The first sentence from a recent paper in RNA:
Noncoding RNAs (ncRNAs) are widespread transcripts occurring from yeast to human, but their functions remain unclear (Kapranov et al. 2002; Rinn et al. 2003; Yelin et al. 2003; Cheng et al. 2005; Davis and Ares 2006;Neil et al. 2009).
Um, what the heck! ncRNAs have been known in plants for quite some time – at least 5 years.
Oh well. The paper itself is interesting – talking about how short intragenic RNAs* modulate transcription of their associated gene. The suggestion (based on experimental data) that the specific ncRNAs in this case are not transcribed by polII adds yet one more twist to the interconnections between polymerases, chromatin modifications, and regulation.
And, yes, it’s almost for certain that these things happen in plants.
Inter- and intragenic noncoding transcription is widespread in eukaryotic genomes; however, the purpose of these types of transcription is still poorly understood. Here, we show that intragenic sense-oriented transcription within the budding yeast ASP3 coding region regulates a constitutively and immediately accessible promoter for the transcription of full-length ASP3. Expression of this short intragenic transcript is independent of GATA transcription factors, which are essential for the activation of full-length ASP3, and independent of RNA polymerase II (RNAPII). Furthermore, we found that an intragenic control element is required for the expression of this noncoding RNA (ncRNA). Continuous expression of the short ncRNA maintains a high level of trimethylation of histone H3 at lysine 4 (H3K4me3) at the ASP3 promoter and makes this region more accessible for RNAPII to transcribe the full length ASP3. Our results show for the first time that intragenic noncoding transcription promotes gene expression.
The citation and link:
Huang YC, Chen HT, Teng SC. 2010. Intragenic transcription of a noncoding RNA modulates expression of ASP3 in budding yeast. RNA 16, 2086-2093.
* – short intragenic RNAs are non-coding RNAs (ncRNAs) that are transcribed from within a larger gene or transcription unit. The ones described in this report are in the sense orientation, but antisense short intragenic ncRNAs are also possible.