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

Václav Brázda,Jan Kolomazník,Oldřich Trenz,Jiří Šťastný,Jan Havlík

doi:10.3390/ijms222312857

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.

Highlights

In addition to the basic DNA structure first described by Watson and Crick in 1953 [1], new findings show many nucleic acid structures differing from this canonical B-DNA structure
R-loops have been suggested as hot-spots for double-stranded breaks leading to DNA damage and human diseases [29,30]
Many tools exist for analyzing other non-B DNA structures in silico, the options for R-loop analyses are limited

Summary

Introduction

In addition to the basic DNA structure first described by Watson and Crick in 1953 [1], new findings show many nucleic acid structures differing from this canonical B-DNA structure. The formation of R-loops plays a role in DNA replication, mutations, and homologous recombination, but it is suggested to be an inducer of trinucleotide repeat expansion associated with human neuromuscular degenerative diseases [14,15]. Negative supercoiling of DNA during transcription facilitates the formation of local nucleic acid structures, including cruciform and R-loop [18,19]. There are several tools to study inverted repeats that form cruciform, G-quadruplexes, and other non-B DNA structures in nucleic acids [11,21–24], in silico tools for the prediction of R-loops are limited [22]. The R-loop tracker tool has been implemented as part of the DNA Analyser web server, and this completely new implementation enables server-based prediction of R-loops while integrating its results with other tools for nucleic acids analyses, internal crossevaluation of results with experimental data, easy export and correlation analyses with other genome features and markers, and enhanced visualization outputs. The R-loop tracker tool is integrated into the web pages of DNA Analyser tools http://bioinformatics.ibp.cz/ (accessed on 28 October 2021) and freely accessible

Methods

Results

Conclusion