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Related Concept Videos

Alternative RNA Splicing02:18

Alternative RNA Splicing

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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.
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...
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Splicing is the process by which eukaryotic RNA is edited before its translation into protein. The RNA strand transcribed from eukaryotic DNA is called the primary transcript. The primary transcripts that become mRNAs are called precursor messenger RNAs (pre-mRNAs). Eukaryotic pre-mRNA contains alternating sequences of exons and introns. Exons are nucleotide sequences that code for proteins, whereas introns are the non-coding regions. In RNA splicing, introns are removed and exons are bonded...
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Exon Recombination02:32

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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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Conservative Site-specific Recombination and Phase Variation02:53

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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Protein domains are small structurally independent units that are part of a single amino acid chain.  Although these domains are often structurally independent, they may rely on synergistic effects to perform their functions as part of a larger protein. Protein domains may be conserved within the same organism, as well as across different organisms.
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Updated: Jul 23, 2025

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Building alternative splicing and evolution-aware sequence-structure maps for protein repeats.

Antoine Szatkownik1, Diego Javier Zea2, Hugues Richard1

  • 1Sorbonne Université, CNRS, IBPS, Laboratoire de Biologie Computationnelle et Quantitative (LCQB), 75005 Paris, France; Bioinformatics Unit, Genome Competence Center (MF1), Robert Koch Institute, 13353 Berlin, Germany.

Journal of Structural Biology
|July 15, 2023
PubMed
Summary
This summary is machine-generated.

We developed ASPRING to identify alternatively spliced protein repeats, revealing over 5,000 conserved repeats that modulate protein interactions and offer new therapeutic targets.

Keywords:
AlphaFold modelsAlternative splicingProtein evolutionProtein interactionsProtein repeats

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Structural Biology

Background:

  • Alternative splicing of protein repeats fine-tunes protein interaction networks.
  • Understanding repeat diversity is crucial for protein function.
  • Existing methods lack comprehensive analysis of alternatively spliced repeats.

Purpose of the Study:

  • To develop a robust method (ASPRING) for identifying alternatively spliced protein repeats.
  • To map protein repeat sequences to 3D structures using evolutionary graphs.
  • To analyze the role of these repeats in protein interactions.

Main Methods:

  • Developed ASPRING, a novel method for identifying alternatively spliced repeats.
  • Utilized alternative splicing-aware hierarchical graphs for sequence-structure mapping.
  • Applied stringent sequence-based similarity criteria across multiple species.
  • Performed joint sequence and structure analysis to identify specificity signatures.

Main Results:

  • Identified over 5,000 evolutionary conserved repeats across human genes and orthologs.
  • Characterized specificity-determining sequence signatures within these repeats.
  • Assessed the impact of alternatively spliced repeats on protein interactions.
  • Demonstrated widespread alternative repeat usage in modulating protein interactions.

Conclusions:

  • Alternative splicing of protein repeats is a widespread mechanism for regulating protein interactions.
  • ASPRING provides a powerful tool for discovering and analyzing these repeats.
  • Findings open new avenues for targeting repeat-mediated interactions therapeutically.