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qKAT: Quantitative Semi-automated Typing of Killer-cell Immunoglobulin-like Receptor Genes
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Published on: March 6, 2019

Haplotype-specific sequence encoding the protein kinase, interferon-inducible double-stranded RNA-dependent activator

S Chida1, H Hohjoh, M Hirai

  • 1Department of Human Genetics, Graduate School of Medicine, University of Tokyo, Japan.

Immunogenetics
|February 28, 2001
PubMed

Insights

The protein kinase, interferon-inducible double-stranded RNA-dependent activator (PRKRA) gene in the HLA-DR subregion is a processed pseudogene, likely originating from a functional gene on Chromosome 2. This pseudogene

Area of Science:

  • Genetics
  • Immunology
  • Molecular Biology

Background:

  • The protein kinase, interferon-inducible double-stranded (ds)RNA-dependent activator (PRKRA) is a dsRNA-binding protein crucial for interferon's antiviral activity.
  • Previous studies suggested an intronless PRKRA gene sequence within the human leukocyte antigen (HLA) DR subregion.

Purpose of the Study:

  • To investigate and characterize the PRKRA gene's location and nature within the human genome.
  • To determine the origin and relationship of the PRKRA sequence in the HLA DR subregion.

Main Methods:

  • Southern blotting and polymerase chain reaction (PCR) using homozygous typing cell lines for HLA genes.
  • Fluorescence in situ hybridization (FISH) with PRKRA as a probe.
  • Sequence-database homology search.

Main Results:

  • The PRKRA sequence in the DR subregion was found to be dependent on the DR53 group.
  • FISH analysis revealed PRKRA signals on Chromosome (Chr) 6p21.3 (DR53-dependent) and Chr 2q31.2-q32.1 (consistently detected).
  • Homology searches indicated an intron-containing PRKRA gene on Chr 2, suggesting the Chr 6 sequence is a processed pseudogene (PRKRApsi).

Conclusions:

  • The PRKRA gene found in the HLA DR subregion is a processed pseudogene (PRKRApsi).
  • This pseudogene likely originated from a functional PRKRA gene on Chr 2q31.2-q32.1.
  • The generation of PRKRApsi appears linked to the DR53 group's common ancestor.

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