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

RNA Biol. 2016 Sep;13(9):772-82. doi: 10.1080/15476286.2016.1191738. Epub 2016 Jun 30.


The origin of replication complex subunit ORC1 is important for DNA replication. The gene is known to encode a meiotic transcript isoform (mORC1) with an extended 5'-untranslated region (5'-UTR), which was predicted to inhibit protein translation. However, the regulatory mechanism that controls the mORC1 transcript isoform is unknown and no molecular biological evidence for a role of mORC1 in negatively regulating Orc1 protein during gametogenesis is available. By interpreting RNA profiling data obtained with growing and sporulating diploid cells, mitotic haploid cells, and a starving diploid control strain, we determined that mORC1 is a middle meiotic transcript isoform. Regulatory motif predictions and genetic experiments reveal that the activator Ndt80 and its middle sporulation element (MSE) target motif are required for the full induction of mORC1 and the divergently transcribed meiotic SMA2 locus. Furthermore, we find that the MSE-binding negative regulator Sum1 represses both mORC1 and SMA2 during mitotic growth. Finally, we demonstrate that an MSE deletion strain, which cannot induce mORC1, contains abnormally high Orc1 levels during post-meiotic stages of gametogenesis. Our results reveal the regulatory mechanism that controls mORC1, highlighting a novel developmental stage-specific role for the MSE element in bi-directional mORC1/SMA2 gene activation, and correlating mORC1 induction with declining Orc1 protein levels. Because eukaryotic genes frequently encode multiple transcripts possessing 5'-UTRs of variable length, our results are likely relevant for gene expression during development and disease in higher eukaryotes.

Keywords: 5′-UTR; Bi-directional promoter; MSE; NDT80; ORC1; SMA2; SUM1; isoform; meiosis; sporulation.

MeSH terms

  • Binding Sites
  • Cluster Analysis
  • DNA-Binding Proteins / metabolism*
  • Datasets as Topic
  • Gene Expression Profiling
  • Gene Expression Regulation, Fungal
  • Meiosis / genetics*
  • Models, Biological
  • Nucleotide Motifs
  • Origin Recognition Complex / genetics*
  • Promoter Regions, Genetic
  • Protein Binding
  • RNA Isoforms
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism*
  • Saccharomyces cerevisiae Proteins / genetics*
  • Saccharomyces cerevisiae Proteins / metabolism*
  • Spores, Fungal / genetics
  • Transcription Factors / metabolism*
  • Transcription, Genetic*


  • DNA-Binding Proteins
  • NDT80 protein, S cerevisiae
  • ORC1 protein, S cerevisiae
  • Origin Recognition Complex
  • RNA Isoforms
  • Saccharomyces cerevisiae Proteins
  • Sma2 protein, S cerevisiae
  • Transcription Factors