The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1's meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae

Abstract

BOI1 and BOI2 are paralogs important for the actin cytoskeleton and polar growth. BOI1 encodes a meiotic transcript isoform with an extended 5'-untranslated region predicted to impair protein translation. It is, however, unknown how the isoform is repressed during mitosis, and if Boi1 is present during sporulation. By interpreting microarray data from MATa cells, MATa/α cells, a starving MATα/α control, and a meiosis-impaired rrp6 mutant, we classified BOI1's extended isoform as early meiosis-specific. These results were confirmed by RNA-Sequencing, and extended by a 5'-RACE assay and Northern blotting, showing that meiotic cells induce the long isoform while the mitotic isoform remains detectable during meiosis. We provide evidence via motif predictions, an in vivo binding assay and genetic experiments that the Rpd3/Sin3/Ume6 histone deacetylase complex, which represses meiotic genes during mitosis, also prevents the induction of BOI1's 5'-extended isoform in mitosis by direct binding of Ume6 to its URS1 target. Finally, we find that Boi1 protein levels decline when cells switch from fermentation to respiration and sporulation. The histone deacetylase Rpd3 is conserved, and eukaryotic genes frequently encode transcripts with variable 5'-UTRs. Our findings are therefore relevant for regulatory mechanisms involved in the control of transcript isoforms in multi-cellular organisms.

Transcription of a 5’ extended mRNA isoform directs dynamic chromatin changes and interference of a downstream promoter

“…During budding yeast meiosis, more than 190 genes express an extended 5’ leader sequence ( Brar et al, 2012 ). Some examples have been further confirmed and show a clear inhibitory effect on expression from the downstream promoter ( Liu et al, 2015 ; Xie et al, 2016 ). However, how the expression of different mRNA isoforms regulate gene expression remains unexplored at the genome-wide level.…”

Kinetochore inactivation by expression of a repressive mRNA

“…Analysis of the mRNA-seq and ribosome profiling datasets of meiotic yeast revealed hundreds of transcripts with potential luti-like signatures ( Brar et al, 2012 ). In support of this idea, two other genes, ORC1 and BOI1 , have been shown to express meiosis-specific transcript isoforms with uORF-containing leader extensions ( Xie et al, 2016 and Liu et al, 2015 ). Rather than dissecting each candidate luti-mRNA on a case by case basis, future studies that integrate additional genome-wide datasets to measure stage-specific transcription factor binding sites, transcription-coupled chromatin modification states, mRNA translation status with isoform specificity and protein abundance would result in a high-confidence map of luti-mRNAs and aid in the dissection of their cellular functions.…”

Tunable Transcriptional Interference at the Endogenous Alcohol Dehydrogenase Gene Locus inDrosophila melanogaster

“…In addition to non-coding RNAs, mRNA isoforms have also been linked to transcriptional interference. For genes with more than one promoter, transcription from the distal promoter may not only produce a distinct mRNA isoform, but could also lead to the repression of an mRNA isoform transcribed from the open reading frame (ORF)-proximal gene promoter (Corbin and Maniatis, 1989;Moseley et al, 2002;Sehgal et al, 2008;Liu et al, 2015;Chen et al, 2017). In addition, since distinct mRNA isoforms may differ in their translational efficiency, regulation of promoter choice may impact gene expression at the protein level.…”