Fig. 4: MUSHER enhances PIR1 expression independently of its role in DOG1 regulation. | Nature Communications

Fig. 4: MUSHER enhances PIR1 expression independently of its role in DOG1 regulation.

From: Chromatin retained MUSHER lncRNA integrates ABA and DOG1 signalling pathways to enhance Arabidopsis seeds dormancy

Fig. 4

a Volcano plot showing differentially expressed genes for WT and msh-1 selected using DESeq2; absolute log2FC >  log2 (1.5), FDR  <  0.05, n = 4. DOG1 and PIR1 genes are highlighted. The number of downregulated (down) and upregulated (up) genes is provided on the plot. b Diagram of 3′RNA-seq reads for PIR1 locus in WT and msh-1 mutant. Schematic diagram showing PIR1 locus: exons (grey rectangles), 3’UTR region (grey arrow) c The PIR1 relative expression level in freshly harvested seeds (primary dormancy) of WT, msh-1 and dog1-4 mutants, normalised to UBC21 and relative to WT. Data are presented as mean values of four biological replicates +/− SD (p-value from the two-tailed t-test, *p < 0.05). *p < 0.05. d The PIR1 relative expression level in WT msh-1, dog1-4 and cpl1-7 mutant seeds, after 5 days of SD induction, normalised to UBC21 and relative to WT. Data are presented as mean values of four biological replicates +/− SD (p-value from the two-tailed t-test, *p < 0.05). e Pol II f H3 g H3K4me3 and h H3K27me3 occupancy was measured by ChIP-qPCR in WT, msh-1. (n = 4) H3K4me3 and H3K27me3 values were normalised to H3 and to ACTIN7 (AT5G09810); Pol II and H3 were normalised to ACTIN7 (AT5G09810). For all ChIP experiments *P < 0.05, ns - not significant (two-tailed t-test). Error bars represent the standard deviation of four biological replicates. H3, H3K4me3 and H3K27me3 (f–h) ChIP were done side by side and share NoAB control shown on panel h.

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