Modeling the relationship of diverse genomic signatures to gene expression levels with the regulation of long-range enhancer-promoter interactions
Modeling the relationship of diverse genomic signatures to gene expression levels with the regulation of long-range enhancer-promoter interactions
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通过远程增强子-启动子相互作用的调节，模拟不同基因组特征与基因表达水平的关系
DOI：
10.1007/s41048-019-0089-z
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发表时间：
2019-06
影响因子：
--
通讯作者：
Jian-Jun Meng
中科院分区：
文献类型：
--
作者：
Zhen-Xing Feng;Qian-Zhong Li;Jian-Jun Meng
增强子-启动子（E-P）相互作用是基因表达顺式调控的重要组成部分。然而，要全面研究基因表达与远程调控的关系。E-P相互作用是监管网络中的一个主要挑战。这些类型的基因表达。在不同基因组特征的调控下，我们提出了一种计算方法来研究相关性。基因表达水平与不同基因组特征之间的关系。本文基于。远程E-P相互作用的数据集，我们从多个签名中提取特征参数(例如，。表观遗传标记，转录因子)，并使用回归模型预测基因表达水平。在我们的结果中，我们发现预测的表达值与测量值具有良好的相关性。在各细胞系中，相互作用组和非相互作用组的表达值以及相互作用组的相关值均高于相应的非相互作用组。表明远端增强子可能与不同的基因组特征协同作用，以促进基因的克隆。目的基因的表达水平。通过比较基因表达的重要特征。在同一细胞系中相互作用组和非相互作用组之间的水平，我们发现。重要的特异性特征影响远端增强子调控的基因表达。我们的研究。提供了关于不同特征在基因表达调控中的作用的额外见解。远端增强器。
Enhancer–promoter (E–P) interaction is an essential component of cis-regulatory regulation for gene.expression. However, to comprehensively study the gene expression with the regulation of long-range.E–P interactions is a major challenge in the regulatory networks. As these types of gene expression are.regulated by diverse genomic signatures, we presented a computational method to study the rela-.tionships between gene expression levels and diverse genomic signatures. In this paper, based on the.datasets of long-range E–P interactions, we extracted feature parameters from multiple signatures (e.g.,.epigenetic marks, transcription factors) and used regression models to predict the gene expression.levels. In our results, we found that the predicted expression values correlated well with the measured.expression values in both the interacting and non-interacting sets, and the correlation values of the.interacting set were higher than that of the corresponding non-interacting set in each cell line, which.indicated that the distal enhancers would cooperate with diverse genomic signatures to facilitate the.expression level of target genes. By comparing the important signature features for the gene expression.levels between the interacting and non-interacting sets in the same cell line, we found that the.important specific signatures affect the gene expression regulated by distal enhancers. Our research.provided additional insights about the roles of diverse signatures in gene expression with the regulation.of distal enhancers.
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影响因子：
46.9
作者：
Ball, Madeleine P.;Li, Jin Billy;Gao, Yuan;Lee, Je-Hyuk;LeProust, Emily M.;Park, In-Hyun;Xie, Bin;Daley, George Q.;Church, George M.
通讯作者：
Church, George M.
影响因子：
64.8
作者：
Heintzman, Nathaniel D.;Hon, Gary C.;Hawkins, R. David;Kheradpour, Pouya;Stark, Alexander;Harp, Lindsey F.;Ye, Zhen;Lee, Leonard K.;Stuart, Rhona K.;Ching, Christina W.;Ching, Keith A.;Antosiewicz-Bourget, Jessica E.;Liu, Hui;Zhang, Xinmin;Green, Roland D.;Lobanenkov, Victor V.;Stewart, Ron;Thomson, James A.;Crawford, Gregory E.;Kellis, Manolis;Ren, Bing
通讯作者：
Ren, Bing
增强子和启动子相互作用长距离。
影响因子：
4
作者：
Krivega, Ivan;Dean, Ann
通讯作者：
Dean, Ann
影响因子：
64.8
作者：
Sanyal, Amartya;Lajoie, Bryan R.;Jain, Gaurav;Dekker, Job
通讯作者：
Dekker, Job
影响因子：
11.4
作者：
Yang, WM;Yao, YL;Seto, E
通讯作者：
Seto, E