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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 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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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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Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models
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Polymorphic differences within HLA-C alleles contribute to alternatively spliced transcripts lacking exon 5.

Femke A I Ehlers1,2,3, Timo I Olieslagers1,3, Mathijs Groeneweg1,3

  • 1Department of Transplantation Immunology, Tissue Typing Laboratory, Maastricht University Medical Center+, Maastricht, The Netherlands.

HLA
|June 1, 2022
PubMed
Summary
This summary is machine-generated.

Human Leukocyte Antigen (HLA) allele polymorphisms influence alternative splicing in HLA-C genes. This study reveals specific HLA-C variants exhibit exon skipping due to genetic variations, impacting gene expression.

Keywords:
HLA-Calternative splicingexon skippingsplicing regulatory elements

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Area of Science:

  • Immunogenetics
  • Molecular Biology
  • Genomics

Background:

  • The human leukocyte antigen (HLA) genes are highly polymorphic.
  • Alternative splicing of HLA genes is not well understood.
  • Understanding HLA-C splicing is crucial for immune response studies.

Purpose of the Study:

  • To investigate the impact of HLA-C allele polymorphism on alternative splicing.
  • To identify specific HLA-C alleles and their splicing variants.
  • To explore the mechanisms underlying allele-specific alternative splicing.

Main Methods:

  • RNA isolation from peripheral blood cells.
  • cDNA synthesis and specific amplification of 12 common HLA-C allele groups.
  • HLA-C sequencing to identify alternative splicing variants.
  • Bioinformatic analysis of intron and exon sequences, including splicing regulatory elements (SREs).

Main Results:

  • Alternative splicing variants with exon 5 skipping were observed in HLA-C*04 and HLA-C*16 alleles.
  • These variants were co-expressed with the mature HLA-C transcript.
  • Polymorphisms in intron 4 did not affect predicted splice sites or branch points.
  • A single nucleotide polymorphism (SNP) in exon 5 of HLA-C*16 altered predicted exonic SREs, unlike HLA-C*04.

Conclusions:

  • HLA-C allele polymorphisms directly influence alternative splicing patterns.
  • Specific SNPs within HLA-C alleles can modulate splicing by affecting SREs.
  • This study provides evidence for genetic control over HLA-C alternative splicing.