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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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Before mRNAs are exported to the cytoplasm, it is crucial to check each mRNA for structural and functional integrity. Eukaryotic cells use several different mechanisms, collectively known as mRNA surveillance, to look for irregularities in mRNAs. Irregular or aberrant mRNA are rapidly degraded by various enzymes. If a defective mRNA escapes the surveillance, it would be translated into a protein which would either be non-functional or not function properly. One of the primary irregularities in...
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Alu insertion variants alter mRNA splicing.

Lindsay M Payer1, Jared P Steranka1, Daniel Ardeljan2

  • 1Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.

Nucleic Acids Research
|November 13, 2018
PubMed
Summary
This summary is machine-generated.

Common inherited Alu insertions can alter RNA splicing, leading to splicing quantitative trait loci (sQTLs). One Alu variant in the CD58 gene may increase multiple sclerosis risk by disrupting normal splicing.

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Area of Science:

  • Genomics and Molecular Biology
  • RNA Biology
  • Genetic Epidemiology

Background:

  • RNA splicing is a critical gene expression process regulated by specific DNA sequences.
  • Alu retrotransposons, mobile genetic elements, can interfere with RNA splicing when inserted near splice sites.
  • Genetic variations, including Alu insertions, can influence splicing patterns and lead to splicing quantitative trait loci (sQTLs).

Purpose of the Study:

  • To investigate whether common inherited polymorphic Alu insertions function as splicing quantitative trait loci (sQTLs).
  • To identify specific Alu variants that alter RNA splicing efficiency.
  • To explore the potential role of Alu-mediated splicing alterations in disease risk, focusing on multiple sclerosis.

Main Methods:

  • Screened intronic Alu variants within 100 base pairs of alternatively used exons for splicing-altering effects.
  • Utilized RT-PCR (Reverse Transcription Polymerase Chain Reaction) analysis to confirm splicing alterations at endogenous loci.
  • Focused on Alu polymorphisms within the CD58 gene, known to be associated with multiple sclerosis risk.

Main Results:

  • Identified five loci (21.7% of those tested) where polymorphic Alu insertions significantly altered splicing.
  • Observed that Alu insertions typically promote exon skipping, but can also increase exon inclusion in some cases.
  • Confirmed an Alu polymorphism in the CD58 gene promotes exon 3 skipping, leading to a frameshifted transcript and acting as an sQTL for CD58.

Conclusions:

  • Alu polymorphisms are a common cause of altered splicing efficiency and can function as sQTLs.
  • The identified Alu variant in CD58 is implicated as a potential causative factor for increased multiple sclerosis risk.
  • This research expands the understanding of Alu elements as regulators of splicing and their contribution to human disease.