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Figure 1 | Epigenetics & Chromatin

Figure 1

From: Chd1 co-localizes with early transcription elongation factors independently of H3K36 methylation and releases stalled RNA polymerase II at introns

Figure 1

Nucleosome occupancy in chd1Δ. (A) Average nucleosome profile for all genes (n =5,207) shows that nucleosome occupancy is reduced at gene bodies in chd1Δ. The X-axis shows genomic position relative to the transcription start site (TSS). The Y-axis represents average read counts per million reads (M). (B) Example of smoothing MNase-seq read data using a spline function. Smoothing removes the noise caused by fluctuations in read coverage that can give erroneous correlation coefficients. Blue line is the raw, binned read count data and the red line is smoothed (C) Smoothing followed by Pearson correlation, called shapeDiff analysis, measures the nucleosome occupancy similarity as 0.31 between wild-type (WT) and chd1Δ over the transcribed region of RPL37B. MET14 has a high correlation coefficient between WT and chd1Δ as determined by shapeDiff due to high similarity of nucleosome occupancy profiles. (D) Average nucleosome profile for RP genes (n =136) shows strong nucleosome disruption upon deletion of CHD1. The shaded bands represent the 95% confidence interval of the data. (E) Quantitation of nucleosome disruption at ribosomal protein (RP) genes after heat shock or upon deletion of CHD1 (chd1Δ). The Y axis shows the correlation coefficient as measured by shapeDiff for genes in each class as indicated on the X-axis.

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