Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

Christian Cole, Andrew Sobala, Cheng Lu, Shawn R. Thatcher, A. Bowman, John W. S. Brown, Pamela J. Green, Geoffrey J. Barton (Lead / Corresponding author), Gyorgy Hutvagner (Lead / Corresponding author)

    Research output: Contribution to journalArticle

    309 Citations (Scopus)

    Abstract

    Deep sequencing technologies such as Illumina, SOLiD, and 454 platforms have become very powerful tools in discovering and quantifying small RNAs in diverse organisms. Sequencing small RNA fractions always identifies RNAs derived from abundant RNA species such as rRNAs, tRNAs, snRNA, and snoRNA, and they are widely considered to be random degradation products. We carried out bioinformatic analysis of deep sequenced HeLa RNA and after quality filtering, identified highly abundant small RNA fragments, derived from mature tRNAs that are likely produced by specific processing rather than from random degradation. Moreover, we showed that the processing of small RNAs derived from tRNA(Gln) is dependent on Dicer in vivo and that Dicer cleaves the tRNA in vitro.

    Original languageEnglish
    Pages (from-to)2147-2160
    Number of pages14
    JournalRNA: a Publication of the RNA Society
    Volume15
    Issue number12
    DOIs
    Publication statusPublished - Dec 2009

    Keywords

    • small RNA
    • miRNA
    • deep sequencing
    • Dicer
    • tRNA
    • SMALL INTERFERING RNAS
    • SMALL SILENCING RNAS
    • ENDOGENOUS SIRNAS
    • ALIGNMENT EDITOR
    • SOMATIC-CELLS
    • MOUSE OOCYTES
    • DROSOPHILA
    • PATHWAY
    • EXPRESSION
    • GENES

    Cite this

    Cole, Christian ; Sobala, Andrew ; Lu, Cheng ; Thatcher, Shawn R. ; Bowman, A. ; Brown, John W. S. ; Green, Pamela J. ; Barton, Geoffrey J. ; Hutvagner, Gyorgy. / Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. In: RNA: a Publication of the RNA Society. 2009 ; Vol. 15, No. 12. pp. 2147-2160.
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    Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. / Cole, Christian; Sobala, Andrew; Lu, Cheng; Thatcher, Shawn R.; Bowman, A.; Brown, John W. S.; Green, Pamela J.; Barton, Geoffrey J. (Lead / Corresponding author); Hutvagner, Gyorgy (Lead / Corresponding author).

    In: RNA: a Publication of the RNA Society, Vol. 15, No. 12, 12.2009, p. 2147-2160.

    Research output: Contribution to journalArticle

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    AU - Sobala, Andrew

    AU - Lu, Cheng

    AU - Thatcher, Shawn R.

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