Androgen responsive intronic non-coding RNAs

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.

Authors thank Junio Cota Silva and Vinícius Coutinho for technical help with RACE experiments. This work was mainly funded by grant 02/132836 from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) to SVA and AMDS, by grant 03465 RG/BIO/LA from TWAS to EMR, by grant 01/107077 to MCS from FAPESP and by fellowships to RL and HIN from FAPESP. Fellowships from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) supported PPA and FF. MCS, AMDS and SVA were partially supported by CNPq.

Authors thank Junio Cota Silva and Vinícius Coutinho for technical help with RACE experiments. This work was mainly funded by grant 02/13283-6 from Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) to SVA and AMDS, by grant 03-465 RG/BIO/LA from TWAS to EMR, by grant 01/10707-7 to MCS from FAPESP and by fellowships to RL and HIN from FAPESP. Fellowships from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) supported PPA and FF. MCS, AMDS and SVA were partially supported by CNPq.