Identification and characterization of novel genotoxic stress-inducible nuclear long noncoding RNAs in mammalian cells

Rena Mizutani, Ai Wakamatsu, Noriyuki Tanaka, Hiroshi Yoshida, Naobumi Tochigi, Yoshio Suzuki, Tadahiro Oonishi, Hidenori Tani, Keiko Tano, Kenichi Ijiri, Takao Isogai, Nobuyoshi Akimitsu

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Abstract

Whole transcriptome analyses have revealed a large number of novel transcripts including long and short noncoding RNAs (ncRNAs). Currently, there is great interest in characterizing the functions of the different classes of ncRNAs and their relevance to cellular processes. In particular, nuclear long ncRNAs may be involved in controlling various aspects of biological regulation, such as stress responses. By a combination of bioinformatic and experimental approaches, we identified 25 novel nuclear long ncRNAs from 6,088,565 full-length human cDNA sequences. Some nuclear long ncRNAs were conserved among vertebrates, whereas others were found only among primates. Expression profiling of the nuclear long ncRNAs in human tissues revealed that most were expressed ubiquitously. A subset of the identified nuclear long ncRNAs was induced by the genotoxic agents mitomycin C or doxorubicin, in HeLa Tet-off cells. There were no commonly altered nuclear long ncRNAs between mitomycin C- and doxorubicin-treated cells. These results suggest that distinct sets of nuclear long ncRNAs play roles in cellular defense mechanisms against specific genotoxic agents, and that particular long ncRNAs have the potential to be surrogate indicators of a specific cell stress.

Original languageEnglish
Article numbere34949
JournalPloS one
Volume7
Issue number4
DOIs
Publication statusPublished - Apr 19 2012

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ASJC Scopus subject areas

  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • General

Cite this

Mizutani, R., Wakamatsu, A., Tanaka, N., Yoshida, H., Tochigi, N., Suzuki, Y., Oonishi, T., Tani, H., Tano, K., Ijiri, K., Isogai, T., & Akimitsu, N. (2012). Identification and characterization of novel genotoxic stress-inducible nuclear long noncoding RNAs in mammalian cells. PloS one, 7(4), [e34949]. https://doi.org/10.1371/journal.pone.0034949