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Related Experiment Videos

Incognito rRNA and rDNA in databases and libraries

I L Gonzalez, J E Sylvester

    Genome Research
    |January 1, 1997
    PubMed
    Summary

    Ribosomal DNA (rDNA) and ribosomal RNA (rRNA) sequences are frequently found in genomic and cDNA databases due to over-representation. This study explains the widespread occurrence and recommends checking submissions for structural RNAs.

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    Area of Science:

    • Genomics
    • Molecular Biology
    • Bioinformatics

    Background:

    • Ribosomal DNA (rDNA) and ribosomal RNA (rRNA) sequences are disproportionately present in genomic and cDNA libraries.
    • This over-representation leads to numerous database entries, particularly in EST databases, often misidentified.

    Discussion:

    • Several factors contribute to the prevalence of rDNA in libraries, including rRNA pseudogenes, mRNA-derived pseudogenes within rDNA, and cDNA derived from rRNA or rDNA transcripts.
    • Genomic DNA contamination in RNA preparations is also a potential source of rDNA sequences.

    Key Insights:

    • Unidentified rDNA sequences are common in public sequence databases.
    • The study identifies multiple mechanisms leading to rDNA over-representation in sequence data.
    • Recommendations are made for improved data submission and validation processes.

    Outlook:

    • Future database submissions should include checks for structural RNAs like rDNA.
    • Enhanced quality control in sequence data submission can improve database accuracy.
    • Further research may elucidate the precise mechanisms and frequencies of rDNA integration into various library types.

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