Massive-scale rna-seq analysis of non ribosomal transcriptome in human trisomy 21

Valerio Costa, Claudia Angelini, Luciana D'Apice, Margherita Mutarelli, Amelia Casamassimi, Linda Sommese, Maria Assunta Gallo, Marianna Aprile, Roberta Esposito, Luigi Leone, Aldo Donizetti, Stefania Crispi, Monica Rienzo, Berardo Sarubbi, Raffaele Calabrò, Marco Picardi, Paola Salvatore, Teresa Infante, Piergiuseppe de Berardinis, Claudio NapoliAlfredo Ciccodicola

Research output: Contribution to journalArticle

47 Citations (Scopus)

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-polyadenilated 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.

Original languageEnglish
Article numbere18493
JournalPLoS One
Volume6
Issue number4
DOIs
Publication statusPublished - 2011

Fingerprint

trisomics
Down Syndrome
Transcriptome
transcriptome
Down syndrome
RNA
RNA Sequence Analysis
High-Throughput Nucleotide Sequencing
Genes
Untranslated RNA
genes
Long Noncoding RNA
Transcription
Untranslated Regions
Technology
Small Untranslated RNA
pathogenesis
sequence analysis
transcription (genetics)
Inborn Genetic Diseases

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Medicine(all)

Cite this

Costa, V., Angelini, C., D'Apice, L., Mutarelli, M., Casamassimi, A., Sommese, L., ... Ciccodicola, A. (2011). Massive-scale rna-seq analysis of non ribosomal transcriptome in human trisomy 21. PLoS One, 6(4), [e18493]. https://doi.org/10.1371/journal.pone.0018493

Massive-scale rna-seq analysis of non ribosomal transcriptome in human trisomy 21. / Costa, Valerio; Angelini, Claudia; D'Apice, Luciana; Mutarelli, Margherita; Casamassimi, Amelia; Sommese, Linda; Gallo, Maria Assunta; Aprile, Marianna; Esposito, Roberta; Leone, Luigi; Donizetti, Aldo; Crispi, Stefania; Rienzo, Monica; Sarubbi, Berardo; Calabrò, Raffaele; Picardi, Marco; Salvatore, Paola; Infante, Teresa; de Berardinis, Piergiuseppe; Napoli, Claudio; Ciccodicola, Alfredo.

In: PLoS One, Vol. 6, No. 4, e18493, 2011.

Research output: Contribution to journalArticle

Costa, V, Angelini, C, D'Apice, L, Mutarelli, M, Casamassimi, A, Sommese, L, Gallo, MA, Aprile, M, Esposito, R, Leone, L, Donizetti, A, Crispi, S, Rienzo, M, Sarubbi, B, Calabrò, R, Picardi, M, Salvatore, P, Infante, T, de Berardinis, P, Napoli, C & Ciccodicola, A 2011, 'Massive-scale rna-seq analysis of non ribosomal transcriptome in human trisomy 21', PLoS One, vol. 6, no. 4, e18493. https://doi.org/10.1371/journal.pone.0018493
Costa V, Angelini C, D'Apice L, Mutarelli M, Casamassimi A, Sommese L et al. Massive-scale rna-seq analysis of non ribosomal transcriptome in human trisomy 21. PLoS One. 2011;6(4). e18493. https://doi.org/10.1371/journal.pone.0018493
Costa, Valerio ; Angelini, Claudia ; D'Apice, Luciana ; Mutarelli, Margherita ; Casamassimi, Amelia ; Sommese, Linda ; Gallo, Maria Assunta ; Aprile, Marianna ; Esposito, Roberta ; Leone, Luigi ; Donizetti, Aldo ; Crispi, Stefania ; Rienzo, Monica ; Sarubbi, Berardo ; Calabrò, Raffaele ; Picardi, Marco ; Salvatore, Paola ; Infante, Teresa ; de Berardinis, Piergiuseppe ; Napoli, Claudio ; Ciccodicola, Alfredo. / Massive-scale rna-seq analysis of non ribosomal transcriptome in human trisomy 21. In: PLoS One. 2011 ; Vol. 6, No. 4.
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