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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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Intact DNA strands can be found in fossils, while scientists sometimes struggle to keep RNA intact under laboratory conditions. The structural variations between RNA and DNA underlie the differences in their stability and longevity. Because DNA is double-stranded, it is inherently more stable. The single-stranded structure of RNA is less stable but also more flexible and can form weak internal bonds. Additionally, most RNAs in the cell are relatively short, while DNA can be up to 250 million...
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Proteins that regulate transcription can do so either via direct contact with RNA Polymerase or through indirect interactions facilitated by adaptors, mediators, histone-modifying proteins, and nucleosome remodelers. Direct interactions to activate transcription is seen in bacteria as well as in some eukaryotic genes. In these cases, upstream activation sequences are adjacent to the promoters, and the activator proteins interact directly with the transcriptional machinery. For example, in...
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Alternative RNA Splicing02:18

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Alternative RNA splicing is the regulated splicing of exons and introns to produce different mature mRNAs from a single pre-mRNA. Unlike in constitutive splicing where a single gene produces a single type of mRNA, alternative splicing allows an organism to produce multiple proteins from a single gene and plays an important role in protein diversity.
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Multiple Sequence Alignments Enhance Boundary Definition of RNA Structures.

Radhakrishnan Sabarinathan1,2, Christian Anthon3, Jan Gorodkin4

  • 1Center for Non-Coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, University of Copenhagen, Grønnegårdsvej 3, 1870 Frederiksberg C, Denmark. sabari@rth.dk.

Genes
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Accurately defining RNA structured domains is crucial for gene finding and motif discovery. Our study shows multiple sequence alignments significantly improve boundary prediction for non-coding RNAs compared to single sequences.

Keywords:
RNA domainRNA secondary structureRNA structure boundarynon-coding RNA gene finder

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Area of Science:

  • Computational Biology
  • Bioinformatics
  • Genomics

Background:

  • Structured domains within non-coding RNAs (ncRNAs) possess distinct molecular functions.
  • Accurate identification of these structured domain boundaries is essential for ncRNA gene finder programs and motif discovery.
  • Current methods often lack precision in defining RNA structure boundaries, especially in comparative genomics.

Purpose of the Study:

  • To compare boundary definition methods for RNA structured domains using single sequences versus multiple sequence alignments.
  • To introduce RNAbound, a novel method for identifying RNA structured domain boundaries based on conserved base-pairing probabilities.
  • To evaluate the performance of RNAbound and another method on human ncRNA families.

Main Methods:

  • Comparison of single sequence and multiple sequence alignment approaches for RNA structured domain boundary prediction.
  • Development and application of the RNAbound method, utilizing probabilities of evolutionarily conserved base pairings.
  • Testing on Rfam families with annotated structured RNA regions and multiple sequence alignments from 14 species.

Main Results:

  • Multiple sequence alignments enhance boundary prediction for branched RNA structures compared to single sequences, irrespective of the method used.
  • RNAbound demonstrates improved boundary predictions for branched structures like transfer RNAs (tRNAs) and small nucleolar RNAs (snoRNAs) using multiple sequence alignments.
  • Median differences in boundary prediction were -6 and -11.5 nucleotides for left and right boundaries, respectively, for branched structures with RNAbound.

Conclusions:

  • Multiple sequence alignments are superior to single sequences for predicting the boundaries of structured RNA domains, particularly branched structures.
  • The RNAbound method, leveraging evolutionary conservation, offers improved accuracy in defining RNA structured domain boundaries.
  • Precise boundary definition is critical for advancing RNA structure modeling, clustering, and motif discovery in ncRNA research.