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Related Concept Videos

RNA Splicing01:32

RNA Splicing

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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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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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Comparing Copy Number Variations and SNPs02:26

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Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
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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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Genetic Variation01:25

Genetic Variation

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Genetic variation is the diversity in DNA sequences found among individuals of the same species. This diversity is crucial for a species' survival because it helps organisms adapt to environmental changes. Genetic variation begins with fertilization, where an egg and sperm cell merge. Each of these cells carries 23 chromosomes, up to 46 in the fertilized egg. Chromosomes are long DNA strands that contain genes, the basic units of heredity.
Genes exist in different versions called alleles,...
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Exon Recombination02:32

Exon Recombination

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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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Alternative splicing induces sample-level variation in gene-gene correlations.

Yihao Lu1, Brandon L Pierce1,2, Pei Wang3

  • 1Department of Public Health Sciences, University of Chicago, 5841 South Maryland Ave, MC2000, Chicago, IL, 60637, USA.

BMC Genomics
|December 10, 2024
PubMed
Summary
This summary is machine-generated.

Gene splicing variation impacts gene expression correlations, influencing how genes interact. Accounting for these splicing-expression interactions improves the accuracy of gene co-expression analysis, especially in bulk tissue data.

Keywords:
Alternative splicingGene–gene correlationIsoformSample-level variationTotal expression

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Area of Science:

  • Genomics
  • Transcriptomics
  • Bioinformatics

Background:

  • Most genes are multi-exonic and undergo alternative splicing, producing various mRNA isoforms.
  • Different isoforms can have distinct expression levels and functional roles.
  • Bulk tissue RNA-sequencing (RNA-seq) quantifies total gene expression (TE) across isoforms and cell types.

Purpose of the Study:

  • To investigate the impact of alternative splicing variation on gene-gene correlation.
  • To develop a method for analyzing gene-gene correlations that accounts for splicing effects.

Main Methods:

  • Utilized a variance-component model to test TE-TE correlations between co-expressed genes.
  • Incorporated splicing variation and splicing-by-TE interaction effects into the model.
  • Analyzed data from the Genotype-Tissue Expression (GTEx) project (V8).

Main Results:

  • Identified 38,146 significant TE-splicing interaction gene pairs in GTEx lung tissue.
  • Observed strong tissue-specificity of TE-splicing interaction effects across 13 GTEx brain tissues.
  • Demonstrated that accounting for splicing variation enhances result reproducibility and reduces confounding in bulk tissue data analysis.

Conclusions:

  • Splicing variation interacts with total gene expression (TE), affecting co-expressed genes and causing tissue-specific variability in gene-gene correlations.
  • Accounting for TE-splicing interaction effects improves the robustness and reduces confounding in gene-gene correlation estimations from bulk tissue expression data.