title: Potential G-quadruplexes in the human long non-coding transcriptome.
abstract: DNA G-quadruplexes are known as modulators of transcription. More recently G-quadruplexes, located in the untranslated regions of the mRNA of protein coding genes, have been described to negatively regulate gene expression at the post transcriptional/ translational levels. Here we describe the possibility of the existence of G-quadruplexes in non-coding RNA (ncRNA) and discuss their potential biological roles. Using an in house prediction tool (Quadfinder) we observe a significant occurrence and distribution of G-quadruplexes in ncRNA of various sizes. We also observe that most of non-coding RNAs harboring these potential quadruplex motifs peak at the sizes ranging from 200-300 bases. More importantly we report enrichment for single and dinucleotide loops indicating a degree of high stability of these G-quadruplexes and their potential functions in vivo. Subsequent in vitro analyses of a subset of these sequences were performed which support our predictions.
authors.affiliation: Institute for Genomics and Integrative Biology, CSIR, New Delhi, India.
authors.forename: Gopal Gunanathan
authors.initials: GG
authors.lastname: Jayaraj
authors.forename: Satyaprakash
authors.initials: S
authors.lastname: Pandey
authors.forename: Vinod
authors.initials: V
authors.lastname: Scaria
authors.forename: Souvik
authors.initials: S
authors.lastname: Maiti
mesh_terms: D001483:Base Sequence; D002942:Circular Dichroism; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D054856:G-Quadruplexes; D020869:Gene Expression Profiling / Q000379:methods; D006801:Humans; D059372:Nucleotide Motifs; D020871:RNA Stability; D022661:RNA, Untranslated / Q000235:genetics*; D059467:Transcriptome
chemical_list: D022661:RNA, Untranslated