subdivision into four classes are shown; those with at least 2-fold higher CBP occupancy in gd7 compared to wt (gd7 Up), similar levels of CBP occupancy (gd7 Unchanged), at least 2-fold less occupancy in gd7 (gd7 Down), and wt CBP peaks with no or background levels of binding in gd7 (gd7 Lost). (XLSX) Table S3 Overlap between CBP ChIP-seq raw data from 2 to 4 hour old wt or gd7 embryos and all or the 300 most strongly occupied regions for 40 sequence specific transcription factors [21,22]. Overlap of ChIP-seq raw data with increasing cut-off is shown. (XLSX) Table S4 Overlap between the 300 most strongly occupied regions for 40 sequence specific transcription factors [21,22] and CBP ChIP-seq peaks from 2 to 4 hour old wt or gd7 embryos. (XLSX) Table S5 Overlap between CBP ChIP-seq peaks from 2 to 4 hour old wt or gd7 embryos and all regions for 40 sequence specific transcription factors [21,22]. Overlap of ChIP-seq peaks with increasing cut-off is shown. Also, overlap of CBP peaks with the transcription factors after subdivision into four classes are shown; those with at least 2-fold higher CBP occupancy in gd7 compared to wt (gd7 Up), similar levels of CBP occupancy (gd7 Unchanged), at least 2-fold less occupancy in gd7 (gd7 Down), and wt CBP peaks with no or background levels of binding in gd7 (gd7 Lost). (XLSX) Table S6 Binding of CBP, Dorsal, and indicated histone modifications at Dorsal target genes, expressed as fold over References 1. Bedford DC, Kasper LH, Fukuyama T, Brindle PK (2010) Target gene context influences the transcriptional requirement for the KAT3 family of CBP and p300 histone acetyltransferases. Epigenetics 5: 9–15. 2. Heintzman ND, Hon GC, Hawkins RD, Kheradpour P, Stark A, et al. (2009) Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature 459: 108–112. 3. Visel A, Blow MJ, Li Z, Zhang T, Akiyama JA, et al. 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