Efficient and comprehensive ChIP-seq for HoxA9 is possible in myeloid cells from EPC mice and in a human cell line low in granule proteases. (A) Integrated Genome Viewer (IGV)–generated example of ChIP-seq profiles across the established HoxA9 target Myb. Results from murine cells (upper panel). Four replicate samples and an IgG control are shown. For comparison, HoxA9 precipitation data from T cells³¹  are included. Replicates I to III were prepared from EPC HSPCs transformed by HA-tagged HoxA9; for replicate IV, triple Flag–tagged HoxA9 was used. Chromatin was precipitated with anti-HA or anti-Flag antibodies. The color-coded ribbon represents a heat map of conservation between mammal species, with the highest conservation depicted in red. ChIP-seq results from human AML cell line MV4;11 that is naturally low in granule proteases (lower panel). Endogenous HOXA9 was precipitated by anti-HOXA9 antibodies. (B) Distribution of HoxA9 peaks across genomic elements. (C) De novo motif search across the 1000 top scoring and highest confidence HoxA9/HOXA9 peaks. Shown are all recurrent motifs with a significant homology to a consensus binding site for a TF (family) that occurred in >15% of all identified peaks. P values and frequency (%) are given. (D) Motif distribution across HoxA9/HOXA9 peaks, as in panel C. The localization of consensus sites with respect to the identified HoxA9/HOXA9 peak center is plotted. (E) The genomic sequence of HoxA9 peaks is conserved across higher mammals. The metagene plot depicts sequence-conservation scores of all HoxA9 peaks compared with 60 species of Euarchontoglires (a clade of mammals including rodents, lagomorphs, tree shrews, colugos, and primates; http://hgdownload.cse.ucsc.edu/goldenPath/mm10/phastCons60way/).