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R-loopBase: a knowledgebase for genome-wide R-loop formation and regulation.

Ruoyao Lin1, Xiaoming Zhong2, Yongli Zhou1

  • 1State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Chemistry and Biomedicine Innovation Center (ChemBIC), Nanjing University, Nanjing 210023, China.

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R-loopBase integrates genomics and literature data to map R-loop (RNA-DNA hybrid) locations and regulatory networks. This resource aids research into R-loops

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • R-loops (RNA-DNA hybrids) are crucial in physiological and pathological processes, but their genomic localization and regulatory networks remain poorly understood.
  • Challenges in R-loop research stem from controversies regarding genomic localization and incomplete knowledge of regulatory mechanisms.

Purpose of the Study:

  • To establish a comprehensive resource, R-loopBase, for systematic integration of genomics and literature data on R-loops.
  • To address challenges in R-loop research by providing high-confidence R-loop localization and regulatory information.

Main Methods:

  • Systematic integration of 107 high-quality genome-wide R-loop mapping datasets from 11 different technologies.
  • Literature mining and multi-omics analyses to curate R-loop regulatory proteins and their targeted R-loops across species.
  • Integration of billions of functional genomic annotations with interactive data analysis tools.

Main Results:

  • A reference set of human R-loop zones for high-confidence localization and identification of conservative genomic features associated with R-loop formation.
  • The most comprehensive list to date of R-loop regulatory proteins and their targeted R-loops, revealing a global regulatory network.
  • Interactive interfaces for searching, visualizing, downloading, and analyzing R-loops and their regulators within a genomic context.

Conclusions:

  • R-loopBase provides a valuable, integrated resource for the R-loop research community.
  • The platform facilitates research into R-loop dynamics and their potential links to cancers and neurological diseases.
  • R-loopBase is designed for accessibility, enabling users with varying bioinformatics backgrounds to utilize the data effectively.