Research Institute of Bio-System Informatics, Tohoku Chemical Co., Ltd., 6-15-5 Mitake, Morioka 020-0122, Iwate, Japan.
Department of Biochemistry and Genome Biology, Hirosaki University Graduate School of Medicine, 5 Zaifu-cho, Hirosaki 036-8562, Aomori, Japan.
Genes (Basel). 2022 Mar 7;13(3):472. doi: 10.3390/genes13030472.
Accumulating evidence suggests that the physical interactions between genomic regions play critical roles in the regulation of genome functions, such as transcription and epigenetic regulation. Various methods to detect the physical interactions between genomic regions have been developed. We recently developed a method to search for genomic regions interacting with a locus of interest in a non-biased manner that combines pull-down of the locus using engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) and next-generation sequencing (NGS) analysis (enChIP-Seq). The clustered regularly interspaced short palindromic repeats (CRISPR) system, consisting of a nuclease-dead form of Cas9 (dCas9) and a guide RNA (gRNA), or transcription activator-like (TAL) proteins, can be used for enChIP. In enChIP-Seq, it is necessary to compare multiple datasets of enChIP-Seq data to unambiguously detect specific interactions. However, it is not always easy to analyze enChIP-Seq datasets to subtract non-specific interactions or identify common interactions. To facilitate such analysis, we developed the enChIP-Seq analyzer software. It enables easy extraction of common signals as well as subtraction of non-specific signals observed in negative control samples, thereby streamlining extraction of specific enChIP-Seq signals. enChIP-Seq analyzer will help users analyze enChIP-Seq data and identify physical interactions between genomic regions.
越来越多的证据表明，基因组区域之间的物理相互作用在调节基因组功能方面起着关键作用，如转录和表观遗传调控。已经开发了各种方法来检测基因组区域之间的物理相互作用。我们最近开发了一种方法，用于以无偏倚的方式搜索与感兴趣基因座相互作用的基因组区域，该方法结合了使用工程化 DNA 结合分子介导的染色质免疫沉淀 (enChIP) 和下一代测序 (NGS) 分析 (enChIP-Seq) 下拉感兴趣基因座。由核酸酶失活形式的 Cas9 (dCas9) 和指导 RNA (gRNA) 或转录激活子样 (TAL) 蛋白组成的成簇规律间隔短回文重复序列 (CRISPR) 系统可用于 enChIP。在 enChIP-Seq 中，有必要比较多个 enChIP-Seq 数据集，以明确检测特定相互作用。然而，分析 enChIP-Seq 数据集以减去非特异性相互作用或识别常见相互作用并不总是那么容易。为了便于这种分析，我们开发了 enChIP-Seq 分析器软件。它可以轻松提取共同信号，并减去阴性对照样品中观察到的非特异性信号，从而简化了特定 enChIP-Seq 信号的提取。enChIP-Seq 分析器将帮助用户分析 enChIP-Seq 数据并识别基因组区域之间的物理相互作用。
