title: The role of antisense long noncoding RNA in small RNA-triggered gene activation.
abstract: Long noncoding RNAs (lncRNAs) are known to regulate neighboring protein-coding genes by directing chromatin remodeling complexes, imprinting, and X-chromosome inactivation. In this study, we explore the function of lncRNAs in small RNA-triggered transcriptional gene activation (TGA), a process in which microRNAs (miRNAs) or small interfering RNAs (siRNAs) associated with Argonaute (Ago) proteins induce chromatin remodeling and gene activation at promoters with sequence complementarity. We designed a model system with different lncRNA and chromatin environments to elucidate the molecular mechanisms required for mammalian TGA. Using RNA-fluorescence in situ hybridization (FISH) and rapid amplification of cDNA ends (RACE)-PCR, we demonstrated that small RNA-triggered TGA occurs at sites where antisense lncRNAs are transcribed through the reporter gene and promoter. Small RNA-induced TGA coincided with the enrichment of Ago2 at the promoter region, but Ago2-mediated cleavage of antisense lncRNAs was not observed. Moreover, we examined the allele-specific effects of lncRNAs through a Cre-induced inversion of a poly(A) sequence that was designed to block the transcription of antisense lncRNAs through the reporter gene region in an inducible and reversible manner. Termination of nascent antisense lncRNAs abrogated gene activation triggered by small RNAs, and only allele-specific cis-acting antisense lncRNAs, but not trans-acting lncRNAs, were capable of rescuing TGA. Hence, this model revealed that antisense lncRNAs can mediate TGA in cis and not in trans, serving as a molecular scaffold for a small RNA-Ago2 complex and chromatin remodeling.
authors.affiliation: Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA.
authors.forename: Xizhe
authors.initials: X
authors.lastname: Zhang
authors.affiliation: Department of Molecular and Cellular Biology, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA.
authors.forename: Haitang
authors.initials: H
authors.lastname: Li
authors.affiliation: Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA Department of Molecular and Cellular Biology, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA jburnett@coh.org jrossi@coh.org.
authors.forename: John C
authors.initials: JC
authors.lastname: Burnett
authors.affiliation: Irell and Manella Graduate School of Biological Sciences, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA Department of Molecular and Cellular Biology, Beckman Research Institute at the City of Hope, Duarte, California 91010, USA.
authors.forename: John J
authors.initials: JJ
authors.lastname: Rossi
mesh_terms: D000818:Animals; D060565:Argonaute Proteins / Q000235:genetics*; D042002:Chromatin Assembly and Disassembly; D006367:HeLa Cells; D006801:Humans; D017404:In Situ Hybridization, Fluorescence; D046912:Multiprotein Complexes / Q000235:genetics; D011401:Promoter Regions, Genetic; D016372:RNA, Antisense / Q000235:genetics*; D062085:RNA, Long Noncoding / Q000235:genetics*; D034741:RNA, Small Interfering; D015533:Transcriptional Activation / Q000235:genetics*
chemical_list: C466422:AGO2 protein, human; D060565:Argonaute Proteins; D046912:Multiprotein Complexes; D016372:RNA, Antisense; D062085:RNA, Long Noncoding; D034741:RNA, Small Interfering
keywords: Argonaute 2; RNA-FISH; TGA; lncRNA; shRNA; transcriptional gene activation