Fig. 7: ChIP reveals increased histone acetylation and propionylation at propionate-responsive genes.
a, 13C tracing of propionyl-CoA sourced from propiogenic substrates (isoleucine/valine) or exogenous propionate to identify propionylation sites on histone H3 under baseline and elevated propionate signaling, respectively. Lysine propionylation was identified by LC–MS/MS. Heat map shows label-free quantification intensity for the various lysines (x axis). The modifications include stable (unlabeled) propionylation (Pro) (‘unlab C3’) or (iso)butyration (‘unlab C4’) or propionylation with one labeled carbon from 1-13C-propionate (1-13C Pro) or three labeled carbons from 13C Ile/Val (3-13C Pro). Gray indicates no signal detected. Intensity is expressed as log10. Residues grouped by brackets are present on the same peptide fragment. b, Reference-normalised ChIP-seq in female amWT and amPA mouse hearts, using antibodies against histone H3K27ac and pan-propionylation (Kpr). ChIP-seq tracks are shown at the Pde9a and Mme promoter loci. c, Overlap of H3K27ac and Kpr peaks in female amWT mice. d, Correlation of H3K27ac and Kpr levels at H3K27ac peaks in female amPA mice. e, Metaplots showing the mean level of H3K27ac or Kpr at active gene promoters in female amWT or amPA mice relative to the transcriptional start site (TSS). f, Median log2(fold change (FC)) (amPA to amWT) in H3K27ac or Kpr levels for genes that are upregulated, downregulated or unaffected in PA. Error bars show 95% confidence intervals. ****P < 0.0001. g, ChIP–qPCR at the Pde9a and Mme promoters using antibodies against H3K27ac (n = 8 biologically independent samples per genotype), pan-Kpr (n = 3 amWT and n = 5 amPA biologically independent samples) and H3K23pr (n = 3 biologically independent samples per genotype). Locations of primer pairs are shown in b. Unpaired two-tailed t-tests. */** P < 0.05/<0.01. Mean ± s.e.m. h, ChIP–qPCR at the promoters of Pde9a, Mme and Gsta3 for H3K27ac in male or female amWT and amPA mice. PA was associated with a significant increase in H3K27ac only in females. n = 4 biologically independent samples. Ordinary two-way ANOVA with Tukey’s multiple comparisons test. */*** P < 0.05/<0.001. Mean ± s.e.m. F, female; Ile, isoleucine; M, male; Unlab, unlabeled; Unmodif., unmodified; Val, valine.
