Figure 2.

Characterization of DSCAM-AS1 SE in MCF-7 cells. (a) WashU genome browser view of the DSCAM-AS1 genomic locus, which is reported in association with apoERα ChIP-Seq and RNA-Seq reads enrichment in siCTR-(red) or siERα-(blue) transfected MCF-7 cells; and with GRO-Seq, ChIP-Seq profiles of histone modifications and DNase hypersensitivity signals (yellow), RNA-Pol II and eight TFs (teal-blue) obtained from vehicle treated MCF-7 cells (see the Materials and Methods section for detailed data source). ERα and CTCF ChIA-PET data performed in MCF-7 grown in full medium from ENCODE project are also included [26]. The coordinates of the predicted SE and aERBSs are reported at the top as black and orange boxes, respectively. ChIP-Seq genomic signal profiles are reported as read count per million sequenced reads. (b,c) Bar plots reporting ERα fold enrichment over IgG signal by ChIP-qPCR at DSCAM-AS1 promoter and E5-E6-enhancers, TFF1 promoter (positive control) and KCNQ1OT1 promoter (negative control), in MCF-7 cells grown in HD medium transfected with siERα or siCTR (b); treated for 45′ with 17β-estradiol (E2) or vehicle (veh) (c). Standard error of four biological replicates; p-value by unpaired t-test: ** p < 0.01; (d) Left. Qualitative PCR reactions with primers detecting DSCAM-AS1 promoter interaction with E5 or E6 enhancer sites; primers detecting DSCAM-AS1 genomic region or non-interacting region; Right. Qualitative PCR reactions with primers detecting P2RY2 promoter-enhancer interaction; primers detecting P2RY2 genomic region or non-interacting region. All reactions were loaded on 2% agarose gel. Undigested and Digested samples represent DNA controls recovered during 3C libraries production.