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 language | English |
|---|---|
| Article number | e18493 |
| Journal | PLoS One |
| Volume | 6 |
| Issue number | 4 |
| DOIs | |
| Publication status | Published - 2011 |
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ASJC Scopus subject areas
- Agricultural and Biological Sciences(all)
- Biochemistry, Genetics and Molecular Biology(all)
- Medicine(all)
Cite this
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 journal › Article
}
TY - JOUR
T1 - Massive-scale rna-seq analysis of non ribosomal transcriptome in human trisomy 21
AU - Costa, Valerio
AU - Angelini, Claudia
AU - D'Apice, Luciana
AU - Mutarelli, Margherita
AU - Casamassimi, Amelia
AU - Sommese, Linda
AU - Gallo, Maria Assunta
AU - Aprile, Marianna
AU - Esposito, Roberta
AU - Leone, Luigi
AU - Donizetti, Aldo
AU - Crispi, Stefania
AU - Rienzo, Monica
AU - Sarubbi, Berardo
AU - Calabrò, Raffaele
AU - Picardi, Marco
AU - Salvatore, Paola
AU - Infante, Teresa
AU - de Berardinis, Piergiuseppe
AU - Napoli, Claudio
AU - Ciccodicola, Alfredo
PY - 2011
Y1 - 2011
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=79955399112&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79955399112&partnerID=8YFLogxK
U2 - 10.1371/journal.pone.0018493
DO - 10.1371/journal.pone.0018493
M3 - Article
C2 - 21533138
AN - SCOPUS:79955399112
VL - 6
JO - PLoS One
JF - PLoS One
SN - 1932-6203
IS - 4
M1 - e18493
ER -