Extended Data Fig. 10. Chromatin immunoprecipitation reveals increased histone acetylation and propionylation at propionate-responsive genes.
(a) Proportion of genes marked by a peak of H3K27ac, Kpr, or both modifications at the promoter, for unaffected and differentially expressed genes in amPA mice. (b) Overlap of H3K27ac or Kpr peaks in female amWT and amPA mice. (c) Log2-fold change in H3K27ac or Kpr levels in amPA mice relative to amWT mice at the promoters of active genes that are unaffected or sensitive to both PA in vivo and propionate in vitro. Dashed line shows the median log2-fold change for unaffected genes. Upper and lower hinges showing 25th and 75th percentile, respectively. Upper and lower whiskers extend to the largest and smallest datapoints within 1.5 times the interquartile range of either hinge. (d) Concentration-dependence of propionate effect on H3K27ac ChIP-qPCR at Pde9a and Mme promoters in NRVMs. N = 4 matched biologically independent samples per condition from 4 isolations. Repeated measures one-way ANOVA with Dunnett’s multiple comparisons test. * P < 0.05. Mean ± SEM. (e) Reference-normalised ChIP-seq for H3K27ac in cultured neonatal rat ventricular myocytes, either untreated (nrCON) or treated with 6 mM propionate (nrPRO) for 48-h. ChIP-seq tracks are shown at Pde9a and Mme. (f) Metaplots showing the mean level of H3K27ac at active gene promoters in cultured neonatal rat ventricular myocytes treated with 6 mM propionate (nrPRO) for 48-h or control (nrCON). (g) Overlap of H3K27ac peaks in untreated (nrCON) NRVMs or myocytes treated with 6 mM propionate for 48-h (nrPRO). (h) Median log2-fold change in H3K27ac in treated (nrPRO) versus untreated (nrCON) myocytes for genes that are up-regulated, down-regulated or unaffected by propionate treatment in vitro. Error bars show 95% confidence intervals. **** P < 0.0001. (i) ChIP-qPCR at the Pde9a and Mme promoters for H3K27ac and Kpr cultured myocytes, showing increase in nrPRO, relative to nrCON. N = 4 biologically independent samples per condition from 4 isolations. */** P < 0.05/0.01. Mean ± SEM.