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. 2022 Mar 28;50(7):3727–3744. doi: 10.1093/nar/gkac175

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© The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 1. — Glucose starvation increases H3K9 methylation in rDNA. (A) Time course of ChIP-qPCR experiments examining H3K9me2 levels in 18S (filled squares) and 28S rDNA (open circles) (mean ± SEM: n = 3). (B) Data of ChIP-qPCR showing the H3K9me3 levels in 18S (filled squares) and 28S rDNA (open circles) (mean ± SEM: n = 3). (C) ChIP-qPCR showing the total H3 levels in 18S (filled squares) and 28S rDNA (open circles) after glucose starvation (mean ± SEM: n = 3). (D) Graph showing the ratios of H3K9me2 (filled rhombus) and H3K9me3 (open triangles) relative to total H3. The average values of H3K9me2 and H3K9me3 in the three independent experiments are compared with that of the total H3 in the three independent experiments. Times indicate minutes after glucose starvation. (E) ChIP-qPCR data showing the amount of H3 in 18S rDNA, the act1⁺ gene, and the promoter of the fbp1⁺ gene in a glucose-rich medium (mean + SEM: n = 3). (F) Graph showing the ratio of H3K9me2 relative to total H3 in 18S rDNA, the act1⁺ gene and the promoter of the fbp1⁺ gene. The average values of H3K9me2 in the three independent experiments are compared with that of total H3 in the three independent experiments. (G) ChIP-seq profile of H3K9me2 in rDNA during glucose-rich (upper) and -poor conditions (lower). Red horizontal lines indicate the positions of regions with highly methylated H3K9 under glucose-rich conditions. The schematic diagram at the bottom indicates the rDNA annotated region. White arrows indicate the direction of transcription. The y-axis exhibits log₂ ratio of IP/input (0–4). (H and I) Enrichment of HP1 and Chp1 in 18S rDNA and dg (peri-centromere). GFP-Swi6 (H) and Chp1 (I) are shown (mean + SEM: n = 6). Samples for glucose starvation were taken at 120 min. (J) ChIP-qPCR of Nuc1-FLAG, a component of RNA polymerase I, in each rDNA element. 0, 15, 30 min indicate the time in glucose-starved medium (mean + SEM: n = 3). (K) Graph showing the amount of newly synthesized (nascent) 18S rRNA before and after glucose starvation (mean + SD: n = 3). Nascent 18S rRNA levels were normalized with that of act1⁺ mRNA.