Nucleic Acids Research, 2009, Vol. 37, No. 16 5339 Figure 6. Identiﬁcation of a region of high homology among activating Ly49 genes. (A) Alignment of 50 regions of inhibitory and activating Ly49 genes. A region, located in exon 1, with high homology among activating receptors only, is boxed (dashed line). The region of transcriptional start site is indicated by the solid black line above the alignment. Promoter region sequences of Ly49d and h of NOD, Ly49p and r of 129/S6 as well as Ly49a, c, d, e, f, g and h of the B6 strain are shown. Ly49a, c, e, f and g are inhibitory genes and all other sequences are from activating genes. CpG dinucleotides are also highlighted. The sequence used as probe in the supershift experiment is indicated for Ly49d with box (solid line). Potential YY1 binding sites (CCAT and ACAT) are shown in bold font. (B) Double-stranded probes harbouring the region of interest in exon 1 for the activating Ly49d and h of the B6 strain and the corresponding region for the inhibitory Ly49a and Ly49c were used in gel-shift experiments with nuclear extract from FACS-sorted T-cells and IL-2 cultured NK cells. A YY1 antibody was used for supershift assays. The bracket indicates the protein complexes bound most signiﬁcantly by the activating Ly49d and h probes but not the inhibitory Ly49a and c in both NK and T-cells. The arrow indicates another protein complex speciﬁc to the activating Ly49 probes that disappears (supershifts) in the presence of anti-YY1 in both NK and T-cells.