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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

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.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Alternative RNA Splicing02:18

Alternative RNA Splicing

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.
There are five types of alternative RNA splicing that vary in the ways the pre-mRNA segments are removed or retained in the mature mRNA. The first...
Mutations01:35

Mutations

Mutations are changes in the sequence of DNA. These changes can occur spontaneously or they can be induced by exposure to environmental factors. Mutations can be characterized in a number of different ways: whether and how they alter the amino acid sequence of the protein, whether they occur over a small or large area of DNA, and whether they occur in somatic cells or germline cells.
Chromosomal Alterations Are Large-Scale Mutations
While point mutations are changes in a single nucleotide in...
Mutations01:39

Mutations

Overview
Mutations01:39

Mutations

Overview
Translation01:31

Translation

Lesson: Translation
Translation is the process of synthesizing proteins from the genetic information carried by messenger RNA (mRNA). Following transcription, it constitutes the final step in the expression of genes. This process is carried out by ribosomes, complexes of protein and specialized RNA molecules. Ribosomes, transfer RNA (tRNA), and other proteins produce a chain of amino acids—the polypeptide—as the end product of translation.
Translation Produces the Building Blocks of Life

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Related Experiment Video

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Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

Disease-associated mutations that alter the RNA structural ensemble.

Matthew Halvorsen1, Joshua S Martin, Sam Broadaway

  • 1Biomedical Sciences Department, University at Albany, Albany, New York, USA.

Plos Genetics
|September 3, 2010
PubMed
Summary

Disease-associated Single Nucleotide Polymorphisms (SNPs) in untranslated regions (UTRs) can alter RNA structure, causing disease. We identified these "RiboSNitches" using our SNPfold algorithm, linking genetic variations to altered mRNA conformations and disease phenotypes.

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Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

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Related Experiment Videos

Last Updated: Jun 9, 2026

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells
10:34

Probing RNA Structure with Dimethyl Sulfate Mutational Profiling with Sequencing In Vitro and in Cells

Published on: December 9, 2022

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12:26

Optical Tweezers to Study RNA-Protein Interactions in Translation Regulation

Published on: February 12, 2022

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes
11:58

Using In Vitro and In-cell SHAPE to Investigate Small Molecule Induced Pre-mRNA Structural Changes

Published on: January 30, 2019

Area of Science:

  • Genomics
  • RNA Biology
  • Medical Genetics

Background:

  • Genome-wide association studies (GWAS) frequently detect disease-associated mutations in non-coding genomic regions.
  • A significant portion of the human genome is transcribed, suggesting non-coding variants may impact RNA structure and function.
  • Disease phenotypes may arise from structural rearrangements in regulatory regions of RNA transcripts caused by genetic variations.

Purpose of the Study:

  • To identify disease-associated Single Nucleotide Polymorphisms (SNPs) located in untranslated regions (UTRs) that significantly alter RNA secondary structure.
  • To investigate the potential of these SNP-induced structural changes in UTRs to cause disease phenotypes.
  • To introduce the concept of "RiboSNitches" – regulatory RNAs where SNPs induce structural changes leading to disease.

Main Methods:

  • Genome-wide analysis of disease-associated SNPs from the Human Gene Mutation Database (HGMD) mapping to gene UTRs.
  • Utilized partition function calculations to analyze the ensemble of possible RNA conformations, rather than minimum free energy approaches.
  • Employed Boltzmann sampling for sub-optimal RNA structures to characterize SNP-induced conformational changes.

Main Results:

  • Identified disease-associated SNPs in human UTRs that significantly alter global RNA conformation.
  • Found multiple SNPs in UTRs associated with six disease states (Hyperferritinemia Cataract Syndrome, beta-Thalassemia, Cartilage-Hair Hypoplasia, Retinoblastoma, COPD, Hypertension) that modify mRNA structural ensembles.
  • Observed SNP-induced conformational changes in 5' UTRs (e.g., FTL, RB1) analogous to bacterial riboswitches.

Conclusions:

  • Propose the existence of "RiboSNitches," where specific SNPs in UTRs cause structural alterations leading to disease.
  • The SNPfold algorithm effectively identifies potential RiboSNitches by integrating GWAS data with mRNA structural ensemble analysis.
  • This approach offers a novel mechanism for understanding genetic contributions to disease through RNA structure modulation.