High resolution mapping of enhancer-promoter interactions.
High resolution mapping of enhancer-promoter interactions.
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增强器促销相互作用的高分辨率映射。
DOI：
10.1371/journal.pone.0122420
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Gifford D
中科院分区：
文献类型：
--
作者：
Reeder C;Closser M;Poh HM;Sandhu K;Wichterle H;Gifford D
RNA聚合酶II china - pet数据揭示了在特定细胞类型中具有活性的增强子以及这些增强子通过染色质相互作用调节的基因。用于分析ChIA-PET数据的最常用的计算方法是ChIA-PET工具，它可以发现空间分辨率不足以准确识别单个增强子的相互作用锚点。我们介绍Germ，一种计算方法，估计任何两个狭义定义的基因组位置共同被RNA聚合酶II占用的可能性。Germ采用盲反卷积方法同时估计RNA聚合酶II占用的可能性，以及相对于RNA聚合酶II占用的位置的读对排列模型。这两种类型的信息都被用来估计RNA聚合酶II共同占据任何两个基因组位置的可能性。我们应用胚胎干细胞的RNA聚合酶II china - pet数据来鉴定与转录起始位点共同占据的基因组位置。我们发现这些基因组位置与ChIP-Seq测量的活性增强子的特征比使用ChIA-PET工具鉴定的位置更接近。我们还将Germ应用于运动神经元祖细胞的RNA聚合酶II china - pet数据。基于Germ的结果，我们观察到细胞利用细胞类型特异性和细胞类型独立的调节相互作用的组合来调节基因表达。
RNA Polymerase II ChIA-PET data has revealed enhancers that are active in a profiled cell type and the genes that the enhancers regulate through chromatin interactions. The most commonly used computational method for analyzing ChIA-PET data, the ChIA-PET Tool, discovers interaction anchors at a spatial resolution that is insufficient to accurately identify individual enhancers. We introduce Germ, a computational method that estimates the likelihood that any two narrowly defined genomic locations are jointly occupied by RNA Polymerase II. Germ takes a blind deconvolution approach to simultaneously estimate the likelihood of RNA Polymerase II occupation as well as a model of the arrangement of read alignments relative to locations occupied by RNA Polymerase II. Both types of information are utilized to estimate the likelihood that RNA Polymerase II jointly occupies any two genomic locations. We apply Germ to RNA Polymerase II ChIA-PET data from embryonic stem cells to identify the genomic locations that are jointly occupied along with transcription start sites. We show that these genomic locations align more closely with features of active enhancers measured by ChIP-Seq than the locations identified using the ChIA-PET Tool. We also apply Germ to RNA Polymerase II ChIA-PET data from motor neuron progenitors. Based on the Germ results, we observe that a combination of cell type specific and cell type independent regulatory interactions are utilized by cells to regulate gene expression.
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影响因子：
12.3
作者：
Li G;Fullwood MJ;Xu H;Mulawadi FH;Velkov S;Vega V;Ariyaratne PN;Mohamed YB;Ooi HS;Tennakoon C;Wei CL;Ruan Y;Sung WK
通讯作者：
Sung WK
影响因子：
4.3
作者：
Rajagopal N;Xie W;Li Y;Wagner U;Wang W;Stamatoyannopoulos J;Ernst J;Kellis M;Ren B
通讯作者：
Ren B
影响因子：
20.3
作者：
Li, Y;McClintick, J;Chan, RJ
通讯作者：
Chan, RJ
影响因子：
4.3
作者：
Guo Y;Mahony S;Gifford DK
通讯作者：
Gifford DK
影响因子：
4.5
作者：
Busser BW;Taher L;Kim Y;Tansey T;Bloom MJ;Ovcharenko I;Michelson AM
通讯作者：
Michelson AM