title: Formation of DNA:RNA hybrid G-quadruplexes of two G-quartet layers in transcription: expansion of the prevalence and diversity of G-quadruplexes in genomes.
abstract: G-quadruplexes are implicated in important cellular processes. Previous studies mostly focused on intramolecular G-quadruplexes of three or more G-quartets. Those composed of two G-quartets were only shown to form in single-stranded oligonucleotides. On the basis of electrophoresis, DMS footprinting, fluorescence labeling, and photo-cross-linking, we detected the formation of DNA:RNA hybrid G-quadruplexes (HQs) of two G-quartets during the transcription of DNA duplexes. These HQs have a lifetime on the minute scale and are stabilized by a stabilizing ligand. They are far shorter-lived than the HQs of three G-quartets, which last for hours. The occurrence of putative formation motifs of such HQs shows a transcription-dependent strand-biased selection, thus supporting their formation and function in genomes. They are present in almost all human genes in large amounts. We speculate that the two-G-quartet HQs may be a distinct type of G-quadruplexes that may play a role in timely responsive processes and for purposes of fine-tuning.
authors.affiliation: State Key Laboratory of Biomembrane and Membrane Biotechnology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101 (P. R. China).
authors.forename: Shan
authors.initials: S
authors.lastname: Xiao
authors.forename: Jia-yu
authors.initials: JY
authors.lastname: Zhang
authors.forename: Jun
authors.initials: J
authors.lastname: Wu
authors.forename: Ren-yi
authors.initials: RY
authors.lastname: Wu
authors.forename: Ye
authors.initials: Y
authors.lastname: Xia
authors.forename: Ke-wei
authors.initials: KW
authors.lastname: Zheng
authors.forename: Yu-hua
authors.initials: YH
authors.lastname: Hao
authors.forename: Xiang
authors.initials: X
authors.lastname: Zhou
authors.forename: Zheng
authors.initials: Z
authors.lastname: Tan
mesh_terms: D004247:DNA / Q000235:genetics*; D054856:G-Quadruplexes / Q000187:drug effects*; D016678:Genome / Q000235:genetics*; D006801:Humans; D009841:Oligonucleotides / Q000235:genetics*; D015995:Prevalence; D012313:RNA / Q000235:genetics*
chemical_list: D009841:Oligonucleotides; D012313:RNA; D004247:DNA
keywords: DNA; G-quadruplexes; RNA; genomes; transcription