Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines

Junko Tomikawa, Hiroko Shimokawa, Masahiro Uesaka, Naoki Yamamoto, Yuji Mori, Hiroko Tsukamura, Kei Ichiro Maeda, Takuya Imamura

Research output: Contribution to journalArticle

25 Citations (Scopus)

Abstract

Agrowing number of noncoding RNAs (ncRNAs) are thought to be involved in sequence-specific alterations of epigenetic processes, mostly causing gene repression. In this study, promoterassociated ncRNAs (pancRNAs >200 nucleotides in size) that were endogenously generated from the sense strand at Map2b, antisense strand at Nefl, and both strands at Vim were investigated regarding their epigenetic potential as positive or negative regulators in rat pheochromocytoma (PC12) and fibroblast (normal rat kidney) cell lines. The respective antisense pancRNAs were associated with several active chromatin marks at the Nefl and Vim promoters. Forced expression of fragments expressing the antisense pancRNAs caused sequence-specific DNA demethylation, whereas a decrease of expression induced methylation of the same sequences. In contrast, perturbing the expression of the two sense pancRNAs did not change the DNA methylation status. These results suggest that a fraction of naturally occurring ncRNAs acts in cis as a single-stranded form and that the transcriptional orientation of pancRNA is important for the establishment of sequence-specific epigenetic modifications consistent with open chromatin structure.

Original languageEnglish
Pages (from-to)34788-34799
Number of pages12
JournalJournal of Biological Chemistry
Volume286
Issue number40
DOIs
Publication statusPublished - Oct 7 2011
Externally publishedYes

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Untranslated RNA
Epigenomics
Rats
Genes
Cells
Cell Line
Chromatin
Genetic Epigenesis
Methylation
Pheochromocytoma
DNA Methylation
Fibroblasts
Nucleotides
Kidney
DNA

All Science Journal Classification (ASJC) codes

  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines. / Tomikawa, Junko; Shimokawa, Hiroko; Uesaka, Masahiro; Yamamoto, Naoki; Mori, Yuji; Tsukamura, Hiroko; Maeda, Kei Ichiro; Imamura, Takuya.

In: Journal of Biological Chemistry, Vol. 286, No. 40, 07.10.2011, p. 34788-34799.

Research output: Contribution to journalArticle

Tomikawa, J, Shimokawa, H, Uesaka, M, Yamamoto, N, Mori, Y, Tsukamura, H, Maeda, KI & Imamura, T 2011, 'Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines', Journal of Biological Chemistry, vol. 286, no. 40, pp. 34788-34799. https://doi.org/10.1074/jbc.M111.275750
Tomikawa, Junko ; Shimokawa, Hiroko ; Uesaka, Masahiro ; Yamamoto, Naoki ; Mori, Yuji ; Tsukamura, Hiroko ; Maeda, Kei Ichiro ; Imamura, Takuya. / Single-stranded noncoding RNAs mediate local epigenetic alterations at gene promoters in rat cell lines. In: Journal of Biological Chemistry. 2011 ; Vol. 286, No. 40. pp. 34788-34799.
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