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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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The basic structure of RNA consists of a string of ribonucleotides attached by phosphodiester bonds. Although most RNA is single-stranded, it can form complex secondary and tertiary structures. Such structures play essential roles in the regulation of transcription and translation.
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RNA Polymerase (RNAP) is conserved in all animals, with bacterial, archaeal, and eukaryotic RNAPs sharing significant sequence, structural, and functional similarities. Among the three eukaryotic RNAPs, RNA Polymerase II is most similar to bacterial RNAP in terms of both structural organization and folding topologies of the enzyme subunits. However, these similarities are not reflected in their mechanism of action.
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Mapping RNA-RNA Interactions Globally Using Biotinylated Psoralen
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KARR-seq reveals cellular higher-order RNA structures and RNA-RNA interactions.

Tong Wu1,2, Anthony Youzhi Cheng3,4,5, Yuexiu Zhang6

  • 1Department of Chemistry, University of Chicago, Chicago, IL, USA.

Nature Biotechnology
|January 18, 2024
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Summary
This summary is machine-generated.

KARR-seq reveals how RNA molecules form higher-order structures and interact within cells. This new method shows translation impacts mRNA structure and identifies viral-host RNA interactions.

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • RNA structure and interactions are crucial for cellular functions but remain poorly understood.
  • The assembly of RNA and RNA-binding proteins into higher-order structures is largely unknown.
  • Interactions between RNA molecules and their roles in facilitating functions require further investigation.

Purpose of the Study:

  • To develop a novel method for detecting RNA-RNA interactions and higher-order RNA structures within cells.
  • To investigate the impact of translation on mRNA structure.
  • To explore viral-host RNA interactions and their potential role in viral replication.

Main Methods:

  • KARR-seq utilizes N3-kethoxal labeling and multifunctional chemical crosslinkers.
  • This technique covalently traps and determines RNA-RNA interactions and higher-order RNA structures.
  • KARR-seq operates independently of local protein binding to RNA, ensuring RNA-centric analysis.

Main Results:

  • KARR-seq accurately depicts higher-order RNA structures and detects widespread intermolecular RNA-RNA interactions.
  • Translation was found to repress mRNA compaction under both native and stress conditions.
  • The higher-order RNA structures of respiratory syncytial virus (RSV) and vesicular stomatitis virus (VSV) were determined.

Conclusions:

  • KARR-seq is a sensitive and accurate method for studying RNA structures and interactions in vivo.
  • Translation plays a significant role in regulating mRNA compaction.
  • Identified viral-host RNA interactions may offer new insights into viral replication regulation.