title: Myriad Triple-Helix-Forming Structures in the Transposable Element RNAs of Plants and Fungi.
abstract: The ENE (element for nuclear expression) is a cis-acting RNA structure that protects viral or cellular noncoding RNAs (ncRNAs) from nuclear decay through triple-helix formation with the poly(A) tail or 3'-terminal A-rich tract. We expanded the roster of nine known ENEs by bioinformatic identification of ∼200 distinct ENEs that reside in transposable elements (TEs) of numerous non-metazoan and one fish species and in four Dicistrovirus genomes. Despite variation within the ENE core, none of the predicted triple-helical stacks exceeds five base triples. Increased accumulation of reporter transcripts in human cells demonstrated functionality for representative ENEs. Location close to the poly(A) tail argues that ENEs are active in TE transcripts. Their presence in intronless, but not intron-containing, hAT transposase genes supports the idea that TEs acquired ENEs to counteract the RNA-destabilizing effects of intron loss, a potential evolutionary consequence of TE horizontal transfer in organisms that couple RNA silencing to splicing deficits.
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.
authors.forename: Kazimierz T
authors.initials: KT
authors.lastname: Tycowski
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA.
authors.forename: Mei-Di
authors.initials: MD
authors.lastname: Shu
authors.affiliation: Department of Molecular Biophysics and Biochemistry, Howard Hughes Medical Institute, Yale University School of Medicine, 295 Congress Avenue, New Haven, CT 06536, USA. Electronic address: joan.steitz@yale.edu.
authors.forename: Joan A
authors.initials: JA
authors.lastname: Steitz
mesh_terms: D001483:Base Sequence; D002467:Cell Nucleus / Q000235:genetics; D017124:Conserved Sequence / Q000235:genetics; D004251:DNA Transposable Elements / Q000235:genetics*; D005658:Fungi / Q000235:genetics*; D057809:HEK293 Cells; D006801:Humans; D007438:Introns / Q000235:genetics; D009690:Nucleic Acid Conformation; D010944:Plants / Q000235:genetics*; D020871:RNA Stability / Q000235:genetics; D012331:RNA, Fungal / Q000737:chemistry* / Q000235:genetics; D012333:RNA, Messenger / Q000235:genetics; D018749:RNA, Plant / Q000737:chemistry* / Q000235:genetics; D012367:RNA, Viral / Q000737:chemistry / Q000235:genetics; D019895:Transposases / Q000235:genetics / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D012331:RNA, Fungal; D012333:RNA, Messenger; D018749:RNA, Plant; D012367:RNA, Viral; D019895:Transposases