The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development

Abstract

It was recently reported that the sizes of many mRNAs change when budding yeast cells exit mitosis and enter the meiotic differentiation pathway. These differences were attributed to length variations of their untranslated regions. The function of UTRs in protein translation is well established. However, the mechanism controlling the expression of distinct transcript isoforms during mitotic growth and meiotic development is unknown. In this study, we order developmentally regulated transcript isoforms according to their expression at specific stages during meiosis and gametogenesis, as compared to vegetative growth and starvation. We employ regulatory motif prediction, in vivo protein-DNA binding assays, genetic analyses and monitoring of epigenetic amino acid modification patterns to identify a novel role for Rpd3 and Ume6, two components of a histone deacetylase complex already known to repress early meiosis-specific genes in dividing cells, in mitotic repression of meiosis-specific transcript isoforms. Our findings classify developmental stage-specific early, middle and late meiotic transcript isoforms, and they point to a novel HDAC-dependent control mechanism for flexible transcript architecture during cell growth and differentiation. Since Rpd3 is highly conserved and ubiquitously expressed in many tissues, our results are likely relevant for development and disease in higher eukaryotes.

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

“…Contrary to early meiotic transcript isoforms present in mitotic ume6 cells, 23 one would not expect middle meiotic transcript isoforms such as mORC1 to strongly accumulate in a fermenting sum1 mutant because their activator Ndt80 is undetectable in cells cultured in rich medium. Indeed, we find that mORC1 is weakly de-repressed in fermenting JHY222 sum1 cells and during incubation in sporulation medium.…”

“…9,23,24 Initially, we focused on meiotic lncRNAs and later on developmentally regulated transcript isoforms with extended 5 0 -UTRs. Published tiling array data are available at the ReproGenomics Viewer (RGV, rgv.genouest.org; Fig.…”

“…9,23 The ORC1 locus is, however, an interesting case: its mRNA is cell cycle regulated in mitotically growing cells and strongly induced during meiotic development, although the the protein it encodes is a priori dispensable after pre-meiotic DNA replication is finished.…”

“…23 In the case of ORC1, tiling array data and RNA-Sequencing data from starving SK1 MATa/a cells cultured in sporulation medium indicate that they do not induce the long isoform. We conclude that mORC1's transcriptional activation or its stability (or both) depend on meiosis ( Fig.…”

“…8 implies. 13,23 A key question that we sought to answer is which regulator activates mORC1 and SMA2 at the onset of meiotic Mphase. The presence of an MSE prompted us to assay mORC1 induction in an ndt80 mutant strain and we found that the long transcript isoform does not accumulate to normal levels in the absence of Ndt80.…”