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Related Concept Videos

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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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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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Updated: Sep 8, 2025

G2-seq: A High Throughput Sequencing-based Technique for Identifying Late Replicating Regions of the Genome
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Quantitative, Convenient, and Efficient Genome-Wide R-Loop Profiling by ssDRIP-Seq in Multiple Organisms.

Wei Xu1,2,3, Kuan Li1,2, Qin Li1,2

  • 1Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China.

Methods in Molecular Biology (Clifton, N.J.)
|June 15, 2022
PubMed
Summary

We developed ssDRIP-seq, a precise method for genome-wide R-loop detection. This technique accurately profiles DNA:RNA hybrids across diverse organisms, advancing R-loop biology research.

Keywords:
GenomeNext-generation sequencingNoncoding RNANucleic acidR-loop

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Area of Science:

  • Genomics
  • Molecular Biology
  • Chromatin Biology

Background:

  • R-loops are crucial three-stranded DNA:RNA hybrid structures involved in essential biological processes.
  • Accurate, efficient, and unbiased genome-wide R-loop detection methods are critical for understanding their functions.
  • Existing methods may lack the adaptability or precision required across diverse organisms.

Purpose of the Study:

  • To present a straightforward, highly efficient, and adaptable protocol for genome-wide, strand-specific R-loop profiling.
  • To enable precise detection of R-loop formation across a wide range of organisms.
  • To provide a robust method for advancing R-loop biology.

Main Methods:

  • Genomic DNA extraction and fragmentation using restriction enzymes.
  • Immunoprecipitation of DNA:RNA hybrids.
  • Single-stranded DNA adaptor ligation followed by next-generation sequencing (ssDRIP-seq).
  • Application of a bioinformatic pipeline for data analysis.

Main Results:

  • ssDRIP-seq provides high-resolution, comprehensive, and strand-specific R-loop mapping.
  • The method demonstrates high reproducibility and sensitivity.
  • Successful application in diverse organisms including prokaryotes (E. coli), eukaryotes (yeast, mammalian cells/tissues), and plants (Arabidopsis, rice).

Conclusions:

  • ssDRIP-seq is a versatile and powerful tool for genome-wide R-loop profiling.
  • This method significantly contributes to the study of R-loop functions in various biological contexts.
  • The protocol's broad applicability facilitates comparative R-loop biology studies across kingdoms.