(A) Dissection of the putative regulatory elements in the proximal and the upstream promoter regions of H2A.Z-1 and H2A.Z-2. Elements whose relevance for H2A.Z promoter activity has been experimentally demonstrated are indicated in black boxes. The position relative to the transcription start site in the alignment, shown in Additional files 1 and 2, is indicated in each case. (B) Phylogenetic relationships among H2A.Z promoter regions in mammalian representatives. The numbers for internal nodes in the topology indicate confidence values for the groups defined (BS/IBT), both based on 1000 replications and only shown when a value is greater than 50%. Numbers in parentheses and in boldface near species names indicate the sequence variant copy and the number of sequences analysed, respectively (see Additional file 3). The tree was rooted with the H2A.Ze sequence from sea urchin, representing an early chordate in which H2A.Z-1 and H2A.Z-2 variants are not yet differentiated. (C) Logos representation of the amino acid residues at postions 15, 39 and 128 in H2A.Z-1 and H2A.Z-2. The sequences used to create the logos were the same as in (B).