E-MTAB-1736 - Transcription profiling by array of ultraconserved regions (UCRs) from human A375 cells treated with 20 uM of reverse transcriptase inhibitor efavirenz

Status
Released on 1 January 2014, last updated on 2 May 2014
Organism
Homo sapiens
Samples (5)
Array (1)
Protocols (6)
Description
Background: LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode their own reverse transcriptase (RT). They are expressed at low levels in normal cells and abundantly in cancer cells. RT down-regulation, by either RNA interference to LINE-1 elements, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation in cancer cells and to antagonize tumor growth in animal models. Results: We report that the RT inhibitor efavirenz effectively inhibit proliferation of a variety of human tumorigenic cell lines while only slightly affecting the proliferation of human normal fibroblast cell line, a difference that nicely matches RT expression in the former cell lines and its lack in the latter. The finding of Alu and LINE-1 containing DNA:RNA hybrid molecules - identified by CsCl density gradients - selectively in cancer but not in normal cells, suggests that RNA transcripts from these retroelements are candidate substrates for reverse transcription. These hybrids disappear in tumor cells treated with efavirenz, under the same conditions which induce an extensive reprogrammed expression profiles for protein-coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alus sequences. Conclusions: A novel RT-dependent mechanism governs the balance between single-stranded and double-stranded RNA production. In cancer cells, the abundant LINE-1-encoded RT reverse-transcribes retroelement-derived mRNAs, generating RNA:DNA hybrids. We propose that this impairs the formation of double-stranded RNAs and the ensuing production of small regulatory RNAs, with a direct impact on gene expression. RT inhibition restores the ‘normal’ small RNA profile and the regulatory networks that depend on them. Thus, the retrotransposon-encoded RT drives an epigenetic mechanism crucial to maintenance of the transformed state in tumor cells.
Experiment types
transcription profiling by array, co-expression, compound treatment design, in vitro
Contact
Citation
A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase in human cells. Ilaria Sciamanna; Alberto Gualtieri; Cristina Cossetti; Emanuele Felice Osimo; Manuela Ferracin Gianfranco Macchia; Eleonora Aricò; Gianni Prosseda; Patrizia Vitullo; Tom Misteli; Corrado Spadafora.
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-MTAB-1736.idf.txt
Sample and data relationshipE-MTAB-1736.sdrf.txt
Raw data (1)E-MTAB-1736.raw.1.zip
Processed data (1)E-MTAB-1736.processed.1.zip
Array designA-MEXP-2317.adf.txt
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