title: Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.
abstract: Hybridization- and tag-based technologies have been successfully used in Down syndrome to identify genes involved in various aspects of the pathogenesis. However, these technologies suffer from several limits and drawbacks and, to date, information about rare, even though relevant, RNA species such as long and small non-coding RNAs, is completely missing. Indeed, none of published works has still described the whole transcriptional landscape of Down syndrome. Although the recent advances in high-throughput RNA sequencing have revealed the complexity of transcriptomes, most of them rely on polyA enrichment protocols, able to detect only a small fraction of total RNA content. On the opposite end, massive-scale RNA sequencing on rRNA-depleted samples allows the survey of the complete set of coding and non-coding RNA species, now emerging as novel contributors to pathogenic mechanisms. Hence, in this work we analysed for the first time the complete transcriptome of human trisomic endothelial progenitor cells to an unprecedented level of resolution and sensitivity by RNA-sequencing. Our analysis allowed us to detect differential expression of even low expressed genes crucial for the pathogenesis, to disclose novel regions of active transcription outside yet annotated loci, and to investigate a plethora of non-polyadenylated long as well as short non coding RNAs. Novel splice isoforms for a large subset of crucial genes, and novel extended untranslated regions for known genes--possibly novel miRNA targets or regulatory sites for gene transcription--were also identified in this study. Coupling the rRNA depletion of samples, followed by high-throughput RNA-sequencing, to the easy availability of these cells renders this approach very feasible for transcriptome studies, offering the possibility of investigating in-depth blood-related pathological features of Down syndrome, as well as other genetic disorders.
authors.affiliation: Institute of Genetics and Biophysics A. Buzzati-Traverso, CNR, Naples, Italy.
authors.forename: Valerio
authors.initials: V
authors.lastname: Costa
authors.forename: Claudia
authors.initials: C
authors.lastname: Angelini
authors.forename: Luciana
authors.initials: L
authors.lastname: D'Apice
authors.forename: Margherita
authors.initials: M
authors.lastname: Mutarelli
authors.forename: Amelia
authors.initials: A
authors.lastname: Casamassimi
authors.forename: Linda
authors.initials: L
authors.lastname: Sommese
authors.forename: Maria Assunta
authors.initials: MA
authors.lastname: Gallo
authors.forename: Marianna
authors.initials: M
authors.lastname: Aprile
authors.forename: Roberta
authors.initials: R
authors.lastname: Esposito
authors.forename: Luigi
authors.initials: L
authors.lastname: Leone
authors.forename: Aldo
authors.initials: A
authors.lastname: Donizetti
authors.forename: Stefania
authors.initials: S
authors.lastname: Crispi
authors.forename: Monica
authors.initials: M
authors.lastname: Rienzo
authors.forename: Berardo
authors.initials: B
authors.lastname: Sarubbi
authors.forename: Raffaele
authors.initials: R
authors.lastname: Calabrò
authors.forename: Marco
authors.initials: M
authors.lastname: Picardi
authors.forename: Paola
authors.initials: P
authors.lastname: Salvatore
authors.forename: Teresa
authors.initials: T
authors.lastname: Infante
authors.forename: Piergiuseppe
authors.initials: P
authors.lastname: De Berardinis
authors.forename: Claudio
authors.initials: C
authors.lastname: Napoli
authors.forename: Alfredo
authors.initials: A
authors.lastname: Ciccodicola
mesh_terms: D017398:Alternative Splicing; D004314:Down Syndrome; D015870:Gene Expression; D020869:Gene Expression Profiling; D006801:Humans; D007438:Introns; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics*
chemical_list: D012313:RNA