Figure 7. YY1 Controls PAIR Function and Long-Range Interactions across the Igh Locus.

(A) 4C-seq analysis of ex vivo sorted Rag1^Cre/+Yy1^fl/fl pro-B cells (Figures S6B and S6C), control Rag2^−/− pro-B cells, and thymocytes with the viewpoint Eµ-HD (red). The Eµ-3′CBE interaction is highlighted in orange. A red asterisk indicates the loss of D_H sequences by D_H-J_H rearrangements in the recombination-proficient Rag1^Cre/+Yy1^fl/fl pro-B cells.

(B) Identification of YY1 peaks in the Igh locus by Bio-ChIP-sequencing of cultured pro-B cells from Yy1^ihCd2/+Rosa26^BirA/BirARag2^−/− mice. Vertical bars below the Bio-ChIP-seq track identify significant YY1 peaks that were called by MACS with a p value of <10⁻¹⁰. For comparison, the Pax5-binding and DHS site patterns of Rag2^−/− pro-B cells are shown (Revilla-I-Domingo et al., 2012).

(C) YY1 binding at PAIR elements and associated V_H3609 genes.

(D and E) Analysis of YY1-dependent gene expression. The expression values (RPKM) of selected genes (D) and RNA-seq profiles of the antisense transcripts originating from PAIR4 and PAIR6 (E) are shown for Rag1^Cre/+Yy1^fl/fl (red) and control Rag1^Cre/+Yy1^fl/+ (black) pro-B cells together with the standard error of the mean (based on two RNA-seq experiments for each genotype).

See also Figure S6.