Prediction of Polycomb target genes in mouse embryonic stem cells
Prediction of Polycomb target genes in mouse embryonic stem cells
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DOI：
10.1016/j.ygeno.2010.03.012
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发表时间：
2010-07-01
期刊：
影响因子：
4.4
通讯作者：
Yuan, Guo-Cheng
中科院分区：
文献类型：
--
作者：
Liu, Yingchun;Shao, Zhen;Yuan, Guo-Cheng
多梳蛋白(Polycomb group，PcG)是重要的表观遗传调节蛋白，然而哺乳动物的潜在靶向机制仍然知之甚少。我们开发了一种计算方法来预测小鼠胚胎干细胞中全基因组的PcG靶基因。我们使用TF结合和基序信息作为预测因子，并应用贝叶斯加性回归树(BART)模型进行分类。我们的模型具有很好的预测精度。性能主要可以用五个TF特征(ZF5、Tcfcp2l1、CTCF、E2F1、Myc)来解释。我们对H3K27me3和基因表达数据的分析表明，基因组序列与整体PcG靶标可塑性高度相关。我们还比较了小鼠和果蝇的PcG靶序列签名，发现它们有显著的不同。我们的预测可能有助于在哺乳动物中从头寻找多梳状反应元件(PRE)。(C)2010 Elsevier Inc.保留所有权利。
Polycomb group (PcG) proteins are important epigenetic regulators, yet the underlying targeting mechanism in mammals is still poorly understood. We have developed a computational approach to predict genome-wide PcG target genes in mouse embryonic stem cells. We use TF binding and motif information as predictors and apply the Bayesian Additive Regression Trees (BART) model for classification. Our model has good prediction accuracy. The performance can be mainly explained by five TF features (Zf5, Tcfcp2l1, Ctcf, E2f1, Myc). Our analysis of H3K27me3 and gene expression data suggests that genomic sequence is highly correlated with the overall PcG target plasticity. We have also compared the PcG target sequence signatures between mouse and Drosophila and found that they are strikingly different. Our predictions may be useful for de novo search for Polycomb response elements (PRE) in mammals. (C) 2010 Elsevier Inc. All rights reserved.