Supplementary Figure 8: Iron depletion causes defects in RNA processing similar to those observed in the mtl1 mutant cells.
From: Iron homeostasis regulates facultative heterochromatin assembly in adaptive genome control
(a) Schematic of cryptic introns detected using RNA-seq in wild-type cells untreated or treated with 250µM Dip, and mtl1-1 mutant cells grown at 30 °C. The arcs below or above the line represent intron junction reads that map to the bottom or top DNA strands. (b) Hierarchical clustering of the indicated strains based on Pearson's correlation coefficients determined using RNA-seq (log2 fold change versus wild-type cells grown at 30 °C). Pairwise comparisons were performed (n = 6380 transcripts per comparison) and Pearson's correlation coefficients were converted into a color gradient. RNA-seq data for Dip-treated wild-type and clr4Δ cells grown at 18 °C and 30 °C were compared to various RNA processing mutants such as RNAi components (ago1Δ and dcr1Δ), nuclear RNA elimination factors (mmi1Δ, erh1Δ, red1Δ and mtl1-1), and CCR4-NOT complex (ccr4Δ) cultured at 30 °C. cwf10-1 splicing factor mutant was cultured at 26 °C. Also included is Clr6 HDAC mutant (clr6-1) grown at 30 °C that shows de-repression of genes affected by clr4Δ at 18 °C. Notice the high correlation between RNA processing mutant mtl1-1 and cells depleted for iron or lacking Clr4. (c) Density plots comparing transcripts (n = 6380) in mtl1-1 cells grown at 30 °C and wild-type cells treated with 250 µM Dip and grown at 30 °C (upper) or 18 °C (lower). Pearson's correlation coefficients (r) and the P values of the linear regressions are indicated. Source Data for Supplementary Fig. 8a are available with the paper online.
