Dome-stage histone modifications.
<p><b>(A)</b> Heatmaps of CUT&RUN coverage as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003239#pbio.3003239.g001" target="_blank">Fig 1F</a> showing individual replicates. <b>(B)</b> Strand-specific...
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2025
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| Tóm tắt: | <p><b>(A)</b> Heatmaps of CUT&RUN coverage as in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.3003239#pbio.3003239.g001" target="_blank">Fig 1F</a> showing individual replicates. <b>(B)</b> Strand-specific sphere-stage nascent RNA-seq coverage over the two promoter classes, High H3K4me2/3 and Low H3K4me2/3. Heatmaps are centered on the TSS with ±0.5 kb context. RPKM = Reads per kilobase per million transcripts. <b>(C)</b> Heatmaps of regions stratified by the fourth principal component (PC4) of the pooled PCA, which H3K56ac strongly contributes to. H3K56ac has been proposed to be an Oct4-associated enhancer mark in mouse ES cells (Tan and colleagues, 2013). PC4 high = ATAC-seq regions with PC4 values greater than the 1 standard deviation from 0, PC4 low = less than −1 * standard deviation. Enhancers stratified by PC4 have differential H3K56ac, but do not differ in other enhancer-associated marks. Parallel heatmaps of Nanog, Pou5f3 (Oct4 homolog), and Sox19b ChIP-seq coverage (data from Miao and colleagues, 2022) demonstrate no correlation with PC4/ H3K56ac. No differences are seen among promoters either. Thus, H3K56ac likely does not define a distinct regulatory element class in zebrafish embryos. <b>(D)</b> Heatmaps of regions enriched for H3K122ac (>2-fold over IgG), stratified by H3K27ac co-enrichment (<1.25-fold or >1.5-fold), showing very few regions marked by H3K122ac without H3K27ac. Pradeepa and colleagues (2016) identified a subclass of H3K122ac+/H3K64ac+/H3K27ac− enhancers in mouse, but enhancers with that pattern do not seem to be prevalent in zebrafish embryos.</p> <p>(EPS)</p> |
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