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Data mining of imperfect double-stranded RNA in 3 ' untranslated regions of eukaryotic mRNAs

  1. Author:
    Le, S. Y.
    Maizel, J. V.

  2. Author Address

    Natl Canc Inst, Ctr Canc Res Nanobiol Program, CCR, NIH, Frederick, MD 21702 USA.;Le, SY, Natl Canc Inst, Ctr Canc Res Nanobiol Program, CCR, NIH, Bldg 469,Room 151, Frederick, MD 21702 USA.;shuyun@ncifcrf.gov
    1. Year: 2007
    2. Date: Sep
  2. Journal: Biomolecular Engineering
    1. 24
    2. 3
    3. Pages: 351-359
  4. Type of Article: Article
  5. ISSN: 1389-0344
  1. Abstract:

    Recent developments in the study of RNA silencing indicate that double-stranded RNA (dsRNA) can be used in eukaryotes to block expression of a corresponding cellular gene. There is also a large class of small non-coding RNAs having potential to form a distinct, stable stem-loop in numbers of eukaryotic genomes. We had reported that a large imperfect dsRNA structure with hundreds of base-pairs (bp) in the 3' untranslated region (3'UTR) of cytotoxic ribonuclease was correlated with the translation suppression. In this study, we search for such dsRNAs in a 3'UTR database. The occurrence rate of large dsRNA in 3'UTRs ranges from 0.01% in plant to 0.30% in vertebrate mRNAs. However, small imperfect dsRNAs of similar to 30 bp are much more prevalent than large ones. The small dsRNAs are statistically very significant and uniquely well-ordered. Most of them have the conserved structural features of pre-miRNAs. Our data mining of the dsRNAs in the 3'UTR database can be used to explore RNA-based regulation of gene expression. (C) 2007 Elsevier B.V. All rights reserved.

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External Sources

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  2. DOI: 10.1016/j.bioeng.2007.02.006
  3. View record in Web of Science®
  4. WOS: 000250187400011

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