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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
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Ribosome profiling or ribo-sequencing is a deep sequencing technique that produces a snapshot of active translation in a cell. It selectively sequences the mRNAs protected by ribosomes to get an insight into a cell’s translation landscape at any given point in time.
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Related Experiment Video

Updated: Dec 14, 2025

Studying DNA Looping by Single-Molecule FRET
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Characterization of R-Loop Structures Using Single-Molecule R-Loop Footprinting and Sequencing.

Maika Malig1,2, Frederic Chedin3

  • 1Department of Molecular and Cellular Biology and Genome Center, University of California Davis, Davis, CA, USA.

Methods in Molecular Biology (Clifton, N.J.)
|July 19, 2020
PubMed
Summary

Single Molecule R-Loop Footprinting (SMRF-seq) maps individual R-loops using DNA:RNA hybrid and single-stranded DNA chemical reactivity. This novel method provides high-resolution, strand-specific R-loop detection at the single-molecule level.

Keywords:
DNA:RNA hybridNon-denaturing bisulfite conversionR-loopSMRT sequencingTranscription

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • R-loops are nucleic acid structures crucial for cellular processes but implicated in diseases like cancer.
  • Current methods like DRIP-seq offer genome-wide R-loop mapping but lack single-molecule resolution.
  • Existing techniques rely on the S9.6 antibody, limiting independent validation.

Purpose of the Study:

  • To develop a novel method for high-resolution, single-molecule R-loop detection.
  • To characterize R-loops independently of antibody-based approaches.
  • To enable ultra-deep, strand-specific R-loop mapping.

Main Methods:

  • Single Molecule R-Loop Footprinting (SMRF-seq) utilizes chemical reactivity of displaced single-stranded DNA (ssDNA).
  • Non-denaturing sodium bisulfite treatment targets the ssDNA strand within R-loops.
  • Single molecule long-read sequencing provides the readout for R-loop mapping.

Main Results:

  • SMRF-seq successfully maps individual R-loops at kilobase resolution.
  • The method generates high-resolution, strand-specific R-loop maps.
  • SMRF-seq achieves ultra-deep coverage, revealing R-loop dynamics.

Conclusions:

  • SMRF-seq offers a powerful, antibody-independent approach for R-loop analysis.
  • This technique enhances our understanding of R-loop roles in normal and pathological conditions.
  • SMRF-seq enables unprecedented insights into R-loop formation and function at the single-molecule level.