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.

在2014财政年度，我们已经完成了该项目所需的主要生物信息学分析，使用CAGE实验方案从不同发育阶段的多种果蝇细胞类型收集的转录组数据。我们决定重点关注：1）IV类da神经元发育时程，以及2）IV类与I-III类细胞类型的规格。我们进行了以下分析：1。基于它们的序列组成和形状（它们是尖锐的峰还是广泛分布的）表征表达的启动子，以及它们如何被差异化利用。果蝇特异性转录因子结合位点基序的收集和聚类及其在果蝇基因组中的位置预测。由于缺乏可用的果蝇特异性结合基序，我们收集和合并基序基于它们的相似性.基于收集的基序集和可用的ChIP-seq和ChIP-chip数据对差异表达的启动子进行调控分析。我们已经提出了一个候选调节因素的列表，并正在进行实验验证。分析样本的重复转录组分析。我们发现某些重复序列根据发育阶段或细胞类型而差异表达，我们正试图确定这些差异背后的调控控制。

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