title: Formation of triple-helical structures by the 3'-end sequences of MALAT1 and MENβ noncoding RNAs.
abstract: Stability of the long noncoding-polyadenylated nuclear (PAN) RNA from Kaposi's sarcoma-associated herpesvirus is conferred by an expression and nuclear retention element (ENE). The ENE protects PAN RNA from a rapid deadenylation-dependent decay pathway via formation of a triple helix between the U-rich internal loop of the ENE and the 3'-poly(A) tail. Because viruses borrow molecular mechanisms from their hosts, we searched highly abundant human long-noncoding RNAs and identified putative ENE-like structures in metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) and multiple endocrine neoplasia-β (MENβ) RNAs. Unlike the PAN ENE, the U-rich internal loops of both predicted cellular ENEs are interrupted by G and C nucleotides and reside upstream of genomically encoded A-rich tracts. We confirmed the ability of MALAT1 and MENβ sequences containing the predicted ENE and A-rich tract to increase the levels of an intronless β-globin reporter RNA. UV thermal denaturation profiles at different pH values support formation of a triple-helical structure composed of multiple U•A-U base triples and a single C•G-C base triple. Additional analyses of the MALAT1 ENE revealed that robust stabilization activity requires an intact triple helix, strong stems at the duplex-triplex junctions, a G-C base pair flanking the triplex to mediate potential A-minor interactions, and the 3'-terminal A of the A-rich tract to form a blunt-ended triplex lacking unpaired nucleotides at the duplex-triplex junction. These examples of triple-helical, ENE-like structures in cellular noncoding RNAs, are unique.
authors.affiliation: Department of Molecular Biophysics, Howard Hughes Medical Institute, Yale University School of Medicine, New Haven, CT 06536, USA.
authors.forename: Jessica A
authors.initials: JA
authors.lastname: Brown
authors.forename: Max L
authors.initials: ML
authors.lastname: Valenstein
authors.forename: Therese A
authors.initials: TA
authors.lastname: Yario
authors.forename: Kazimierz T
authors.initials: KT
authors.lastname: Tycowski
authors.forename: Joan A
authors.initials: JA
authors.lastname: Steitz
mesh_terms: D001483:Base Sequence; D004252:DNA Mutational Analysis; D006801:Humans; D006863:Hydrogen-Ion Concentration; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009711:Nucleotides / Q000235:genetics; D020871:RNA Stability / Q000235:genetics; D062085:RNA, Long Noncoding / Q000737:chemistry* / Q000235:genetics*; D016415:Sequence Alignment; D044366:Transition Temperature
chemical_list: C557041:MALAT1 long non-coding RNA, human; D009711:Nucleotides; D062085:RNA, Long Noncoding