(A) Schematic of the domain structure of the full-length mouse Chd1 (1-1711) used to generate the N-terminal FLAG-tagged construct. A region corresponding to the Chd1 ATP-binding pocket is shown below and aligned to various homologues from Saccharomyces cerevisiae and Drosophila melanogaster. The arrow indicates the conserved lysine residue mutated to form the dominant negative. (B) MEFs stably expressing either FLAG-tagged wild-type Chd1 or the dominant negative K510R were subjected to western analysis with a two-fold dilution series. Untransfected MEFs were used as a reference. (C) A representative genome browser snapshot of ChIP-seq data (all fragment lengths) indicating the high occupancy of PolII, wildtype-Chd1 and K510R-Chd1 at gene promoters. PolII distribution was determined in cells expressing wildtype-Chd1 using the N20 antibody. Normalized counts are indicated on the y-axis. (D) Chd1 binding to the 5′ end of genes was determined by ChIP-seq. Here, all recovered DNA fragments, irrespective of length, were analyzed. Each row of the heatmap represents the binding pattern across the −0.5 kb to +2 kb region flanking the TSS. Genes were ranked by the level of PolII occupancy in the −100 to +300 bp region, as measured by ChIP-seq in the MEFs expressing wildtype Chd1, using the N20 antibody that binds to the N-terminus of the largest subunit of PolII. (E) Analyzing only the short DNA fragments recovered (35–75 bp) allows precise mapping of Chd1, indicating that wildtype Chd1 binding tracks into the gene body, whereas K510R-Chd1 accumulates just downstream of the TSS. The genome-wide average is shown across the 4 kb encompassing the TSS.