Cytoplasmic Control of Sense-Antisense mRNA Pairs

Abstract

Transcriptome analyses have revealed that convergent gene transcription can produce many 3'-overlapping mRNAs in diverse organisms. Few studies have examined the fate of 3'-complementary mRNAs in double-stranded RNA-dependent nuclear phenomena, and nothing is known about the cytoplasmic destiny of 3'-overlapping messengers or their impact on gene expression. Here, we demonstrate that the complementary tails of 3'-overlapping mRNAs can interact in the cytoplasm and promote post-transcriptional regulatory events including no-go decay (NGD) in Saccharomyces cerevisiae. Genome-wide experiments confirm that these messenger-interacting mRNAs (mimRNAs) form RNA duplexes in wild-type cells and thus have potential roles in modulating the mRNA levels of their convergent gene pattern under different growth conditions. We show that the post-transcriptional fate of hundreds of mimRNAs is controlled by Xrn1, revealing the extent to which this conserved 5'-3' cytoplasmic exoribonuclease plays an unexpected but key role in the post-transcriptional control of convergent gene expression.

Native elongating transcript sequencing reveals global anti-correlation between sense and antisense nascent transcription in fission yeast

“…In S. cerevisiae, sense/antisense pairing has been debated, as it was first reported that sense and antisense transcripts never coexist in the same cell (Castelnuovo et al 2013). However, recent studies confirmed that although transcribed in a bimodal fashion, sense and antisense RNAs can coexist within the same cell (Nguyen et al 2014;Lenstra et al 2015) and form dsRNA structures in vivo (Drinnenberg et al 2011;Sinturel et al 2015;Wery et al 2016). In S. pombe, the most likely explanation is that Dicer and the asXUT/ mRNA duplexes are prevented for interaction due to different subcellular localization.…”

“…TSS and TTS correspond to gene (mRNA) transcription start site and transcription termination site, respectively. Note that the TSS to TTS region was first scaled to 1000 (virtual) nt, and the signal associated to each nucleotide was scaled upon polynomial interpolation, as previously described (Sinturel et al 2015). The shading surrounding each line denotes the 95% confidence interval.…”

sRNA-mediated activation of gene expression by inhibition of 5'-3’ exonucleolytic mRNA degradation

“…Xrn1 depletion of 5’ monophosphorylated RNA was performed as described in Sinturel et al (2015). Briefly, 15 µg of total RNA was digested for 1 hr at 37°C with 2 units of XrnI in NEB buffer 3.…”

Additional layer of regulation via convergent gene orientation in yeasts

“…Transcriptome analyses have shown that convergent gene pairs can produce tail-to-tail 3'-overlapping mRNA pairs that can theoretically form mRNA duplexes in S. cerevisiae Wilkening et al 2013) and in other eukaryotes (Jen et al 2005;Makalowska et al 2005;Sanna et al 2008). We previously demonstrated that such mRNAs duplexes exist extensively and can interact in the cytoplasm in Saccharomyces cerevisiae (Sinturel et al 2015). Some of these mRNA-mRNA interactions are apparently strong enough to promote post-transcriptional regulatory events by blocking ribosome elongation, as illustrated by mRNA duplex formation between OCA2 and POR1 mimRNAs.…”

“…Some of these mRNA-mRNA interactions are apparently strong enough to promote post-transcriptional regulatory events by blocking ribosome elongation, as illustrated by mRNA duplex formation between OCA2 and POR1 mimRNAs. Indeed, OCA2 mRNA was previously shown to overlap the protein coding sequence of POR1 mRNA, block ribosome elongation and trigger the no-go decay pathway (Doma and Parker 2006;Passos et al 2009;Sinturel et al 2015).…”