AHT-ChIP-seq can be used to simultaneously map multiple levels of transcriptional control. (A) Representation from UCSC genome browser, a 50 kb region around the non-coding RNA AK038602 on mouse chromosome 16. Data generated by AHT-ChIP-seq for five DNA binding regions are shown: HNF4A, CEBPA, RAD21, p300 and H3K4me3. The height of each track (y-axis) corresponds with sequence read depth. Beneath the enrichment track is the RefSeq genome annotation. (B) Correlation heat map based on peak location identified by MACS, with three layers of annotation: biological replicate (greens), technical replicate identification (greys) and factors: RAD21 (purple), H3K4me3 (red), HNF4A (blue), p300 (yellow) and CEBPA (black).