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. 2021 Aug 20;49(16):9174–9193. doi: 10.1093/nar/gkab690

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© The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 4. — The CENP-A^HCP-3 domains/peaks on the endogenous chromosomes and on the prorogated AC. (A) Representative enrichment of CENP-A^HCP-3 and CENP-A^HCP-3 domains/peaks on chromosome I by current ChIP-seq replicates and previous ChIP-chip replicates. (B) The localization of CENP-A^HCP-3 enrichment on endogenous chromosomes between two ChIP-seq replicates are highly correlated. (C) The localization of CENP-A^HCP-3 enrichment on endogenous chromosomes detected by ChIP-seq is highly correlated to previous ChIP-chip results (18). The signal for each data set represents the average of two independent replicates. (D) Histogram plots of CENP-A^HCP-3 domain/peak sizes in endogenous chromosomes (left panel) and in AC (right panel). (E) Circos plot of CENP-A^HCP-3 domains/peaks on all endogenous chromosomes (left panel) and on all 49 AC contigs, including the longest contig tig8258 (right panel). The outside circle shows the CENP-A^HCP-3 domains/peaks called by MACS2. Y-axis is the signal value (overall enrichment) for the domains/peaks. The inside circle indicate the CENP-A^HCP-3 domains/peaks density in 10-kb windows. (F) Representative CENP-A^HCP-3 enrichment in a 800-kb region in endogenous Chromosome II (7200–8000 kb) and in AC contig tig8258 (200–1000 kb). CENP-A^HCP-3 domains/peaks were indicated as grey bars. The dashed box (1 319 126–1 347 939 bp) indicates the region enriched with yeast mitochondrial DNA (the zoom-in is shown in Figure 5A). (G) Dot plots of AT-content (%) of each CENP-A^HCP-3 domain/peak against its size in endogenous chromosomes (left panel) and in AC (right panel). The 2D density plots were indicated by contour lines (bin = 7). The linear regression line to the scatter plot model was shown with 95% confidence region (grey shading). The average C. elegans genomic and AC AT-contents are indicated by the blue dotted lines, respectively. (H) The empirical cumulative distribution functions (ECDF) of interval distances between CENP-A^HCP-3 domains/peaks on endogenous chromosomes (blue) and AC (red). (I) The CENP-A^HCP-3 enrichment profiles and heatmaps of the 2-kb flanking regions surrounding the center of each CENP-A^HCP-3 domain/peak for endogenous chromosomes and AC. Consensus CENP-A^HCP-3 domains/peaks are separated into four clusters by k-means clustering. The profile plots (upper panel) show the average ChIP signals of each cluster. The ChIP signals of each domain/peak are shown in the clustered heatmaps (lower panel), in which the color coding on the right indicates the log₂ CENP-A^HCP-3 ratio. The schematic on the left and right show the possible distribution of CENP-A^HCP-3 nucleosomes interspaced in between H3 nucleosomes.

Figure 4. — The CENP-A^HCP-3 domains/peaks on the endogenous chromosomes and on the prorogated AC. (A) Representative enrichment of CENP-A^HCP-3 and CENP-A^HCP-3 domains/peaks on chromosome I by current ChIP-seq replicates and previous ChIP-chip replicates. (B) The localization of CENP-A^HCP-3 enrichment on endogenous chromosomes between two ChIP-seq replicates are highly correlated. (C) The localization of CENP-A^HCP-3 enrichment on endogenous chromosomes detected by ChIP-seq is highly correlated to previous ChIP-chip results (18). The signal for each data set represents the average of two independent replicates. (D) Histogram plots of CENP-A^HCP-3 domain/peak sizes in endogenous chromosomes (left panel) and in AC (right panel). (E) Circos plot of CENP-A^HCP-3 domains/peaks on all endogenous chromosomes (left panel) and on all 49 AC contigs, including the longest contig tig8258 (right panel). The outside circle shows the CENP-A^HCP-3 domains/peaks called by MACS2. Y-axis is the signal value (overall enrichment) for the domains/peaks. The inside circle indicate the CENP-A^HCP-3 domains/peaks density in 10-kb windows. (F) Representative CENP-A^HCP-3 enrichment in a 800-kb region in endogenous Chromosome II (7200–8000 kb) and in AC contig tig8258 (200–1000 kb). CENP-A^HCP-3 domains/peaks were indicated as grey bars. The dashed box (1 319 126–1 347 939 bp) indicates the region enriched with yeast mitochondrial DNA (the zoom-in is shown in Figure 5A). (G) Dot plots of AT-content (%) of each CENP-A^HCP-3 domain/peak against its size in endogenous chromosomes (left panel) and in AC (right panel). The 2D density plots were indicated by contour lines (bin = 7). The linear regression line to the scatter plot model was shown with 95% confidence region (grey shading). The average C. elegans genomic and AC AT-contents are indicated by the blue dotted lines, respectively. (H) The empirical cumulative distribution functions (ECDF) of interval distances between CENP-A^HCP-3 domains/peaks on endogenous chromosomes (blue) and AC (red). (I) The CENP-A^HCP-3 enrichment profiles and heatmaps of the 2-kb flanking regions surrounding the center of each CENP-A^HCP-3 domain/peak for endogenous chromosomes and AC. Consensus CENP-A^HCP-3 domains/peaks are separated into four clusters by k-means clustering. The profile plots (upper panel) show the average ChIP signals of each cluster. The ChIP signals of each domain/peak are shown in the clustered heatmaps (lower panel), in which the color coding on the right indicates the log₂ CENP-A^HCP-3 ratio. The schematic on the left and right show the possible distribution of CENP-A^HCP-3 nucleosomes interspaced in between H3 nucleosomes.