(A F) H&E staining of the duodenum in the indicated genotypes at E16.5 (A, D), E18.5

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1 Fig. S1. Brg1 ablation leads to abnormal villous structure in the duodenum in the perinatal period (A F) H&E staining of the duodenum in the indicated genotypes at E16.5 (A, D), E18.5 (B, E), and P0.5 (C, F). Scale bars: 100 µm.

2 Fig. S2. Loss of Brg1 results in downregulation of the Notch signaling pathway in the duodenum during embryonic development. Relative expression levels of Hes1, Hes5, HeyL, and Math1 in the duodenum of the indicated genotypes at E17.5, as determined by q-pcr (n=4). * p < 0.05, ** p < 0.01.

3 Fig. S3 Expression of Notch target genes in the ileum. (A, B) Hes1 staining of the ileum in the indicated genotypes. Scale bars: 50 µm. (C) Relative expression levels of Hes1, Hes5, and HeyL in the ileum in the indicated genotypes at P4, as determined by q-pcr (n=4). * p < 0.05, ** p < 0.01.

5 Fig.S4. Analysis of intestinal overexpression of Notch 1 ICD in mice (A E) Histological analyses of the duodenum of Villin-Cre; Rosa NotchIC (VN) mice at P4. H&E staining (A), Alcian blue staining (B), Cleaved caspase 3 staining (C), Ki67 staining (D), and Hes1 staining (E). Scale bars: 100 µm. (F I) Length of villi (F) (n=4), number of Goblet cells (G) (n=3), apoptotic cells (H) (n=3), and Ki67-positive cells (I) (n=3) in the duodenum of the indicated genotypes at P4. * p < 0.05, ** p < 0.01, *** p < (J) Relative expression levels of Hes1 in the duodenum of the indicated genotypes at P4, as determined by q-pcr (n=4). * p < 0.05, ** p < 0.01, *** p <

7 Fig.S5. β-catenin stabilization does not reverse the phenotypes of Brg1-mutant mice (A, L) Relative expression levels of genes involved in the Wnt signaling pathway in the duodenum of Villin-Cre; Brg1 f/f mice at P4, as determined by q-pcr (n>3). * p < 0.05, ** p < 0.01, *** p < (B G) Histological analyses of the duodenum of Villin-Cre; Brg1 f/f ; Ctnnb1 f/f(exon3) (VBB) mice at P4. H&E staining (B), Alcian blue staining (C), Cleaved caspase 3 staining (D), Ki67 staining (E), GFP/E-Cadherin co-staining of the duodenum of Lgr5-GFP; VBB mice at P4 (F), and Hes1 staining (G). Scale bars: 100 µm (B-D), 50 µm (E G). (H K) Length of villi (H) (n=4), number of Goblet cells (I) (n=3), apoptotic cells (J) (n=3), and Ki67-positive cells (K) (n=3) in duodenum of the indicated genotypes at P4. * p < 0.05, ** p < 0.01, *** p < (M) Relative expression levels of genes involved in the Notch signaling pathway in the duodenum of the indicated genotypes at P4, as determined by q-pcr (n=4). * p < 0.05, ** p < 0.01, *** p <

8 Fig.S6. Brm expression pattern in the murine intestine. (A D) Brm staining of the duodenum (A, B) and the ileum (C, D) of the indicated genotypes. Scale bars: 50 µm.

