title: Identification of RNA polymerase III-transcribed Alu loci by computational screening of RNA-Seq data.
abstract: Of the ∼ 1.3 million Alu elements in the human genome, only a tiny number are estimated to be active in transcription by RNA polymerase (Pol) III. Tracing the individual loci from which Alu transcripts originate is complicated by their highly repetitive nature. By exploiting RNA-Seq data sets and unique Alu DNA sequences, we devised a bioinformatic pipeline allowing us to identify Pol III-dependent transcripts of individual Alu elements. When applied to ENCODE transcriptomes of seven human cell lines, this search strategy identified ∼ 1300 Alu loci corresponding to detectable transcripts, with ∼ 120 of them expressed in at least three cell lines. In vitro transcription of selected Alus did not reflect their in vivo expression properties, and required the native 5'-flanking region in addition to internal promoter. We also identified a cluster of expressed AluYa5-derived transcription units, juxtaposed to snaR genes on chromosome 19, formed by a promoter-containing left monomer fused to an Alu-unrelated downstream moiety. Autonomous Pol III transcription was also revealed for Alus nested within Pol II-transcribed genes. The ability to investigate Alu transcriptomes at single-locus resolution will facilitate both the identification of novel biologically relevant Alu RNAs and the assessment of Alu expression alteration under pathological conditions.
authors.affiliation: Department of Life Sciences, University of Parma, 43124 Parma, Italy Department of Clinical and Experimental Medicine, University of Parma, 43126 Parma, Italy.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Conti
authors.affiliation: Department of Life Sciences, University of Parma, 43124 Parma, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Carnevali
authors.affiliation: Department of Clinical Sciences and Community Health, University of Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via S. Barnaba, 8-20122 Milano, Italy.
authors.forename: Valentina
authors.initials: V
authors.lastname: Bollati
authors.affiliation: Department of Clinical Sciences and Community Health, University of Milano and Fondazione IRCCS Cà Granda Ospedale Maggiore Policlinico, Via S. Barnaba, 8-20122 Milano, Italy.
authors.forename: Silvia
authors.initials: S
authors.lastname: Fustinoni
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095-7239, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.affiliation: Department of Life Sciences, University of Parma, 43124 Parma, Italy giorgio.dieci@unipr.it.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Dieci
mesh_terms: D020087:Alu Elements; D020869:Gene Expression Profiling; D020868:Gene Silencing; D056426:Genetic Loci; D023281:Genomics / Q000379:methods; D006801:Humans; D012320:RNA Polymerase III / Q000378:metabolism*; D017423:Sequence Analysis, RNA; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic; D059467:Transcriptome
chemical_list: D014157:Transcription Factors; D012320:RNA Polymerase III