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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.
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A single nucleotide polymorphism or SNP is a single nucleotide variation at a specific genomic position in a large population. It is the most prevalent type of sequence variation found in the human genome. Point mutations that occur in more than 1% of the population qualify as SNPs. These are present once every 1000 nucleotides on an average in the human genome. Replacement of a purine with another purine (A/G) or a pyrimidine with another pyrimidine (C/T) is known as a transition. In contrast,...
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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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In eukaryotic cells, transcripts made by RNA polymerase are modified and processed before exiting the nucleus. Unprocessed RNA is called precursor mRNA or pre-mRNA to distinguish it from mature mRNA.
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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Systematically developing a registry of splice-site creating variants utilizing massive publicly available

Naoko Iida1, Ai Okada1, Yoshihisa Kobayashi2

  • 1Division of Genome Analysis Platform Development, National Cancer Center Research Institute, Tokyo, Japan.

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|January 9, 2025
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Summary
This summary is machine-generated.

We developed a new method to find splice-site creating variants (SSCVs) using transcriptome data, identifying over 30,000 SSCVs, including those linked to diseases. This discovery aids in understanding splicing and developing new therapies.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Genomic variants affecting splicing are crucial in genetic disorders and cancer.
  • Novel splice-site creating variants (SSCVs) are difficult to detect and often missed in genomic studies.
  • SSCVs are promising targets for splice-switching antisense oligonucleotide (ASO) therapies.

Purpose of the Study:

  • To develop a novel computational framework for identifying SSCVs using only transcriptome data.
  • To create a comprehensive registry of SSCVs from large-scale transcriptome datasets.
  • To investigate the characteristics and implications of SSCVs, including their role in Alu exonization and disease.

Main Methods:

  • Development of a novel framework to screen for SSCVs using transcriptome sequence data.
  • Application of the framework to 322,072 publicly available transcriptomes.
  • Analysis of identified SSCVs for disease relevance, Alu exonization patterns, and evolutionary relationships.

Main Results:

  • Identification of 30,130 SSCVs, with 5121 impacting disease-causing variants.
  • Characterization of Alu exonization via SSCVs, including hotspots and evolutionary insights.
  • Discovery of novel gain-of-function SSCVs in the NOTCH1 gene, suppressible by ASOs.

Conclusions:

  • A systematic approach for automated SSCV discovery facilitates the study of splicing mechanisms.
  • The identified SSCV catalog serves as a valuable resource for drug discovery and therapeutic development.
  • The findings highlight the potential of ASOs in targeting and correcting splicing defects caused by SSCVs.