Hershman Steve G, Chen Qijun, Lee Julia Y, Kozak Marina L, Yue Peng, Wang Li-San, Johnson F Brad
College of Arts and Sciences and Vagelos Scholars Program, University of Pennsylvania, Philadelphia, PA, USA.
Nucleic Acids Res. 2008 Jan;36(1):144-56. doi: 10.1093/nar/gkm986. Epub 2007 Nov 13.
Although well studied in vitro, the in vivo functions of G-quadruplexes (G4-DNA and G4-RNA) are only beginning to be defined. Recent studies have demonstrated enrichment for sequences with intramolecular G-quadruplex forming potential (QFP) in transcriptional promoters of humans, chickens and bacteria. Here we survey the yeast genome for QFP sequences and similarly find strong enrichment for these sequences in upstream promoter regions, as well as weaker but significant enrichment in open reading frames (ORFs). Further, four findings are consistent with roles for QFP sequences in transcriptional regulation. First, QFP is correlated with upstream promoter regions with low histone occupancy. Second, treatment of cells with N-methyl mesoporphyrin IX (NMM), which binds G-quadruplexes selectively in vitro, causes significant upregulation of loci with QFP-possessing promoters or ORFs. NMM also causes downregulation of loci connected with the function of the ribosomal DNA (rDNA), which itself has high QFP. Third, ORFs with QFP are selectively downregulated in sgs1 mutants that lack the G4-DNA-unwinding helicase Sgs1p. Fourth, a screen for yeast mutants that enhance or suppress growth inhibition by NMM revealed enrichment for chromatin and transcriptional regulators, as well as telomere maintenance factors. These findings raise the possibility that QFP sequences form bona fide G-quadruplexes in vivo and thus regulate transcription.
尽管在体外对G-四链体（G4-DNA和G4-RNA）进行了充分研究，但其在体内的功能才刚刚开始被阐明。最近的研究表明，在人类、鸡和细菌的转录启动子中，具有分子内G-四链体形成潜力（QFP）的序列有所富集。在这里，我们对酵母基因组中的QFP序列进行了调查，同样发现这些序列在上游启动子区域有强烈的富集，在开放阅读框（ORF）中也有较弱但显著的富集。此外，有四项发现与QFP序列在转录调控中的作用一致。第一，QFP与组蛋白占有率低的上游启动子区域相关。第二，用N-甲基中卟啉IX（NMM）处理细胞，NMM在体外能选择性结合G-四链体，会导致具有QFP启动子或ORF的基因座显著上调。NMM还会导致与核糖体DNA（rDNA）功能相关的基因座下调，而rDNA本身具有高QFP。第三，在缺乏G4-DNA解旋酶Sgs1p的sgs1突变体中，具有QFP的ORF被选择性下调。第四，对增强或抑制NMM生长抑制作用的酵母突变体进行筛选，发现染色质和转录调节因子以及端粒维持因子有所富集。这些发现增加了QFP序列在体内形成真正的G-四链体从而调节转录的可能性。
