Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq.
Isoform diversity and regulation in peripheral and central neurons revealed through RNA-Seq.
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DOI：
10.1371/journal.pone.0030417
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发表时间：
2012
期刊：
影响因子：
3.7
通讯作者：
Lemmon VP
中科院分区：
文献类型：
--
作者：
Lerch JK;Kuo F;Motti D;Morris R;Bixby JL;Lemmon VP
为了充分了解神经系统中细胞类型的特性和功能，需要了解同种型多样性水平上的神经元基因表达。在这里，我们将转录组的下一代测序（RNA-Seq）应用于在轴突生长许可基质上生长的纯化的感觉神经元和小脑颗粒神经元（CGN）。分析的目的是揭示神经元类型特异性亚型，作为了解其内在生长能力的基因表达模式的前奏。全球基因表达模式与其他细胞类型中发现的基因表达模式相当，因为绝大多数基因以低丰度表达。近18%的基因位点产生一个以上的转录本。超过8000种亚型的差异表达，在不同的神经元类型或独特的表达在一个或另一个不同程度。感觉神经元比CGN表达更多的基因和基因亚型。为了开始了解差异基因/亚型表达的机制，我们鉴定了特异性存在于差异表达亚型上游基因组序列中的转录因子结合位点，并分析了microRNA（miRNA）靶位点的3′非翻译区（3′ UTR）。我们的分析定义了两种神经元类型的异构体多样性与不同的轴突生长能力，并开始阐明在两个神经元群体的复杂的转录景观。
To fully understand cell type identity and function in the nervous system there is a need to understand neuronal gene expression at the level of isoform diversity. Here we applied Next Generation Sequencing of the transcriptome (RNA-Seq) to purified sensory neurons and cerebellar granular neurons (CGNs) grown on an axonal growth permissive substrate. The goal of the analysis was to uncover neuronal type specific isoforms as a prelude to understanding patterns of gene expression underlying their intrinsic growth abilities. Global gene expression patterns were comparable to those found for other cell types, in that a vast majority of genes were expressed at low abundance. Nearly 18% of gene loci produced more than one transcript. More than 8000 isoforms were differentially expressed, either to different degrees in different neuronal types or uniquely expressed in one or the other. Sensory neurons expressed a larger number of genes and gene isoforms than did CGNs. To begin to understand the mechanisms responsible for the differential gene/isoform expression we identified transcription factor binding sites present specifically in the upstream genomic sequences of differentially expressed isoforms, and analyzed the 3′ untranslated regions (3′ UTRs) for microRNA (miRNA) target sites. Our analysis defines isoform diversity for two neuronal types with diverse axon growth capabilities and begins to elucidate the complex transcriptional landscape in two neuronal populations.
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影响因子：
3.5
作者：
Blackmore, Murray G.;Moore, Darcie L.;Smith, Robin P.;Goldberg, Jeffrey L.;Bixby, John L.;Lemmon, Vance P.
通讯作者：
Lemmon, Vance P.
影响因子：
16.2
作者：
Belgard TG;Marques AC;Oliver PL;Abaan HO;Sirey TM;Hoerder-Suabedissen A;García-Moreno F;Molnár Z;Margulies EH;Ponting CP
通讯作者：
Ponting CP
影响因子：
5.3
作者：
Christie, Kimberly J.;Webber, Christine A.;Zochodne, Douglas W.
通讯作者：
Zochodne, Douglas W.
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL
影响因子：
25
作者：
Liu, Kai;Lu, Yi;Lee, Jae K.;Samara, Ramsey;Willenberg, Rafer;Sears-Kraxberger, Ilse;Tedeschi, Andrea;Park, Kevin Kyungsuk;Jin, Duo;Cai, Bin;Xu, Bengang;Connolly, Lauren;Steward, Oswald;Zheng, Binhai;He, Zhigang
通讯作者：
He, Zhigang