Figure 6. Footprint analysis of endogenous protamine locus.

To identify potential regulators of prior endogenous protamine transcription the CENTIPEDE footprint analysis was relaxed to test the occupancy status of additional motifs found within the 5 Mb region centered on the mouse protamine locus. Footprints (2 kb CENTIPEDE window; see Methods) overlapping testes enhancers are colored according to their name. Average log₁₀ normalized total testis RNA-seq coverage is depicted in blue. Pink arrow designates the Ctcf site bound upstream of Tnp2. Predicted testis enhancer peaks were provided by the mouse ENCODE project (Methods)³⁶. Additional footprints identified in sperm that do not intersect a testis enhancer are presented in a separate track (motif length, ~20 bp).