Fig. 4: CeSPT-2 histone binding controls chromatin accessibility.
From: The histone chaperone SPT2 regulates chromatin structure and function in Metazoa
a, Distribution of GFP::CeSPT-2 ChIP–seq peaks in different genome locations. b, Metagene profile of GFP::CeSPT-2 occupancy levels within the coding region of its target genes, compared to non CeSPT-2 target genes. c, GFP::CeSPT-2 chromatin occupancy regions were divided in quartiles, and gene expression levels (measured in synchronized WT adult worms) were plotted in each quartile, and compared to CeSPT-2 nontarget genes. The box represents the interquartile range, the whiskers the minimum and maximum (excluding outliers). n, nontargets: 20,117; first quartile: 545; second quartile: 544; third quartile: 544; fourth quartile: 544. Statistical differences: Benjamini–Hochberg-corrected pairwise Mann–Whitney test. ***P < 10−16. d, Chromatin accessibility at CeSPT-2 target genes in spt-2KO-A and spt-2HBM adult worms, measured by ATAC–seq and expressed in reads per million. TSS, transcription start site; TTS, transcription termination site. Two independent replicates of the ATAC–seq experiment were performed. e, Example of ATAC–seq and GFP::CeSPT-2 ChIP–seq tracks. The ATAC–seq signal across the gene body of ddo-2 in WT, spt-2KO-A and spt-2HBM worms is indicated, with the GFP::CeSPT-2 binding profile shown in the bottom profile. f, Fraction of genes with significantly increased accessibility in spt-2KO-A (dark gray) among CeSPT-2 nontarget and target genes. CeSPT-2 targets were divided in quartiles based on their CeSPT-2 enrichment. Statistical difference between CeSPT-2 targets and nontargets was measured by a chi-squared test. Benjamini–Hochberg corrected P values. P, nontargets versus first quartile: 0.0513; nontargets versus second quartile: 0.0035; nontargets versus third quartile: <10−16; nontargets versus fourth quartile: <10−16. g,h, Volcano plot of gene expression levels of CeSPT-2 target genes (g) and nontargets (h) in spt-2 null versus WT worms. Red points indicate genes with FDR <0.001 and log2 fold change >1 or <−1. In Extended Data Fig. 4e: validation by qPCR using independently collected RNA. i, GO analysis of the genes upregulated in the indicated spt-2 mutants. KO_UP, genes upregulated in spt-2 KO worms. ‘p.adjust’ values indicate Benjamini–Hochberg P values obtained through an hypergeometric test.
