ハイスループット・トランスクリプトミクスを通じてのニューロン構造可塑性規制の分析

通过高通量转录组学分析神经元结构可塑性调控

• 批准号: 13F03728
• 负责人: CARNINCI Piero
• 金额: $ 1.47万
• 依托单位: The Institute of Physical and Chemical Research
• 依托单位国家: 日本
• 项目类别: Grant-in-Aid for JSPS Fellows
• 财政年份: 2013
• 资助国家: 日本
• 起止时间: 2013-04-01 至 2015-03-31
• 项目状态: 已结题
• 来源: https://kaken.nii.ac.jp/grant/KAKENHI-PROJECT-13F03728/
• 关键词: Promoters; Transcriptome; Regulatory Analysis; Repeat analysis; Raw data processing and filtering; Data survey; Differential expression analysis; Clustering; Functional analysis

For the FY2014, we have completed the main bioinformatics analyses required for this project, using the collected transcriptome data from multiple Drosophila cell types at different stages of development using the CAGE experimental protocol. We decided to focus on: 1) Class IV da neuron development time course, and 2) specification of Class IV vs. the Class I-III cell types. We performed the following analyses:1. Characterization of the expressed promoters based on their sequence composition and shapes (whether they are sharply peaked or broadly spread), and how they are differentially utilized.2. Collecting and clustering of Drosophila-specific transcription factor binding site motifs and predicting their positions on the Drosophila genome. Due to the lack of available Drosophila-specific binding motifs, we collected and merged motifs based on their similarity.3. Regulatory analysis of the differentially expressed promoters based on the collected motif set and available ChIP-seq and ChIP-chip data. We have come up with a list of candidate regulatory factors and are in the process of validating them experimentally.4. Analysis of the repeat transcriptome for the analyzed samples. We found that certain repeats are differentially expressed according to developmental stages or cell types, and we are trying to determine what regulatory controls are behind these differences.

对于2014财年，我们使用CAGE实验方案在不同开发阶段的多个果蝇细胞类型中收集的转录组数据完成了该项目所需的主要生物信息学分析。我们决定关注：1）IV类神经元开发时间课程，以及2）IV类别与I-III类细胞类型的规范。我们进行了以下分析：1。根据表达启动子的序列组成和形状（无论是峰值或广泛传播）以及如何差异使用的表征。2。果蝇特异性转录因子结合位点基序的收集和聚类，并预测其在果蝇基因组上的位置。由于缺乏可用的果蝇特异性结合基序，我们根据其相似性收集并合并了基序。3。基于收集的基序集以及可用的芯片序列和芯片芯片数据对差异表达的启动子进行调节分析。我们提出了候选监管因素的列表，并正在实验验证它们4。分析分析样品的重复转录组。我们发现，根据发育阶段或细胞类型对某些重复进行差异表达，我们正在尝试确定这些差异背后的调节控制。

项目成果

Analysis of Neuronal Structural Plasticity Regulation through Transcriptomic Approaches

通过转录组学方法分析神经元结构可塑性调节

• 发表时间: 2014
• 作者: Kouki Kato;Tetsuro Muraoka;Takatoshi Higuchi;Nobuaki Mizuguchi;Kazuyuki Kanosue;Kazuya Masuda;Tae Jun Kwon
• 通讯作者: Tae Jun Kwon