R-Loop Tracker: Web Access-Based Tool for R-Loop Detection and Analysis in Genomic DNA Sequences

Abstract

R-loops are common non-B nucleic acid structures formed by a three-stranded nucleic acid composed of an RNA–DNA hybrid and a displaced single-stranded DNA (ssDNA) loop. Because the aberrant R-loop formation leads to increased mutagenesis, hyper-recombination, rearrangements, and transcription-replication collisions, it is regarded as important in human diseases. Therefore, its prevalence and distribution in genomes are studied intensively. However, in silico tools for R-loop prediction are limited, and therefore, we have developed the R-loop tracker tool, which was implemented as a part of the DNA Analyser web server. This new tool is focused upon (1) prediction of R-loops in genomic DNA without length and sequence limitations; (2) integration of R-loop tracker results with other tools for nucleic acids analyses, including Genome Browser; (3) internal cross-evaluation of in silico results with experimental data, where available; (4) easy export and correlation analyses with other genome features and markers; and (5) enhanced visualization outputs. Our new R-loop tracker tool is freely accessible on the web pages of DNA Analyser tools, and its implementation on the web-based server allows effective analyses not only for DNA segments but also for full chromosomes and genomes.

Pathophysiological Role and Diagnostic Potential of R-Loops in Cancer and Beyond

“…It demonstrates highly accurate predictions of the RLFSs detected. The R-loop tracker tool is a similar web-based server that focuses on the prediction of R-loops in genomic DNA with an unlimited input size [ 143 ]. It allows for the cross-evaluation of in silico results with experimental data, if available, and helps correlate these with other genomic features and markers with an enhanced visualization output [ 143 ].…”

“…The R-loop tracker tool is a similar web-based server that focuses on the prediction of R-loops in genomic DNA with an unlimited input size [ 143 ]. It allows for the cross-evaluation of in silico results with experimental data, if available, and helps correlate these with other genomic features and markers with an enhanced visualization output [ 143 ]. In 2017, R-loopDB, a database that contains computationally predicted RLFSs in human genetic regions, was developed.…”

Chromatin Hubs: A biological and computational outlook

“… Category Methods/Tools reviewed Reference Enhancer–promoter interaction prediction Epigenomics-based methods: FANTOM5, PreSTIGE, IM-PET, RIPPLE, TargetFinder, and JEME [111] , [112] , [113] , [114] , [115] , and [116] Sequence-based methods: PEP, EP2vec, SPEID, CNN with TL, and SEPT. [117] , [118] , [119] , [120] , and [121] Network analysis of interaction networks Standard chromatin interaction network analysis: Sandhu et al , Li et al , Chen et al , Thibodeau et al , and Li et al [122] , [123] , [39] , [124] , and [71] Promoter- or enhancer- enriched standard interaction network analysis: Schoenfelder et al and Madsen et al [125] , [126] Multi-scale network analysis [127] Graphlet approach [128] Detection of chromatin hubs around disease-related SNPs [129] Calling special chromatin domains such as TADs, LADs, NADs, etc. TAD callers: TopDom, HiCseg, CaTCH, CHDF, and IC-Finder [130] , [131] , [132] , [133] , and [134] LAD callers: EDD and LADetector [135] , [136] R-Loop / G-quadruplex prediction R-Loop Tracker [137] …”

“…Although R-loops and G-quadruplexes may co-localize, computational tools have been developed to predict each of them. A recent prediction tool for R-loops is “R-Loop Tracker”, a web platform for R-Loop prediction and analysis from genomic DNA [137] .…”

RLSuite: An integrative R-loop bioinformatics framework

“…There are a growing number of publications that describe bioinformatic approaches for the study of R-loops. However, most have focused on the task of predicting R-loop formation from genomic sequences (16)(17)(18)(19)(20)(21) and associated epigenomic marks (22). At present, only two bioinformatic tools for the analysis of R-loop mapping data have been described.…”