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Related Concept Videos

RNA Structure01:23

RNA Structure

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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...
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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 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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Nucleic Acid Structure01:25

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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.
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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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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
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Alignment-free comparative genomic screen for structured RNAs using coarse-grained secondary structure dot plots.

Yuki Kato1,2, Jan Gorodkin3, Jakob Hull Havgaard4

  • 1Department of RNA Biology and Neuroscience, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, 565-0871, Japan. ykato@rna.med.osaka-u.ac.jp.

BMC Genomics
|December 4, 2017
PubMed
Summary

A new method, DotcodeR, efficiently detects structurally similar RNAs in genomes by comparing secondary structure dot plots. This fast approach aids in comparative genomic scans for structured RNAs without sequence alignment.

Keywords:
Gene findingNon-coding RNASecondary structure

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Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Structured non-coding RNAs perform vital cellular functions, yet their genomic annotation remains incomplete.
  • Existing computational tools for RNA structure analysis are often computationally intensive or require pre-aligned sequences, limiting their use in large-scale genomic studies.

Purpose of the Study:

  • To introduce DotcodeR, a novel computational method for the rapid and efficient detection of structurally similar RNAs within genomic sequences.
  • To enable large-scale comparative genomic analyses of structured RNAs without the need for sequence alignment.

Main Methods:

  • DotcodeR compares coarse-grained secondary structure dot plots of RNA sequences at the string level.
  • The method facilitates an all-against-all scan of window pairs across two genomes, bypassing traditional sequence alignment.

Main Results:

  • Computational experiments using simulated and real genomic data confirm the high sensitivity of the DotcodeR method.
  • The approach demonstrates effectiveness in identifying structurally related RNAs.

Conclusions:

  • DotcodeR serves as a valuable pre-filtering tool for comparative genomic scans targeting structured RNAs.
  • The method enhances the efficiency of discovering functionally relevant RNA structures across different genomes.