Additional file 5: Figure S2. of Sex chromosomes drive gene expression and regulatory dimorphisms in mouse embryonic stem cells

Identification of candidate regulatory elements. (A) Top, graphic display of the conservation profiles for regions upstream of Zfx from Dcode.org [64, 110]. The base genome is mouse. Evolutionarily conserved regions (ECRs) of a minimum of 100 bp conserved above 70% sequence identity are displayed as red (intergenic) peaks, with the x-axis representing positions in the base genome and the y-axis representing percentage identity between the base and the aligned genomes. Predicted transcription factor motifs are depicted as colored bars. Arrowhead points to predicted motif of TF expressed more highly in female ES cells. Bottom, UCSC genome browser view of the same regions including histone modifications from ENCODE data in mouse ES cells ( http://genome.ucsc.edu , NCBI37/mm9). (B) Conservation analysis, TF motif prediction and UCSC browser view as in (A) for the Tcf3 gene. Arrowhead points to predicted motif of TF expressed more highly in male ES cells. (C) Conservation analysis, TF motif prediction and UCSC browser view as in (A) for the Apln gene, with arrowheads indicating motifs predicted to bind TFs more highly expressed in male ES cells.