9 Table SI. A list of used primers in RT-PCR experiments. Gene Forward Reverse Math1 5 -GCCTTGCCGGACTCGCTTCTC-3 5 -TCTGTGCCATCATCGCTGTTAGGG-3 Gfi1 5 -AGAAGGCGCACAGCTATCAC-3 5 -GGCTCCATTTTCGACTCGC-3 Noxa 5 -CGAGCCCTGGCCTATATGATA-3 5 -GGGTCCTTTGTAGCTGCTCC-3 Bax 5 -TGAAGACAGGGGCCTTTTTG-3 5 -AATTCGCCGGAGACACTCG-3 Bcl2 5 -GGGAGAACAGGGTATGATAACCG-3 5 -TAGCCCCTCTGTGACAGCTTA-3 Lgr5 5 -TCCTAGAAGAGTTACGTCTTGCT-3 5 -CCTTGGGAATGTGTGTCAAAGC-3 Olfm4 5 -CAGCCACTTTCCAATTTCACTG-3 5 -GCTGGACATACTCCTTCACCTTA-3 Musashi1 5 -TTCATCGGAGGACTCAGTTGG-3 5 -CATCACCAGACACTCTTTCACC-3 Ascl2 5 -AAGCACACCTTGACTGGTACG-3 5 -AAGTGGACGTTTGCACCTTCA -3 Bmi1 5 -AAATCCCCACTTAATGTGTGTCC-3 5 -GGCATCAATGAAGTACCCTCCA-3 Tert 5 -GCACTTTGGTTGCCCAATG-3 5 -,GCACGTTTCTCTCGTTGCG-3 Notch1 5 -GATGGCCTCAATGGGTACAAG-3 5 -TCGTTGTTGTTGATGTCACAGT-3 Notch2 5 -ATGTGGACGAGTGTCTGTTGC-3 5 -GGAAGCATAGGCACAGTCATC-3 Dll1 5 -CAGGACCTTCTTTCGCGTATG-3 5 -AAGGGGAATCGGATGGGGTT-3 Dll4 5 -TTCCAGGCAACCTTCTCCGA-3 5 -ACTGCCGCTATTCTTGTCCC-3 Jag1 5 -CCTCGGGTCAGTTTGAGCTG-3 5 -CCTTGAGGCACACTTTGAAGTA-3 Jag2 5 -CTGTGCAGCGTGTTCAGTG-3 5 -GTGTCCACCATACGCAGATAAC-3 Numb 5 -AAAGCAGTGAAGGCCGTTCT-3 5 -GTTTTCTCGTCCACAACTCTGAG-3 Hes1 5 -ATAGCTCCCGGCATTCCAAG-3 5 -GCGCGGTATTTCCCCAACA-3 Hes5 5 -AGTCCCAAGGAGAAAAACCGA-3 5 -GCTGTGTTTCAGGTAGCTGAC-3 Hes6 5 -ACCACCTGCTAGAATCCATGC-3 5 -GCACCCGGTTTAGTTCAGC-3 HeyL 5 -CAGCCCTTCGCAGATGCAA-3 5 -CCAATCGTCGCAATTCAGAAAG-3 Wnt3a 5 -CTCCTCTCGGATACCTCTTAGTG-3 5 -GCATGATCTCCACGTAGTTCCTG-3 Wnt5a 5 -CAACTGGCAGGACTTTCTCAA-3 5 -CCTTCTCCAATGTACTGCATGTG-3 Fzd1 5 -CAGCAGTACAACGGCGAAC-3 5 -GTCCTCCTGATTCGTGTGGC-3 Fzd2 5 -GCCGTCCTATCTCAGCTATAAGT-3 5 -TCTCCTCTTGCGAGAAGAACATA-3 Fzd3 5 -ATGGCTGTGAGCTGGATTGTC-3 5 -GGCACATCCTCAAGGTTATAGGT-3 Fzd4 5 -TGCCAGAACCTCGGCTACA-3 5 -ATGAGCGGCGTGAAAGTTGT-3 Fzd5 5 -GGTGTGCCAGGAAATCACG-3 5 -CACAAGCGGCCAGAATTGG-3

10 Fzd6 5 -ATGGAAAGGTCCCCGTTTCTG-3 5 -GGGAAGAACGTCATGTTGTAAGT-3 Fzd7 5 -GCCACACGAACCAAGAGGAC-3 5 -CGGGTGCGTACATAGAGCATAA-3 Fzd8 5 -ATGGAGTGGGGTTACCTGTTG-3 5 -CACCGTGATCTCTTGGCAC-3 Rnf43 5 -TCCGAAAGATCAGCAGAACAGA-3 5 -GGACTGCATTAGCTTCCCTTC-3 Znrf3 5 -CACTGTCGGCACAACATCATA-3 5 -GGTAGGGTCACTCTTGGCT-3 Axin2 5 -TGACTCTCCTTCCAGATCCCA-3 5 -TGCCCACACTAGGCTGACA-3 Tcf4 5 -CGAAAAGTTCCTCCGGGTTTG-3 5 -CGTAGCCGGGCTGATTCAT-3 Lef1 5 -TGTTTATCCCATCACGGGTGG-3 5 -CATGGAAGTGTCGCCTGACAG-3 Ctnnb1 5 -ATGGAGCCGGACAGAAAAGC-3 5 -CTTGCCACTCAGGGAAGGA-3 c-myc 5 -TCTCCATCCTATGTTGCGGTC-3 5 -TCCAAGTAACTCGGTCATCATCT-3

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