title: Exploring Ty1 retrotransposon RNA structure within virus-like particles.
abstract: Ty1, a long terminal repeat retrotransposon of Saccharomyces, is structurally and functionally related to retroviruses. However, a differentiating aspect between these retroelements is the diversity of the replication strategies used by long terminal repeat retrotransposons. To understand the structural organization of cis-acting elements present on Ty1 genomic RNA from the GAG region that control reverse transcription, we applied chemoenzymatic probing to RNA/tRNA complexes assembled in vitro and to the RNA in virus-like particles. By comparing different RNA states, our analyses provide a comprehensive structure of the primer-binding site, a novel pseudoknot adjacent to the primer-binding sites, three regions containing palindromic sequences that may be involved in RNA dimerization or packaging and candidate protein interaction sites. In addition, we determined the impact of a novel form of transposon control based on Ty1 antisense transcripts that associate with virus-like particles. Our results support the idea that antisense RNAs inhibit retrotransposition by targeting Ty1 protein function rather than annealing with the RNA genome.
authors.affiliation: RT Biochemistry Section, HIV Drug Resistance Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
authors.forename: Katarzyna J
authors.initials: KJ
authors.lastname: Purzycka
authors.forename: Michal
authors.initials: M
authors.lastname: Legiewicz
authors.forename: Emiko
authors.initials: E
authors.lastname: Matsuda
authors.forename: Linda D
authors.initials: LD
authors.lastname: Eizentstat
authors.forename: Sabrina
authors.initials: S
authors.lastname: Lusvarghi
authors.forename: Agniva
authors.initials: A
authors.lastname: Saha
authors.forename: Stuart F J
authors.initials: SF
authors.lastname: Le Grice
authors.forename: David J
authors.initials: DJ
authors.lastname: Garfinkel
mesh_terms: D001665:Binding Sites; D055029:Inverted Repeat Sequences; D009690:Nucleic Acid Conformation; D059372:Nucleotide Motifs; D012313:RNA / Q000737:chemistry; D016372:RNA, Antisense / Q000378:metabolism; D012343:RNA, Transfer / Q000737:chemistry; D016601:RNA-Binding Proteins / Q000378:metabolism; D018626:Retroelements; D048348:Reverse Transcription; D012440:Saccharomyces / Q000235:genetics; D014771:Virion / Q000235:genetics*
chemical_list: D016372:RNA, Antisense; D016601:RNA-Binding Proteins; D018626:Retroelements; D012313:RNA; D012343:RNA, Transfer