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A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines.

Sciamanna I, Gualtieri A, Cossetti C, Osimo EF, Ferracin M, Macchia G, Aricò E, Prosseda G, Vitullo P, Misteli T, Spadafora C - Oncotarget (2013)

Bottom Line: Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models.The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences.The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production.

View Article: PubMed Central - PubMed

Affiliation: Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy.

ABSTRACT
LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming 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 a previously unrecognized mechanism crucial to the transformed state in tumor cells.

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Related in: MedlinePlus

Alu and LINE-1 content around miRNAs, UCRs and coding genesThe box and whisker plots represent the distribution of numbers of repeated Alu (left panels) and LINE-1 (right panels) elements flanking (+/− 100 Kbp) the indicated sequence classes, i.e. miRNAs (A and A'), UCRs (B and B') and protein-coding genes (C and C'). EFV-downregulated miRNAs (A) and UCRs (B) are highly significantly enriched (**, P≤0.0001) in Alu elements.
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Figure 4: Alu and LINE-1 content around miRNAs, UCRs and coding genesThe box and whisker plots represent the distribution of numbers of repeated Alu (left panels) and LINE-1 (right panels) elements flanking (+/− 100 Kbp) the indicated sequence classes, i.e. miRNAs (A and A'), UCRs (B and B') and protein-coding genes (C and C'). EFV-downregulated miRNAs (A) and UCRs (B) are highly significantly enriched (**, P≤0.0001) in Alu elements.

Mentions: Significant associations were found between EFV-sensitive sequences and retrotransposons. EFV-modulated miRNAs (P <0.0001, supplemetary Figure S2B) and UCRs (P=0.0003, supplemetary Figure S2C) showed statistically significant over-representation of flanking Alu elements compared to EFV-insensitive sequences. In particular, a significant enrichment in Alu content was found in EFV-downregulated subpopulations of miRNAs (Figure 4A) and UCRs (Figure 4B), whereas upregulated sequences did not significantly differ from non-modulated controls. No significant variations were found instead in the distribution of LINE-1 elements among the three groups of sequences (Figure 4A', B', C').


A tumor-promoting mechanism mediated by retrotransposon-encoded reverse transcriptase is active in human transformed cell lines.

Sciamanna I, Gualtieri A, Cossetti C, Osimo EF, Ferracin M, Macchia G, Aricò E, Prosseda G, Vitullo P, Misteli T, Spadafora C - Oncotarget (2013)

Alu and LINE-1 content around miRNAs, UCRs and coding genesThe box and whisker plots represent the distribution of numbers of repeated Alu (left panels) and LINE-1 (right panels) elements flanking (+/− 100 Kbp) the indicated sequence classes, i.e. miRNAs (A and A'), UCRs (B and B') and protein-coding genes (C and C'). EFV-downregulated miRNAs (A) and UCRs (B) are highly significantly enriched (**, P≤0.0001) in Alu elements.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3926826&req=5

Figure 4: Alu and LINE-1 content around miRNAs, UCRs and coding genesThe box and whisker plots represent the distribution of numbers of repeated Alu (left panels) and LINE-1 (right panels) elements flanking (+/− 100 Kbp) the indicated sequence classes, i.e. miRNAs (A and A'), UCRs (B and B') and protein-coding genes (C and C'). EFV-downregulated miRNAs (A) and UCRs (B) are highly significantly enriched (**, P≤0.0001) in Alu elements.
Mentions: Significant associations were found between EFV-sensitive sequences and retrotransposons. EFV-modulated miRNAs (P <0.0001, supplemetary Figure S2B) and UCRs (P=0.0003, supplemetary Figure S2C) showed statistically significant over-representation of flanking Alu elements compared to EFV-insensitive sequences. In particular, a significant enrichment in Alu content was found in EFV-downregulated subpopulations of miRNAs (Figure 4A) and UCRs (Figure 4B), whereas upregulated sequences did not significantly differ from non-modulated controls. No significant variations were found instead in the distribution of LINE-1 elements among the three groups of sequences (Figure 4A', B', C').

Bottom Line: Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models.The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences.The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production.

View Article: PubMed Central - PubMed

Affiliation: Istituto Superiore di Sanità, Viale Regina Elena 299, Rome, Italy.

ABSTRACT
LINE-1 elements make up the most abundant retrotransposon family in the human genome. Full-length LINE-1 elements encode a reverse transcriptase (RT) activity required for their own retrotranpsosition as well as that of non-autonomous Alu elements. LINE-1 are poorly expressed in normal cells and abundantly in cancer cells. Decreasing RT activity in cancer cells, by either LINE-1-specific RNA interference, or by RT inhibitory drugs, was previously found to reduce proliferation and promote differentiation and to antagonize tumor growth in animal models. Here we have investigated how RT exerts these global regulatory functions. We report that the RT inhibitor efavirenz (EFV) selectively downregulates proliferation of transformed cell lines, while exerting only mild effects on non-transformed cells; this differential sensitivity matches a differential RT abundance, which is high in the former and undetectable in the latter. Using CsCl density gradients, we selectively identify Alu and LINE-1 containing DNA:RNA hybrid molecules in cancer but not in normal cells. Remarkably, hybrid molecules fail to form in tumor cells treated with EFV under the same conditions that repress proliferation and induce the reprogramming of expression profiles of coding genes, microRNAs (miRNAs) and ultraconserved regions (UCRs). The RT-sensitive miRNAs and UCRs are significantly associated with Alu sequences. The results suggest that LINE-1-encoded RT governs the balance between single-stranded and double-stranded RNA production. In cancer cells the abundant RT reverse-transcribes retroelement-derived mRNAs forming 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 a previously unrecognized mechanism crucial to the transformed state in tumor cells.

Show MeSH
Related in: MedlinePlus