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

Rongjie Liu, Aparna Gorthi, Yufang Jin, Alexander J Bishop, Yidong Chen

Research output: Contribution to journalArticle

1 Citation (Scopus)

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 ImmunePrecipitation (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.

Original languageEnglish (US)
Pages (from-to)123-136
Number of pages14
JournalInternational Journal of Computational Biology and Drug Design
Volume10
Issue number2
DOIs
StatePublished - 2017

Fingerprint

DNA
Genes
Genome
RNA
Gene Expression
Gene expression
Genomic Instability
Single-Stranded DNA
Nonparametric Statistics
DNA Replication
Carrier Proteins
Binding Sites

Keywords

  • Binding protein sites
  • Biological pathways
  • ChIP-seq
  • Co-regulated genes
  • DNA/RNA hybrid
  • DRIP-seq
  • DRIPer
  • Ontological functions
  • R-loops
  • Target gene expression

ASJC Scopus subject areas

  • Drug Discovery
  • Computer Science Applications

Cite this

Computational tools for genome-wide R-loops identification and characterisation. / Liu, Rongjie; Gorthi, Aparna; Jin, Yufang; Bishop, Alexander J; Chen, Yidong.

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

Research output: Contribution to journalArticle

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