Satoh Jun-Ichi, Kawana Natsuki, Yamamoto Yoji
Department of Bioinformatics and Molecular Neuropathology, Meiji Pharmaceutical University, Tokyo 204-8588, Japan.
Bioinform Biol Insights. 2013 Dec 1;7:357-68. doi: 10.4137/BBI.S13279. eCollection 2013.
The neuron-restrictive silencer factor (NRSF) is a zinc finger transcription factor that represses neuronal gene transcription in non-neuronal cells by binding to the consensus repressor element-1 (RE1) located in regulatory regions of target genes. NRSF silences the expression of a wide range of target genes involved in neuron-specific functions. Previous studies showed that aberrant regulation of NRSF plays a key role in the pathological process of human neurodegenerative diseases. However, a comprehensive set of NRSF target genes relevant to human neuronal functions has not yet been characterized. We performed genome-wide data mining from chromatin immunoprecipitation followed by deep sequencing (ChIP-Seq) datasets of NRSF binding sites in human embryonic stem cells (ESC) and the corresponding ESC-derived neurons, retrieved from the database of the ENCODE/HAIB project. Using bioinformatics tools such as Avadis NGS and MACS, we identified 2,172 NRSF target genes in ESC and 308 genes in ESC-derived neurons based on stringent criteria. Only 40 NRSF target genes overlapped between both data sets. According to motif analysis, binding regions showed an enrichment of the consensus RE1 sites in ESC, whereas they were mainly located in poorly defined non-RE1 sites in ESC-derived neurons. Molecular pathways of NRSF target genes were linked with various neuronal functions in ESC, such as neuroactive ligand-receptor interaction, CREB signaling, and axonal guidance signaling, while they were not directed to neuron-specific functions in ESC-derived neurons. Remarkable differences in ChIP-Seq-based NRSF target genes and pathways between ESC and ESC-derived neurons suggested that NRSF-mediated silencing of target genes is highly effective in human ESC but not in ESC-derived neurons.
神经元限制性沉默因子（NRSF）是一种锌指转录因子，它通过与位于靶基因调控区域的共有抑制元件-1（RE1）结合，在非神经元细胞中抑制神经元基因转录。NRSF使多种参与神经元特异性功能的靶基因表达沉默。先前的研究表明，NRSF的异常调控在人类神经退行性疾病的病理过程中起关键作用。然而，与人类神经元功能相关的NRSF靶基因的完整集合尚未得到表征。我们从人类胚胎干细胞（ESC）和相应的ESC衍生神经元中NRSF结合位点的染色质免疫沉淀测序（ChIP-Seq）数据集中进行全基因组数据挖掘，这些数据集来自ENCODE/HAIB项目数据库。使用诸如Avadis NGS和MACS等生物信息学工具，我们基于严格标准在ESC中鉴定出2172个NRSF靶基因，在ESC衍生神经元中鉴定出308个基因。两个数据集之间只有40个NRSF靶基因重叠。根据基序分析，结合区域在ESC中显示出共有RE1位点的富集，而在ESC衍生神经元中它们主要位于定义不明确的非RE1位点。NRSF靶基因的分子途径与ESC中的各种神经元功能相关，如神经活性配体-受体相互作用、CREB信号传导和轴突导向信号传导，而在ESC衍生神经元中它们并不指向神经元特异性功能。ESC和ESC衍生神经元之间基于ChIP-Seq的NRSF靶基因和途径的显著差异表明，NRSF介导的靶基因沉默在人类ESC中非常有效，但在ESC衍生神经元中则不然。
