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首页> 外文期刊>Current Protocols in Bioinformatics >Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway
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Discovering Transcriptional Regulatory Elements From Run-On and Sequencing Data Using the Web-Based dREG Gateway

机译：使用基于Web的DREG网关从运行和测序数据发现转录调节元件

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摘要

Transcription is a chromatin mark that can be used effectively to identify the location of active enhancers and promoters, collectively known as transcriptional regulatory elements (TREs). We recently introduced dREG, a tool for the identification ofTREs using run-on and sequencing (RO-seq) assays, including global run-on and sequencing (GRO-seq), precision run-on and sequencing (PRO-seq), and chromatin run-on and sequencing (ChRO-seq). In this protocol, we present step-by-step instructions for running dREG on an arbitrary run-on and sequencing dataset. Users provide dREG with bigWig files (in which each read is represented by a single base) representing the location of RNA poly-merase in a cell or tissue sample of interest, and dREG returns a listof genomic regions that are predicted to be active TREs. Finally, we demonstrate the use of dREG regions in discovering transcription factors controlling response to a stimulus and predicting their target genes. Together, this protocol provides detailedinstructions for running dREG on arbitrary run-on and sequencing data.
机译：转录是一种染色质标记，可以有效地用于鉴定活性增强剂和启动子的位置，共同称为转录调节元素（TRES）。我们最近引入了DREG，使用续集和排序（RO-SEQ）测定的识别OFTRES的工具，包括全局续集和测序（GRO-SEQ），精度续集和测序（Pro-SEQ），以及染色质运行和测序（CHRO-SEQ）。在本协议中，我们在任意运行和排序数据集上呈现运行DREG的逐步指令。用户将DREG与BIGWIG文件（其中每个读取由单个基座表示）表示感兴趣的小区或组织样本中RNA多项式的位置，并且渣滓返回预测为活性TRE的基因组区域。最后，我们证明了在发现对刺激响应并预测其靶基因的转录因子时使用渣滓区域。此协议在一起提供了在任意运行和排序数据上运行DREG的详细标记。

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