ArticleNucleic acids research2006
GREM, a technique for genome-wide isolation and quantitative analysis of promoter active repeats.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- Off-target effects of sulforaphane include the derepression of long terminal repeats through histone acetylation events.The Journal of nutritional biochemistry · 2014Trial
- Activation of HERV-K(HML-2) disrupts cortical patterning and neuronal differentiation by increasing NTRK3.Cell stem cell · 2021Article
- Article
- Friends-Enemies: Endogenous Retroviruses Are Major Transcriptional Regulators of Human DNA.Frontiers in chemistry · 2017Review
- Molecular functions of human endogenous retroviruses in health and disease.Cellular and molecular life sciences : CMLS · 2015Review
- Holocarboxylase synthetase interacts physically with nuclear receptor co-repressor, histone deacetylase 1 and a novel splicing variant of histone deacetylase 1 to repress repeats.The Biochemical journal · 2014Article
- Microarray-based identification of individual HERV loci expression: application to biomarker discovery in prostate cancer.Journal of visualized experiments : JoVE · 2013Article
- Epigenetic synergies between biotin and folate in the regulation of pro-inflammatory cytokines and repeats.Scandinavian journal of immunology · 2013Article
- Holocarboxylase synthetase synergizes with methyl CpG binding protein 2 and DNA methyltransferase 1 in the transcriptional repression of long-terminal repeats.Epigenetics · 2013Article
- Article
- Custom human endogenous retroviruses dedicated microarray identifies self-induced HERV-W family elements reactivated in testicular cancer upon methylation control.Nucleic acids research · 2010Article
- A new technique for obtaining whole pathogen transcriptomes from infected host tissues.BioTechniques · 2010Article
- Retroelements and their impact on genome evolution and functioning.Cellular and molecular life sciences : CMLS · 2009Review
- Repression of transposable elements by histone biotinylation.The Journal of nutrition · 2009Article
- Discovery of regulatory elements is improved by a discriminatory approach.PLoS computational biology · 2009Article
- Biotinylation of histones represses transposable elements in human and mouse cells and cell lines and in Drosophila melanogaster.The Journal of nutrition · 2008Article
- Expression patterns of transcribed human endogenous retrovirus HERV-K(HML-2) loci in human tissues and the need for a HERV Transcriptome Project.BMC genomics · 2008Article
- Identification of novel retroid agents in Danio rerio, Oryzias latipes, Gasterosteus aculeatus and Tetraodon nigroviridis.Evolutionary bioinformatics online · 2007Article
- At least 50% of human-specific HERV-K (HML-2) long terminal repeats serve in vivo as active promoters for host nonrepetitive DNA transcription.Journal of virology · 2006Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
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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