Meiosis-induced alterations in transcript architecture and noncoding RNA expression in S. cerevisiae

Abstract

Changes in transcript architecture can have powerful effects on protein expression. Regulation of the transcriptome is often dramatically revealed during dynamic conditions such as development. To examine changes in transcript architecture we analyzed the expression and transcript boundaries of protein-coding and noncoding RNAs over the developmental process of meiosis in Saccharomyces cerevisiae. Custom-designed, high-resolution tiling arrays were used to define the time-resolved transcriptome of cells undergoing meiosis and sporulation. These arrays were specifically designed for the S. cerevisiae strain SK1 that sporulates with high efficiency and synchrony. In addition, new methods were created to define transcript boundaries and to identify dynamic changes in transcript expression and architecture over time. Of 8407 total segments, 699 (8.3%) were identified by our algorithm as regions containing potential transcript architecture changes. Our analyses reveal extensive changes to both the coding and noncoding transcriptome, including altered 59 ends, 39 ends, and splice sites. Additionally, 3910 (46.5%) unannotated expressed segments were identified. Interestingly, subsets of unannotated RNAs are located across from introns (anti-introns) or across from the junction between two genes (anti-intergenic junctions). Many of these unannotated RNAs are abundant and exhibit sporulation-specific changes in expression patterns. All work, including heat maps of the tiling array, annotation for the SK1 strain, and phastCONS conservation analysis, is available at http://groups.molbiosci.northwestern. edu/sontheimer/sk1meiosis.php. Our high-resolution transcriptome analyses reveal that coding and noncoding transcript architectures are exceptionally dynamic in S. cerevisiae and suggest a vast array of novel transcriptional and post-transcriptional control mechanisms that are activated upon meiosis and sporulation.

Extensive Transcript Diversity and Novel Upstream Open Reading Frame Regulation in Yeast

“…They also reported that in the case of uORFs with an AUG start codon, the translational efficiency and ribosome occupancy showed a “strong negative correlation” (Brar et al 2012). A subsequent microarray-based study of meiotic yeast confirmed the presence of abundant transcript architecture changes in meiotic and sporulating yeast (Kim Guisbert et al 2012). …”

Global alterations of the transcriptional landscape during yeast growth and development in the absence of Ume6-dependent chromatin modification

“…Given that the budding yeast transcriptome comprises mRNAs, developmental stage-specific mRNA isoforms with extended 5′- and 3′-UTRs and long non-coding RNAs (lncRNAs), it seems reasonable to assume that Ume6 is not only important for the former two transcript categories, but also for RNAs with little or no coding potential (Cho et al 1998; Chu et al 1998; Primig et al 2000; Wyers et al 2005; Nagalakshmi et al 2008; Xu et al 2009; Lardenois et al 2011, 2014; Kim Guisbert et al 2012; Waern and Snyder 2013). Indeed, we have observed by RT-PCR assays that ume6 / ume6 and rpd3 / rpd3 mutant cells cultured in YPD and YPA accumulate a number of lncRNAs, such as meiotic unannotated transcripts (MUTs), cryptic unstable transcripts (CUTs), and stable unannotated transcripts (SUTs) to higher levels than the wild-type control strain (Y. Liu and B. Xie, unpublished).…”

Ndt80 activates the meiotic ORC1 transcript isoform and SMA2 via a bi-directional middle sporulation element in Saccharomyces cerevisiae

“…6,7 Recent studies using tiling arrays and RNA-Sequencing helped explain this puzzling fact: cells induce a long transcript isoform with an extended 5 0 -UTR proposed to inhibit Orc1 translation. 13,29 However, neither microarrays nor RNA-Seq experiments unambiguously show that the 5 0 -extended isoform is synthesized through to the same transcription termination site (TTS) as the short isoform. We propose that data in previously published work and this study are consistent with the notion that both isoforms use a common TTS as the model in Fig.…”