Androgen responsive intronic non-coding RNAs

Rodrigo Louro, Helder I. Nakaya, Paulo P. Amaral, Fernanda Festa, Mari C. Sogayar, Aline M. da Silva, Sergio Verjovski-Almeida, Eduardo M. Reis

Research output: Contribution to journalArticle

49 Citations (Scopus)

Abstract

Background: Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. Results: Using a custom-built cDNA microarray enriched in intronic transcribed sequences, we found 39 intronic non-coding RNAs for which levels were significantly regulated by androgen exposure. Orientation-specific reverse transcription-PCR indicated that 10 of the 13 were transcribed in the antisense direction. These transcripts are long (0.5-5 kb), unspliced and apparently do not code for proteins. Interestingly, we found that the relative levels of androgen-regulated intronic transcripts could be correlated with the levels of the corresponding protein-coding gene (asGAS6 and asDNAJC3) or with the alternative usage of exons (asKDELR2 and asITGA6) in the corresponding protein-coding transcripts. Binding of the androgen receptor to a putative regulatory region upstream from asMYO5A, an androgen-regulated antisense intronic transcript, was confirmed by chromatin immunoprecipitation. Conclusion: Altogether, these results indicate that at least a fraction of naturally transcribed intronic non-coding RNAs may be regulated by common physiological signals such as hormones, and further corroborate the notion that the intronic complement of the transcriptome play functional roles in the human gene-expression program.

Original languageEnglish (US)
Article number4
JournalBMC Biology
Volume5
DOIs
StatePublished - Mar 1 2007

Fingerprint

Untranslated RNA
androgen
androgens
Androgens
RNA
Transcription
protein
Proteins
proteins
transcription (genetics)
Genes
Chromatin Immunoprecipitation
Nucleic Acid Regulatory Sequences
Biosynthesis
Androgen Receptors
prostatic neoplasms
Microarrays
Oligonucleotide Array Sequence Analysis
Transcriptome
Gene expression

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Structural Biology
  • Ecology, Evolution, Behavior and Systematics
  • Physiology
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)
  • Plant Science
  • Developmental Biology
  • Cell Biology

Cite this

Louro, R., Nakaya, H. I., Amaral, P. P., Festa, F., Sogayar, M. C., da Silva, A. M., ... Reis, E. M. (2007). Androgen responsive intronic non-coding RNAs. BMC Biology, 5, [4]. https://doi.org/10.1186/1741-7007-5-4
Louro, Rodrigo ; Nakaya, Helder I. ; Amaral, Paulo P. ; Festa, Fernanda ; Sogayar, Mari C. ; da Silva, Aline M. ; Verjovski-Almeida, Sergio ; Reis, Eduardo M. / Androgen responsive intronic non-coding RNAs. In: BMC Biology. 2007 ; Vol. 5.
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Louro, R, Nakaya, HI, Amaral, PP, Festa, F, Sogayar, MC, da Silva, AM, Verjovski-Almeida, S & Reis, EM 2007, 'Androgen responsive intronic non-coding RNAs', BMC Biology, vol. 5, 4. https://doi.org/10.1186/1741-7007-5-4

Androgen responsive intronic non-coding RNAs. / Louro, Rodrigo; Nakaya, Helder I.; Amaral, Paulo P.; Festa, Fernanda; Sogayar, Mari C.; da Silva, Aline M.; Verjovski-Almeida, Sergio; Reis, Eduardo M.

In: BMC Biology, Vol. 5, 4, 01.03.2007.

Research output: Contribution to journalArticle

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T1 - Androgen responsive intronic non-coding RNAs

AU - Louro, Rodrigo

AU - Nakaya, Helder I.

AU - Amaral, Paulo P.

AU - Festa, Fernanda

AU - Sogayar, Mari C.

AU - da Silva, Aline M.

AU - Verjovski-Almeida, Sergio

AU - Reis, Eduardo M.

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N2 - Background: Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. Results: Using a custom-built cDNA microarray enriched in intronic transcribed sequences, we found 39 intronic non-coding RNAs for which levels were significantly regulated by androgen exposure. Orientation-specific reverse transcription-PCR indicated that 10 of the 13 were transcribed in the antisense direction. These transcripts are long (0.5-5 kb), unspliced and apparently do not code for proteins. Interestingly, we found that the relative levels of androgen-regulated intronic transcripts could be correlated with the levels of the corresponding protein-coding gene (asGAS6 and asDNAJC3) or with the alternative usage of exons (asKDELR2 and asITGA6) in the corresponding protein-coding transcripts. Binding of the androgen receptor to a putative regulatory region upstream from asMYO5A, an androgen-regulated antisense intronic transcript, was confirmed by chromatin immunoprecipitation. Conclusion: Altogether, these results indicate that at least a fraction of naturally transcribed intronic non-coding RNAs may be regulated by common physiological signals such as hormones, and further corroborate the notion that the intronic complement of the transcriptome play functional roles in the human gene-expression program.

AB - Background: Transcription of large numbers of non-coding RNAs originating from intronic regions of human genes has been recently reported, but mechanisms governing their biosynthesis and biological functions are largely unknown. In this work, we evaluated the existence of a common mechanism of transcription regulation shared by protein-coding mRNAs and intronic RNAs by measuring the effect of androgen on the transcriptional profile of a prostate cancer cell line. Results: Using a custom-built cDNA microarray enriched in intronic transcribed sequences, we found 39 intronic non-coding RNAs for which levels were significantly regulated by androgen exposure. Orientation-specific reverse transcription-PCR indicated that 10 of the 13 were transcribed in the antisense direction. These transcripts are long (0.5-5 kb), unspliced and apparently do not code for proteins. Interestingly, we found that the relative levels of androgen-regulated intronic transcripts could be correlated with the levels of the corresponding protein-coding gene (asGAS6 and asDNAJC3) or with the alternative usage of exons (asKDELR2 and asITGA6) in the corresponding protein-coding transcripts. Binding of the androgen receptor to a putative regulatory region upstream from asMYO5A, an androgen-regulated antisense intronic transcript, was confirmed by chromatin immunoprecipitation. Conclusion: Altogether, these results indicate that at least a fraction of naturally transcribed intronic non-coding RNAs may be regulated by common physiological signals such as hormones, and further corroborate the notion that the intronic complement of the transcriptome play functional roles in the human gene-expression program.

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Louro R, Nakaya HI, Amaral PP, Festa F, Sogayar MC, da Silva AM et al. Androgen responsive intronic non-coding RNAs. BMC Biology. 2007 Mar 1;5. 4. https://doi.org/10.1186/1741-7007-5-4