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. 2017 May 31;6:e23645. doi: 10.7554/eLife.23645

Figure 1. DCC recruitment sites are defined using high resolution ChIP-seq analysis.

(A) The C. elegans dosage compensation complex (DCC) is composed of a modified condensin complex (condensin DC) which is distinguished from condensin I by the SMC-4 variant, DPY-27. The non-condensin subunits SDC-2, SDC-3, and DPY-30 are required for DCC recruitment to the X chromosomes. (B) Peak distribution across each of the six chromosomes. (C) Representative ChIP-seq enrichment for an 80 kb window that includes recruitment element on the X, rex-8. Recruitment sites on the X chromosome were defined as a 400 bp window centered on the SDC-2 ChIP-seq summits that overlap with SDC-3, DPY-30, and DPY-27 peaks and that do not show significant H3K4me3 enrichment. (D) Recruitment sites identified in this study (n = 64) largely overlap with sequences previously shown to recruit DCC to multi-copy extrachromosomal array (n = 47) (Jans et al., 2009; Pferdehirt et al., 2011; McDonel et al., 2006).

DOI: http://dx.doi.org/10.7554/eLife.23645.003

Figure 1.

Figure 1—figure supplement 1. ChIP-seq data suggests that some previously defined rex-sites fail to recruit the DCC in the context of the X chromosome.

Figure 1—figure supplement 1.

(A) SDC-2, SDC-3, DPY-30, DPY-27, and H3K4me3 ChIP-seq enrichment data is plotted for a 1 Mb window. Three previously identified rex-sites (rex-8 (rank 1), rex-28 (rank 35), and rex-29 (rank 50)) are identified as recruitment sites in this study. One previously identified rex-site (rex-27) shows little DCC enrichment and high H3K4me3 enrichment. (B) Plots showing SDC-3 and DPY-27 average ChIP enrichment across a 1 kb window centered on the peak summit. The top three recruitment sites (rank 1–3) are shown in pink; recruitment sites ranked 31–33 are shown in green; recruitment sites ranked 62–64 are shown in blue. Rex-22, rex-27, and rex-30, shown previously to recruit to array but not called recruitment sites in this study, are shown in gray.
DOI: http://dx.doi.org/10.7554/eLife.23645.004

Figure 1—figure supplement 2. Peaks excluded by H3K4me3 overlap do not resemble strong recruitment sites.

Figure 1—figure supplement 2.

(A) Boxplots indicating SDC-2 ChIP-seq enrichment score across each of the defined classes: strong recruitment sites (n = 17), intermediate recruitment sites (n = 16), weak recruitment sites (n = 31), and peaks excluded by H3K4me3 enrichment (n = 9). B) Representative ChIP-seq enrichment for a 100 kb window that includes a peak excluded by H3K4me3 enrichment.
DOI: http://dx.doi.org/10.7554/eLife.23645.005