GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.

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  • Author(s): Buzdin A;Buzdin A; Kovalskaya-Alexandrova E; Gogvadze E; Sverdlov E
  • Source:
    Nucleic acids research [Nucleic Acids Res] 2006 May 12; Vol. 34 (9), pp. e67. Date of Electronic Publication: 2006 May 12.
  • Publication Type:
    Evaluation Study; Journal Article; Research Support, Non-U.S. Gov't
  • Language:
    English
  • Additional Information
    • Source:
      Publisher: Oxford University Press Country of Publication: England NLM ID: 0411011 Publication Model: Electronic Cited Medium: Internet ISSN: 1362-4962 (Electronic) Linking ISSN: 03051048 NLM ISO Abbreviation: Nucleic Acids Res Subsets: MEDLINE
    • Publication Information:
      Publication: 1992- : Oxford : Oxford University Press
      Original Publication: London, Information Retrieval ltd.
    • Subject Terms:
      Promoter Regions, Genetic* ; Terminal Repeat Sequences*; Endogenous Retroviruses/*genetics ; Genomics/*methods; Gene Library ; Humans ; Transcriptional Activation
    • Abstract:
      We developed a technique called GREM (Genomic Repeat Expression Monitor) that can be applied to genome-wide isolation and quantitative analysis of any kind of transcriptionally active repetitive elements. Briefly, the technique includes three major stages: (i) generation of a transcriptome wide library of cDNA 5' terminal fragments, (ii) selective amplification of repeat-flanking genomic loci and (iii) hybridization of the cDNA library (i) to the amplicon (ii) with subsequent selective amplification and cloning of the cDNA-genome hybrids. The sequences obtained serve as 'tags' for promoter active repetitive elements. The advantage of GREM is an unambiguous mapping of individual promoter active repeats at a genome-wide level. We applied GREM for genome-wide experimental identification of human-specific endogenous retroviruses and their solitary long terminal repeats (LTRs) acting in vivo as promoters. Importantly, GREM tag frequencies linearly correlated with the corresponding LTR-driven transcript levels found using RT-PCR. The GREM technique enabled us to identify 54 new functional human promoters created by retroviral LTRs.
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    • Publication Date:
      Date Created: 20060516 Date Completed: 20060530 Latest Revision: 20211020
    • Publication Date:
      20240829
    • Accession Number:
      PMC3303178
    • Accession Number:
      10.1093/nar/gkl335
    • Accession Number:
      16698959