1. BA CD E F Castel_Figure S1, related to Figure 1 Relative mRNA levels (2^-  Ct) RT-qPCR: Hey1 %ChIP/input ChIP: Ab1-RBPJ Sensitivity 1-Specificity GimmeMotifs Transfac M00234 WTRbpj —/— RBPJ Phalloidin Hoechst Hey1 Genes associated to peaks neg16 Rbms1 Atp6v0a4 Krt9 Apobec3 Rps6ka1

2. D C Castel_Figure S2, related to Figure 2 Replicate experiment ChIP:Ab1-RBPJ OnOffNotch:OnOff 6 hours24 hours Constant Inducible p300RBPJ Constant Inducible OnOff 24 hours Notch: OnOff RBPJ Constant Inducible RBPJ Notch:OnOff 24 hours OnOff 6 hours

3. A Castel_Figure S3 Validation with an independent RBPJ polyclonal antibody (Ab2-RBPJ) OnOffNotch:OnOff Ab1-RBPJAb2-RBPJ Constant Inducible Constant Inducible Notch: OnOff Ab1-RBPJ OnOff Ab2-RBPJ B

4. C REST motif in Ab2-RBPJ only sites RBPJ (GM) RBPJ (M00234) REST CREB ETS FE Castel_Figure S3 Frequency D Sensitivity 1-Specificity Ab2-RBPJ only sitesAb1-RBPJ sites %ChIP/input ChIP: Ab1-RBPJChIP: Ab2-RBPJ ChIP on REST sites %ChIP/input ChIP: Ab2-RBPJ Hey1 Genes associated to peaks neg16 Rbms1 Atp6v0a4 Krt9 Apobec3 Rps6ka1 peaks:

5. A C RBPJ/NICD-GFP NICD-GFP only RBPJ only Constant RBPJ only Inducible Castel_Figure S4, related to Figure 3 NICD-GFPGFP HEYL 49kD 38kD 28kD frequency position (bp) B DE

6. F Castel_Figure S4, related to Figure 3

7. Castel_Figure S5, related to Figure 4 A B C