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A pseudogene for human U4 RNA with a remarkable structure.

K Hammarström, G Westin, U Pettersson

    The EMBO Journal
    |January 1, 1982
    PubMed
    Summary
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    Researchers screened a human DNA library for small nuclear RNA U4 sequences. They discovered a U4 RNA pseudogene, suggesting a reverse transcription and integration mechanism for its formation.

    Area of Science:

    • Molecular Biology
    • Genomics
    • RNA Biology

    Background:

    • Small nuclear RNAs (snRNAs) are essential components of the spliceosome.
    • The organization and evolution of snRNA genes in the human genome are not fully understood.
    • Previous studies suggested that some snRNA pseudogenes might arise from reverse transcription.

    Purpose of the Study:

    • To identify sequences complementary to human small nuclear RNA U4 in the genome.
    • To characterize the structure and origin of any identified U4 RNA pseudogenes.
    • To investigate the mechanism of pseudogene formation in the human genome.

    Main Methods:

    • Screening of a human DNA library (Lawn et al., 1978) for U4 RNA complementary sequences.
    • Identification of positive clones through recombinant screening.

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  • Detailed characterization of a positive recombinant clone, including subcloning and partial sequencing.
  • Analysis of the pseudogene structure, including flanking regions and sequence homology.

    • Main Results:

    • Several clones containing sequences complementary to U4 RNA were identified, indicating dispersed U4 sequences in the human genome.
    • One recombinant clone contained a 1.9 kilobase (kb) fragment with a pseudogene for U4 RNA.
    • The U4 RNA pseudogene showed high sequence similarity to the first 68 nucleotides of human U4 RNA.
    • The pseudogene was flanked by perfect direct repeats of 20 base pairs (bp).

    Conclusions:

    • The findings support the model that certain snRNA pseudogenes originate from reverse transcription of RNA followed by integration.
    • This mechanism explains the presence of pseudogenes with structural features like direct repeats.
    • The study contributes to understanding the dynamic nature and evolutionary processes shaping the human genome.