’s effects on genome stability and DNA recombination had already been proven beforehand. Nevertheless, this paper provides evidence for the correlation as well, specifically in Figures 1A-B. In Figure 1A, wild type yeast has a DNA recombination rate of about 20*10^-8 for GTOP. However, Figure 1B shows that when the Top1 protein is mutated and knocked out, this rate is over 100*10^-8. It is important to note that these two charts are scaled very differently. Because recombination is elevated in Top1’s absence, it is implied that Top1 negatively regulates DNA recombination.	complete CACAO 12504

References

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