title: Whole-genome expression analysis of mammalian-wide interspersed repeat elements in human cell lines.
abstract: With more than 500,000 copies, mammalian-wide interspersed repeats (MIRs), a sub-group of SINEs, represent ∼2.5% of the human genome and one of the most numerous family of potential targets for the RNA polymerase (Pol) III transcription machinery. Since MIR elements ceased to amplify ∼130 myr ago, previous studies primarily focused on their genomic impact, while the issue of their expression has not been extensively addressed. We applied a dedicated bioinformatic pipeline to ENCODE RNA-Seq datasets of seven human cell lines and, for the first time, we were able to define the Pol III-driven MIR transcriptome at single-locus resolution. While the majority of Pol III-transcribed MIR elements are cell-specific, we discovered a small set of ubiquitously transcribed MIRs mapping within Pol II-transcribed genes in antisense orientation that could influence the expression of the overlapping gene. We also identified novel Pol III-transcribed ncRNAs, deriving from transcription of annotated MIR fragments flanked by unique MIR-unrelated sequences, and confirmed the role of Pol III-specific internal promoter elements in MIR transcription. Besides demonstrating widespread transcription at these retrotranspositionally inactive elements in human cells, the ability to profile MIR expression at single-locus resolution will facilitate their study in different cell types and states including pathological alterations.
authors.affiliation: Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Carnevali
authors.affiliation: Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Anastasia
authors.initials: A
authors.lastname: Conti
authors.affiliation: Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90095 723, USA.
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
authors.affiliation: Department of Life Sciences, University of Parma, Parma, Italy.
authors.forename: Giorgio
authors.initials: G
authors.lastname: Dieci
mesh_terms: D019295:Computational Biology; D020869:Gene Expression Profiling; D006367:HeLa Cells; D006801:Humans; D020071:Interspersed Repetitive Sequences; D010957:Plasmids; D018626:Retroelements; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic
chemical_list: D018626:Retroelements
keywords: ENCODE; RNA polymerase III; RNA-Seq; SINE; mammalian-wide interspersed repeats