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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. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Ribosome Profiling02:24

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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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DNA Microarrays02:34

DNA Microarrays

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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...
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Sample Preparation for Mass Spectrometry-based Identification of RNA-binding Regions
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Protein-Centric Mapping of RNA-DNA Interactions with RedChIP.

Alexey A Gavrilov1, Sergey V Razin1,2

  • 1Institute of Gene Biology, Russian Academy of Sciences, Moscow, Russia.

Methods in Molecular Biology (Clifton, N.J.)
|November 1, 2025
PubMed
Summary

Researchers developed RedChIP, a new method to map noncoding RNA (ncRNA) interactions with chromatin. This technique identifies specific proteins mediating these crucial RNA-DNA interactions within the cell nucleus.

Keywords:
Cell nucleusChromatinImmunoprecipitationNoncoding RNARNA–DNA interactome

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Noncoding RNAs (ncRNAs) play vital roles in nuclear processes like transcriptional control and genome organization.
  • The precise functions of most identified ncRNAs and their interactions with chromatin remain largely unknown.
  • Existing methods for mapping RNA-chromatin interactions lack the ability to identify involved proteins.

Purpose of the Study:

  • To introduce RedChIP, a novel method for identifying protein-mediated RNA-chromatin interactions genome-wide.
  • To provide a detailed protocol for RedChIP, including experimental nuances and data analysis strategies.
  • To enable the discovery of ncRNAs involved in recruiting protein complexes to specific genomic regions.

Main Methods:

  • RedChIP combines RNA-DNA proximity ligation with chromatin immunoprecipitation (ChIP).
  • This method allows for the genome-wide identification of RNA-chromatin interactions mediated by specific proteins.
  • The protocol details experimental steps and discusses algorithms for sequencing data processing and analysis.

Main Results:

  • RedChIP successfully identifies specific ncRNAs associated with genomic regions occupied by a protein of interest.
  • The method overcomes the limitation of previous techniques by revealing the protein component of RNA-DNA interactions.
  • This facilitates the understanding of how ncRNAs function in recruiting protein complexes to chromatin.

Conclusions:

  • RedChIP is a powerful tool for dissecting the functional roles of ncRNAs in the eukaryotic genome.
  • The method aids in uncovering the mechanisms by which ncRNAs contribute to nuclear organization and gene regulation.
  • RedChIP enables the identification of novel ncRNAs involved in protein-mediated chromatin modulation.