Rawal Pooja, Kummarasetti Veera Bhadra Rao, Ravindran Jinoy, Kumar Nirmal, Halder Kangkan, Sharma Rakesh, Mukerji Mitali, Das Swapan Kumar, Chowdhury Shantanu
G.N. Ramachandran Knowledge Centre for Genome Informatics, Institute of Genomics and Integrative Biology, CSIR, Delhi, India.
Genome Res. 2006 May;16(5):644-55. doi: 10.1101/gr.4508806.
The role of nonlinear DNA in replication, recombination, and transcription has become evident in recent years. Although several studies have predicted and characterized regulatory elements at the sequence level, very few have investigated DNA structure as regulatory motifs. Here, using G-quadruplex or G4 DNA motifs as a model, we have researched the role of DNA structure in transcription on a genome-wide scale. Analyses of >61,000 open reading frames (ORFs) across 18 prokaryotes show enrichment of G4 motifs in regulatory regions and indicate its predominance within promoters of genes pertaining to transcription, secondary metabolite biosynthesis, and signal transduction. Based on this, we predict that G4 DNA may present regulatory signals. This is supported by conserved G4 motifs in promoters of orthologous genes across phylogenetically distant organisms. We hypothesized a regulatory role of G4 DNA during supercoiling stress, when duplex destabilization may result in G4 formation. This is in line with our observations from target site analysis for 55 DNA-binding proteins in Escherichia coli, which reveals significant (P<0.001) association of G4 motifs with target sites of global regulators FIS and Lrp and the sigma factor RpoD (sigma70). These factors together control >1000 genes in the early growth phase and are believed to be induced by supercoiled DNA. We also predict G4 motif-induced supercoiling sensitivity for >30 operons in E. coli, and our findings implicate G4 DNA in DNA-topology-mediated global gene regulation in E. coli.
近年来，非线性DNA在复制、重组和转录中的作用已变得明显。尽管有几项研究在序列水平上预测并表征了调控元件，但很少有研究将DNA结构作为调控基序进行研究。在这里，我们以G-四链体或G4 DNA基序为模型，在全基因组范围内研究了DNA结构在转录中的作用。对18种原核生物中超过61,000个开放阅读框（ORF）的分析表明，G4基序在调控区域富集，并表明其在与转录、次级代谢物生物合成和信号转导相关的基因启动子中占主导地位。基于此，我们预测G4 DNA可能呈现调控信号。这得到了系统发育距离较远的生物体中直系同源基因启动子中保守G4基序的支持。我们假设在超螺旋应激期间G4 DNA具有调控作用，此时双链解稳定可能导致G4形成。这与我们对大肠杆菌中55种DNA结合蛋白的靶位点分析结果一致，该分析揭示了G4基序与全局调节因子FIS和Lrp以及σ因子RpoD（σ70）的靶位点之间存在显著（P<0.001）关联。这些因子共同控制早期生长阶段的>1000个基因，并且被认为是由超螺旋DNA诱导的。我们还预测了大肠杆菌中>30个操纵子对G4基序诱导的超螺旋敏感性，我们的研究结果表明G4 DNA参与了大肠杆菌中DNA拓扑结构介导的全局基因调控。
