Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
Comparative genomics modeling of the NRSF/REST repressor network: From single conserved sites to genome-wide repertoire
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DOI：
10.1101/gr.4997306
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发表时间：
2006-10-01
期刊：
影响因子：
7
通讯作者：
Wold, Barbara
中科院分区：
文献类型：
--
作者：
Mortazavi, Ali;Thompson, Evonne Chen Leeper;Wold, Barbara
我们构建并应用了一个开放源码的信息学框架，称为Cistatics，以努力预测具有大结合位点的转录因子的目标基因谱系。Cistatics使用了两种不同的进化守恒过滤算法和几个分析模块。从神经元抑制因子NRSF/REST的单一保守和生物测试位点开始，Cistatics基于小鼠、人类和狗基因组中保守的位点出现情况生成了一个精细化的PSFM(位置特定频率矩阵)。该模型的预测通过染色质免疫沉淀(CHIP)和定量聚合酶链式反应进行了验证。基因转移试验和芯片浓缩数据的结合为设定成员门槛和对最终的基因队列模型进行排序提供了客观基础，该模型由人类基因组中与733个基因相关的842个高置信度位点组成。在神经元特异性基因本体论(GO)术语和神经元mRNA表达谱中，发现NRSE相关基因在统计学上显著丰富。一项更广泛的进化调查显示，与PSFM模式匹配的NRSE位点在所有完全测序的脊椎动物基因组中存在大致相同的数量，但在无脊椎动物和原脊椎动物基因组中明显缺失，就像NRSF本身一样。一些NRSF/REST位点以重复形式存在，这表明NRSE在古代和现代通过脊椎动物基因组传播的机制。多个预测的位点位于神经元microRNA和剪接因子基因附近，这些基因在体内被检测出NRSF/REST占有率为阳性。由此产生的网络模型整合了转录后控制和翻译控制，包括NRSF及其核心抑制因子Corest上的候选反馈环。
We constructed and applied an open source informatic framework called Cistematic in an effort to predict the target gene repertoire for transcription factors with large binding sites. Cistematic uses two different evolutionary conservation-filtering algorithms in conjunction with several analysis modules. Beginning with a single conserved and biologically tested site for the neuronal repressor NRSF/REST, Cistematic generated a refined PSFM (position specific frequency matrix) based on conserved site occurrences in mouse, human, and dog genomes. Predictions from this model were validated by chromatin immunoprecipitation (ChIP) followed by quantitative PCR. The combination of transfection assays and ChIP enrichment data provided an objective basis for setting a threshold for membership and rank-ordering a final gene cohort model consisting of 842 high- confidence sites in the human genome associated with 733 genes. Statistically significant enrichment of NRSE-associated genes was found for neuron-specific Gene Ontology (GO) terms and neuronal mRNA expression profiles. A more extensive evolutionary survey showed that NRSE sites matching the PSFM model exist in roughly similar numbers in all fully sequenced vertebrate genomes but are notably absent from invertebrate and protochordate genomes, as is NRSF itself. Some NRSF/REST sites reside in repeats, which suggests a mechanism for both ancient and modern dispersal of NRSEs through vertebrate genomes. Multiple predicted sites are located near neuronal microRNA and splicing-factor genes, and these tested positive for NRSF/ REST occupancy in vivo. The resulting network model integrates post-transcriptional and translational controllers, including candidate feedback loops on NRSF and its corepressor, CoREST.