Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.
Massive-scale RNA-Seq analysis of non ribosomal transcriptome in human trisomy 21.
复制标题
DOI：
10.1371/journal.pone.0018493
复制
发表时间：
2011-04-20
期刊：
影响因子：
3.7
通讯作者：
Ciccodicola A
中科院分区：
文献类型：
--
作者：
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
杂交和基于标签的技术已经成功地用于唐氏综合症，以确定涉及发病机制的各个方面的基因。然而，这些技术受到一些限制和缺点的影响，到目前为止，关于罕见的，即使是相关的RNA物种的信息，如长链和小链非编码RNA，是完全缺失的。事实上，没有一本已出版的著作描述了唐氏综合症的整个转录景观。尽管高通量RNA测序的最新进展揭示了转录组的复杂性，但大多数转录组依赖于多聚a富集方案，只能检测到总RNA含量的一小部分。另一方面，在rrna缺失的样本上进行大规模RNA测序，可以调查完整的编码和非编码RNA物种，这些物种现在正在成为致病机制的新贡献者。因此，在这项工作中，我们首次通过rna测序分析了人类三体内皮祖细胞的完整转录组，达到了前所未有的分辨率和灵敏度水平。我们的分析使我们能够检测到对发病机制至关重要的低表达基因的差异表达，揭示了在未注释的位点之外的新活性转录区域，并研究了大量非多聚腺苷化的长和短非编码rna。本研究还发现了大量关键基因的新剪接异构体，以及已知基因的新扩展的非翻译区域——可能是新的miRNA靶点或基因转录的调控位点。将样本的rRNA耗尽，然后进行高通量rna测序，再加上这些细胞的易得性，使得这种方法在转录组研究中非常可行，为深入研究唐氏综合症以及其他遗传疾病的血液相关病理特征提供了可能。
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.
登录
查看更多内容
影响因子：
14.9
作者：
Bruford, Elspeth A.;Lush, Michael J.;Wright, Mathew W.;Sneddon, Tam P.;Povey, Sue;Birney, Ewan
通讯作者：
Birney, Ewan
影响因子：
2.7
作者：
Costa, Valerio;Sommese, Linda;Napoli, Claudio
通讯作者：
Napoli, Claudio
影响因子：
48
作者：
Cloonan, Nicole;Forrest, Alistair R. R.;Grimmond, Sean M.
通讯作者：
Grimmond, Sean M.
影响因子：
2.6
作者：
Holmes, Denise K.;Bates, Nicola;Bellantuono, Ilaria
通讯作者：
Bellantuono, Ilaria
影响因子：
3.5
作者：
FitzPatrick, DR;Ramsay, J;Hastie, ND
通讯作者：
Hastie, ND