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Nucleic Acids Research 2006 34(9):e67; doi:10.1093/nar/gkl335
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Published online 12 May 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
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Methods Online

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

Anton Buzdin*, Elena Kovalskaya-Alexandrova, Elena Gogvadze and Eugene Sverdlov

Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry 16/10 Miklukho-Maklaya, Moscow 117997, Russia

*To whom correspondence should be addressed. Tel: +7 495 330 6329; Fax: +7 495 330 6538; Email: anton{at}humgen.siobc.ras.ru

Received March 16, 2006. Revised April 7, 2006. Accepted April 15, 2006.

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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