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Related Experiment Video

Updated: Dec 30, 2025

RNA Next-Generation Sequencing and a Bioinformatics Pipeline to Identify Expressed LINE-1s at the Locus-Specific Level
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MapR: A Method for Identifying Native R-Loops Genome Wide.

Qingqing Yan1,2, Kavitha Sarma1,2

  • 1Gene Expression and Regulation Program, The Wistar Institute, Philadelphia, Pennsylvania.

Current Protocols in Molecular Biology
|January 17, 2020
PubMed
Summary
This summary is machine-generated.

MapR is a new, sensitive method to map R-loops genome-wide without antibodies. This technique uses RNase H and CUT&RUN to identify DNA:RNA hybrids, aiding R-loop research and disease understanding.

Keywords:
DNA:RNA hybridsR-loopschromatingene expressiontranscription

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Area of Science:

  • Genomics
  • Molecular Biology
  • Chromatin Biology

Background:

  • R-loops are abundant DNA:RNA hybrid structures in eukaryotic and prokaryotic genomes.
  • Understanding R-loop genomic locations is crucial for cellular processes like replication and disease mechanisms.

Purpose of the Study:

  • To develop a novel, antibody-independent method for genome-wide R-loop profiling.
  • To provide a sensitive and efficient tool for R-loop detection.

Main Methods:

  • Developed MapR, a method combining RNase H specificity for DNA:RNA hybrids with CUT&RUN.
  • MapR targets, cleaves, and releases R-loops for subsequent sequencing.
  • The method is antibody-independent and suitable for any cell type.

Main Results:

  • MapR offers high sensitivity and low background for R-loop detection.
  • The method is faster than existing R-loop profiling technologies.
  • MapR does not require the generation of stable cell lines.

Conclusions:

  • MapR is a robust and versatile tool for genome-wide R-loop mapping.
  • This technique facilitates the study of R-loop functions in normal cellular processes and disease.
  • MapR simplifies R-loop analysis across diverse cell types.