Title: Computational tools for genome-wide R-loops identification and characterisation

Authors: Rongjie Liu; Aparna Gorthi; Yufang Jin; Alexander J.R. Bishop; Yidong Chen

Addresses: Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, Texas 78249, USA ' Department of Cellular and Structural Biology, Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA ' Department of Electrical and Computer Engineering, The University of Texas at San Antonio, San Antonio, Texas 78249, USA ' Department of Cellular and Structural Biology, Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA ' Department of Epidemiology and Biostatistics, Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, Texas 78229, USA

Abstract: 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 co-regulated genes. This powerful method will enable biologists to quickly evaluate the relationship of R-loops to nearby binding protein sites and target gene expression.

Keywords: DNA/RNA hybrid; R-loops; DRIP-seq; ChIP-seq; binding protein sites; target gene expression; biological pathways; ontological functions; co-regulated genes; DRIPer.

DOI: 10.1504/IJCBDD.2017.083883

International Journal of Computational Biology and Drug Design, 2017 Vol.10 No.2, pp.123 - 136

Received: 30 Jul 2016
Accepted: 19 Sep 2016

Published online: 15 Apr 2017 *

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