Figure 4. dCas9 block fail to sufficiently recapitulate rex-like boundary on the X-chromosome.

Top: schematic depicting the multi-protein block and the approximate size of the components utilized to prevent condensin from translocating linearly along chromatin. Bottom: Hi-C of wildtype and block strain expressing all components of dCas9-SunTag and single guide RNA (sgRNA). The tick marks point to the block target. The below are ChIP-seq data in dCas9-SunTag expressing strain with (first panel) and without (middle panel) sgRNA. The two ChIP-seq tracks show normalization by input and IgG. Arrows pointing down to the DPY-27 ChIp signal that is apparent when data is normalized to input but not to IgG.

Figure 4—figure supplement 1. Increased ‘chippability’ due to dCas9-SunTag targeting.

Counts per million (CPM) normalized tracks of various ChIP and input data in conditions with (JZ2005) or without (JZ1973) sgRNA expression construct. The mapping quality (MAPQ) score threshold is increased to 20 to prevent mapping at the repetitive target locus. sgRNA expression results in an increased signal at/near the locus when chipped with DPY-27 or IgG. This is not an artifact of cross-reactivity of suntag with protein A/G or changes in sequencing bias of input as exclusion of antibody does not affect the observed tracks. The artifactual signal at the targeted locus only arises in the presence of antibodies.

Figure 4—figure supplement 2. Global effect of Hi-C data in dCas9-SunTag targeting strain.

JZ2005 strain has a global effect on topologically associating domains (TADs) and likely a multi-megabase insertion near the end of chromosome-X.