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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 RNA structurome: transcriptome-wide structure probing with next-generation sequencing.

Chun Kit Kwok1, Yin Tang2, Sarah M Assmann3

  • 1Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA; Center for RNA Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA.

Trends in Biochemical Sciences
|March 24, 2015
PubMed
Summary
This summary is machine-generated.

Determining RNA structure in vivo using next-generation sequencing reveals cellular processes and links to stress and disease. This RNA structurome analysis offers new insights into RNA biology and genome function.

Keywords:
RNA structureRNA structuromenext-generation sequencing (NGS)structure predictionstructure probingtranscriptome

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Area of Science:

  • Molecular Biology
  • Genomics
  • Biochemistry

Background:

  • RNA molecules fold into complex structures essential for diverse biological functions, including gene regulation, ligand sensing, and enzymatic activity.
  • Understanding these intricate RNA structures is crucial for gaining profound insights into living systems.
  • Recent advancements have enabled the determination of RNA structures in vivo across entire transcriptomes.

Purpose of the Study:

  • To review the revolutionary impact of in vivo RNA structure probing coupled with next-generation sequencing (NGS) on the field of RNA biology.
  • To highlight the application of transcriptome-wide in vivo RNA structure determination in various organisms.
  • To discuss the emerging connections between RNA structure, cellular stress, and disease physiology.

Main Methods:

  • In vivo RNA structure probing techniques.
  • Next-generation sequencing (NGS) for transcriptome-wide analysis.
  • Computational analysis of RNA structuromes.

Main Results:

  • Transcriptome-wide RNA structure determination in vivo has been successfully applied to human cells, yeast, and Arabidopsis.
  • Analysis of in vivo RNA structuromes provides critical information on translation control, splicing, polyadenylation, mRNA unfolding, and protein-RNA interactions.
  • Emerging evidence suggests a link between RNA structure and physiological responses to stress and disease.

Conclusions:

  • In vivo RNA structure probing and NGS have revolutionized the study of RNA, enabling the analysis of 'RNA structuromes'.
  • These studies offer novel insights into fundamental cellular processes and the impact of RNA structure on health and disease.
  • This approach opens new avenues for research in RNA biology, genome biology, and related fields.