Computational tools for genome-wide R-loops identification and characterisation
Computational tools for genome-wide R-loops identification and characterisation
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DOI：
10.1504/ijcbdd.2017.10004580
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发表时间：
2017-01-01
影响因子：
--
通讯作者：
Chen, Yidong
中科院分区：
文献类型：
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作者：
Liu, Rongjie;Gorthi, Aparna;Chen, Yidong
R环是基因组中由DNA/RNA杂合体和置换的单链DNA组成的生理结构。R环在多种生物体中被观察到，并在调节基因表达、DNA复制、基因组稳定性和其他功能中发挥重要作用。最近引入的DNA-RNA免疫沉淀（DRIP）方案，随后是下一代测序，进一步推动了不同细胞环境中R环形成的数据积累。在这项研究中，我们提出了一个用户友好的工具DRIPer，用于调查DRIP-seq数据，以与公开的DRIP-seq数据和ENCODE ChIP-seq进行比较。这种比较允许相关性分析和Kolmogorov-Smirnov检验通过给定的基因集来研究关联，这些基因集可以是特定的生物学途径、本体功能或其他共调节基因。这种强大的方法将使生物学家能够快速评估R环与附近结合蛋白位点和靶基因表达的关系。
R-loops are physiologically occurring structures in the genome that composed of a DNA/RNA hybrid and a displaced single-stranded DNA. R-loops have been observed in various organisms and shown to play important roles in regulating gene expression, DNA replication, genome stability, and other functions. The recent introduction of the protocol of DNA-RNA Immune-Precipitation ( DRIP) followed by next-generation sequencing further propels the data accumulation of R-loop formation in different cellular contexts. In this study, we presented a user-friendly tool, DRIPer, for investigating DRIP-seq data to compare against a collection of publicly available DRIP-seq data and ENCODE ChIP-seq. Such comparisons allow correlation analysis and Kolmogorov-Smirnov tests to study associations via a given gene set, which could be for specific biological pathways, ontological functions, or other coregulated genes. This powerful method will enable biologists to quickly evaluate the relationship of R-loops to nearby binding protein sites and target gene expression.