Comparison of parallel high-throughput RNA sequencing between knockout of TDP-43 and its overexpression reveals primarily nonreciprocal and nonoverlapping gene expression changes in the central nervous system of Drosophila.
Comparison of parallel high-throughput RNA sequencing between knockout of TDP-43 and its overexpression reveals primarily nonreciprocal and nonoverlapping gene expression changes in the central nervous system of Drosophila.
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DOI：
10.1534/g3.112.002998
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发表时间：
2012-07
期刊：
影响因子：
--
通讯作者：
Morton DB
中科院分区：
文献类型：
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作者：
Hazelett DJ;Chang JC;Lakeland DL;Morton DB
人类Tar-DNA结合蛋白TDP-43与肌萎缩侧索硬化症(ALS)和其他神经退行性疾病有关。TDP-43包含两个保守的RNA结合基序，并在RNA代谢中发挥作用，包括前mRNA剪接和转录抑制。在这里，我们以果蝇为模型，产生了功能缺失和过表达的Tar-DNA结合蛋白同源基因(TBPH)，以研究它们对中枢神经系统(CNS)转录组的影响。通过使用大规模并行测序方法(RNA-seq)来分析中枢神经系统，我们发现TBPH的缺失导致了广泛的基因激活和剪接变化，其中大部分被TBPH表达的挽救所逆转。相反，TBPH的过度表达会导致基因表达减少。虽然以前的研究表明TDP-43在ALS中既没有表达也有错误表达，但我们的数据显示它们之间的基因表达几乎没有重叠，这表明受TBPH功能丧失和过度表达影响的大部分基因是不同的。结合计算方法来确定可能的TBPH靶标和以前确定的脊椎动物TDP-43靶标的同源基因，我们提供了丰富的基因本体论的全面分析。我们的数据表明，TDP-43在突触传递、突触释放和内吞作用中发挥作用。我们还发现了Wnt和BMP通路的一个潜在的新调节，其许多靶点似乎是保守的。
The human Tar-DNA binding protein, TDP-43, is associated with amyotrophic lateral sclerosis (ALS) and other neurodegenerative disorders. TDP-43 contains two conserved RNA-binding motifs and has documented roles in RNA metabolism, including pre-mRNA splicing and repression of transcription. Here, using Drosophila melanogaster as a model, we generated loss-of-function and overexpression genotypes of Tar-DNA binding protein homolog (TBPH) to study their effect on the transcriptome of the central nervous system (CNS). By using massively parallel sequencing methods (RNA-seq) to profile the CNS, we find that loss of TBPH results in widespread gene activation and altered splicing, much of which are reversed by rescue of TBPH expression. Conversely, TBPH overexpression results in decreased gene expression. Although previous studies implicated both absence and mis-expression of TDP-43 in ALS, our data exhibit little overlap in the gene expression between them, suggesting that the bulk of genes affected by TBPH loss-of-function and overexpression are different. In combination with computational approaches to identify likely TBPH targets and orthologs of previously identified vertebrate TDP-43 targets, we provide a comprehensive analysis of enriched gene ontologies. Our data suggest that TDP-43 plays a role in synaptic transmission, synaptic release, and endocytosis. We also uncovered a potential novel regulation of the Wnt and BMP pathways, many of whose targets appear to be conserved.