Intragenic transcription of a noncoding RNA modulates expression of ASP3 in budding yeast

Abstract

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 fulllength ASP3. Our results show for the first time that intragenic noncoding transcription promotes gene expression.

A current view on long noncoding RNAs in yeast and filamentous fungi

“…ncASP3 is expressed in both cases, when nitrogen is available and upon nitrogen depletion, and maintains an open chromatin configuration at ASP3 by mediating trimethylation of H3K4. Thus, ASP3 is kept in an accessible status, allowing immediate expression upon the onset of NCR (Huang et al 2010 ).…”

LncRNAs: Bridging environmental sensing and gene expression

“…Finally, as more efforts are put forth to decipher the role of the non-coding genome, it must be emphasized that some of these long non-coding RNAs have been detected with translating ribosomes. 88 Although no examples of lncRNAs that produce functional peptides have been documented to date, we should continue to view the term 29 Promotes induction MMF1 Mitochondrial protein YES ASP3 lncRNA 98 Upregulation ASP3 Asparagine catabolism YES PHO84 AS RNA [99][100][101] Repression PHO84 Phosphate metabolism YES SRG1 28,50,51 Repression SER3 Serine / glycine biogenesis YES PHO5 AS RNA 102 Promotes induction PHO5 Phosphate metabolism YES usURA2. 103 Repression URA2 Pyrimidine biogenesis YES usDCI1.…”

Increased Binding of Stroke-Induced Long Non-Coding RNAs to the Transcriptional Corepressors Sin3A and coREST

“…However, our data indicate that the stroke-induced lncRNAs expressed from intragenic loci does not exhibit a cis inhibitory effect. Instead, these lncRNAs might either induce or serve to maintain the expression of the protein-coding transcripts at a normal level by activating the epigenetic signatures as demonstrated previously (Huang et al, 2010). Furthermore, some lncRNAs showed coexpression with their corresponding protein-coding genes while others did not.…”