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Related Concept Videos

RNA-seq03:21

RNA-seq

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 microarray-based...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. 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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
RNA Structure01:19

RNA Structure

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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA) involved in protein synthesis: messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three...
RNA Structure01:23

RNA Structure

Overview
The basic structure of RNA consists of a five-carbon sugar and one of four nitrogenous bases. 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.
Different Types of RNA Have the Same Basic Structure
There are three main types of ribonucleic acid (RNA): messenger RNA (mRNA), transfer RNA (tRNA), and ribosomal RNA (rRNA). All three RNA types consist of a...
Nucleic Acid Structure01:25

Nucleic Acid Structure

The pentose sugar in DNA is deoxyribose, while in RNA the pentose sugar is ribose. The difference between the sugars is the presence of the hydroxyl group on the ribose's second carbon and a hydrogen on the deoxyribose's second carbon. The phosphate residue attaches to the hydroxyl group of the 5′ carbon of one sugar and the hydroxyl group of the 3′ carbon of the sugar of the next nucleotide, which forms  a 5′ to 3′ phosphodiester linkage.
DNA Structure
DNA has a double-helix structure. The...
Ribosome Profiling02:24

Ribosome Profiling

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.
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique helps...

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Sequence-based identification of 3D structural modules in RNA with RMDetect.

José Almeida Cruz1, Eric Westhof

  • 1Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du Centre National de la Recherche Scientifique, Université de Strasbourg, Strasbourg, France.

Nature Methods
|May 10, 2011
PubMed
Summary
This summary is machine-generated.

A new tool, RMDetect, identifies structural RNA modules in RNA sequences. This computational method aids in understanding RNA architecture, ligand binding, and annotating genomic data.

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Area of Science:

  • * Structural biology
  • * Bioinformatics
  • * Computational biology

Background:

  • * Structural RNA modules, defined by non-Watson-Crick base pairs, are crucial for RNA architecture and ligand binding.
  • * These modules are conserved across diverse RNA families and evolutionary history.
  • * Identifying these modules computationally is essential for RNA structure and function analysis.

Purpose of the Study:

  • * To introduce RMDetect, a computational tool for detecting known 3D structural RNA modules.
  • * To enable identification in single and multiple RNA sequences without prior information.
  • * To facilitate the search for specific modules like G-bulge loop, kink-turn, C-loop, and tandem-GA loop.

Main Methods:

  • * Development of the RMDetect computational tool.
  • * Utilized control test sequences to evaluate detection accuracy and false discovery rate.
  • * Scanned a large dataset of 1,444 publicly available RNA sequence alignments.

Main Results:

  • * RMDetect successfully identified all known modules in control sequences with a false discovery rate of 0.23.
  • * Analysis of 1,444 alignments revealed 21 previously unreported structural RNA modules.
  • * A total of 141 known modules were identified across the analyzed RNA alignments.

Conclusions:

  • * RMDetect is an effective tool for identifying known 3D structural RNA modules.
  • * The tool can discover novel RNA modules and refine RNA structure analysis.
  • * Applications include RNA 2D structure refinement, 3D model assembly, and genomic data annotation.