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Related Concept Videos

MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns (non-coding regions of a gene) or intergenic regions (stretches of DNA present between genes). Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself, forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA...
MicroRNAs01:22

MicroRNAs

MicroRNA (miRNA) are short, regulatory RNA transcribed from introns—non-coding regions of a gene—or intergenic regions—stretches of DNA present between genes. Several processing steps are required to form biologically active, mature miRNA. The initial transcript, called primary miRNA (pri-mRNA), base-pairs with itself forming a stem-loop structure. Within the nucleus, an endonuclease enzyme, called Drosha, shortens the stem-loop structure into hairpin-shaped pre-miRNA. After the pre-miRNA ends...
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...
RNA Structure01:23

RNA Structure

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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.
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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...

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A Complete Pipeline for Isolating and Sequencing MicroRNAs, and Analyzing Them Using Open Source Tools
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Analyzing modular RNA structure reveals low global structural entropy in microRNA sequence.

Timothy I Shaw1, Amir Manzour, Yingfeng Wang

  • 1Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA. gatech@uga.edu

Journal of Bioinformatics and Computational Biology
|April 28, 2011
PubMed
Summary

A novel method, unpaired structural entropy (USE), effectively identifies noncoding RNA (ncRNA) genes, like precursor microRNAs (pre-miRNAs), by measuring RNA structure stability. This approach offers improved performance over existing methods for ncRNA gene finding.

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Secondary structure analysis is crucial for noncoding RNA (ncRNA) gene identification.
  • Current secondary structure prediction methods generate many candidates and lack optimal performance.
  • Experimental validation of ncRNA candidates remains a bottleneck.

Purpose of the Study:

  • To introduce and evaluate unpaired structural entropy (USE) as a novel metric for ncRNA structure fold stability.
  • To assess the efficacy of USE in identifying ncRNAs with specific structural features, such as long stem-hairpin loops.
  • To compare the performance of USE against existing measures and classifiers for ncRNA gene prediction.

Main Methods:

  • Investigated unpaired structural entropy (USE) as a measure of RNA structure fold stability.
  • Applied USE to identify ncRNAs, specifically precursor microRNAs (pre-miRNAs), within genomic data.
  • Utilized USE within a Support Vector Machine (SVM) classifier framework.
  • Compared USE performance against previously formulated structural entropy and other pre-miRNA classifiers.

Main Results:

  • USE effectively identifies ncRNAs with long stem-hairpin loop structures, such as pre-miRNAs, from genomic backgrounds.
  • USE demonstrates strong correlation and superior performance compared to other measures on pre-miRNAs.
  • The SVM classifier incorporating USE outperforms existing pre-miRNA classifiers.

Conclusions:

  • Unpaired structural entropy (USE) is a robust and effective metric for predicting ncRNA genes, particularly those with stem-hairpin structures.
  • USE shows significant potential for improving ab initio prediction programs for a broader range of functional RNAs.
  • This method enhances the efficiency of ncRNA discovery, complementing experimental approaches.