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

  1. Minghao Chia
  2. Amy Tresenrider
  3. Jingxun Chen
  4. Gianpiero Spedale
  5. Victoria Jorgensen
  6. Elçin Ünal  Is a corresponding author
  7. Folkert Jacobus van Werven  Is a corresponding author
  1. The Francis Crick Institute, United Kingdom
  2. University of California, Berkeley, United States
6 figures and 3 additional files

Figures

Figure 1 with 1 supplement
NDC80luti transcription represses the NDC80ORF promoter.

(A) Expression pattern of two NDC80 mRNA isoforms during starvation and early meiosis. Diploid control cells (FW4644) or cells harboring the CUP1 promoter fused with IME1 and IME4 (pCUP-IME1/pCUP-IME…

https://doi.org/10.7554/eLife.27420.002
Figure 1—figure supplement 1
NDC80luti transcription represses the NDC80ORF promoter.

(A) The same northern blot and western blot of NDC80 expression during a meiotic time course as described in Figure 1A, except that CIT1 and ribosomal RNA expression levels are also displayed. (B) …

https://doi.org/10.7554/eLife.27420.003
Transcription of NDC80luti promotes H3K4me2 and H3K36me3 in the promoter and 5’ region of NDC80ORF.

(A) NDC80luti transcription promotes histone H3 lysine 4 dimethylation (H3K4me2) in the NDC80ORF promoter. Wild-type (FW1902) and set1Δ (FW3033) cells harboring the pCUP-IME1/pCUP-IME4 were induced …

https://doi.org/10.7554/eLife.27420.004
Figure 3 with 1 supplement
Set2 and Set3 mediate NDC80luti induced gene repression of NDC80ORF.

(A) Set2 and Set3 are required for repression of NDC80ORF expression during early meiosis. Control (FW1902), set2Δ (FW2929), set3Δ (FW2928) and set2Δset3Δ (FW1922) cells harboring pCUP-IME1/pCUP-IME4

https://doi.org/10.7554/eLife.27420.005
Figure 3—figure supplement 1
The Set2 and the Set3 mediate NDC80luti induced gene repression of NDC80ORF.

(A) Quantification of NDC80ORF and NDC80luti levels in the experiment described in Figure 3A. Signals are normalized to SCR1. To control for variation in overall signal between different northern …

https://doi.org/10.7554/eLife.27420.006
Figure 4 with 1 supplement
NDC80luti mediated repression is reversible.

(A) Schematic overview of the experimental set-up. (B) Cells repress NDC80luti and induce NDC80ORF when returned to a nutrient rich environment (YPD). Cells harboring ndt80Δ and pCUP-IME1/pCUP-IME4

https://doi.org/10.7554/eLife.27420.007
Figure 4—figure supplement 1
NDC80luti mediated repression is reversible.

(A) Quantification of NDC80luti during return to rich medium as described in Figure 4B. RNA was extracted, reverse transcribed, and NDC80luti mRNA levels were determined by quantitative PCR. Signals …

https://doi.org/10.7554/eLife.27420.008
Figure 5 with 1 supplement
Gene repression by NDC80luti is tunable.

(A) Adjustable expression of NDC80luti using the LexA-lexO system. Spot assay of cells harboring 0, 1, 2, 3, or 8 lexO binding sites in the NDC80luti promoter (UB8374, UB8358, UB8362, UB8366, …

https://doi.org/10.7554/eLife.27420.009
Figure 5—figure supplement 1
Gene repression by NDC80luti is tunable.

(A) NDC80luti levels in the presence of variable number of lexO sites in the NDC80luti promoter. Cells harboring 0, 1, 2, 3, or 8 lexO and LexA-ER-AD (UB8374, UB8358, UB8362, UB8366, and UB8370) …

https://doi.org/10.7554/eLife.27420.010
Model for NDC80luti mediated repression of NDC80ORF.

During mitosis the NDC80ORF promoter has an open chromatin structure and NDC80ORF is transcribed. During meiotic S-phase and meiotic prophase, transcription of NDC80luti deposits Set1-dependent …

https://doi.org/10.7554/eLife.27420.011

Additional files

Supplementary file 1

Table of yeast strains used in this study.

Table describing genotypes of the strains.

https://doi.org/10.7554/eLife.27420.012
Supplementary file 2

Table of oligo nucleotide sequences used in this study.

Table describing oligo nucleotide sequences used for quantitative PCR and for preparing the northern blot probes.

https://doi.org/10.7554/eLife.27420.013
Transparent reporting form
https://doi.org/10.7554/eLife.27420.014

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