Supplementary Fig. S1. Schematic representation of mouse lines Pax6 fl/fl and mrx-cre used in this study. (A) To generate Pax6 fl/ fl

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Supplementary Fig. S1. Schematic representation of mouse lines Pax6 fl/fl and mrx-cre used in this study. (A) To generate Pax6 fl/ fl, loxp sites flanking exons 3-6 (red arrowheads) were introduced into Pax6 locus by homologous recombination in embryonic stem cells. The paired domain of Pax6 is encoded by exons 5, 5a, 6 and 7. Blue arrowheads represent positions of loxp sites in Pax6 fl/fl mice generated previously (Ashery-Padan et al., 2000). Details of gene targeting are available upon request. (B) To generate mrx-cre, BAC containing 200kb covering the Rx locus was modified by BAC recombineering. The Cre coding region (Cre-pA) was inserted into the Rx translational initiation start site (ATG). Exons are indicated by black boxes. (C) Pax6 fl/fl mice generated in this study were crossed with α-cre to show that amacrine cells are generated in Pax6 fl/fl /α-cre mutants as previously reported (Marquardt et al., 2001). Adult retinal sections were stained with antibodies against amacrine cell markers syntaxin and Vc1.1 (HNK-1 epitope); retinal areas with amacrine cells are indicated with arrowheads. le, lens; ONL, outer nuclear layer; INL, inner nuclear layer; GCL, ganglion cell layer.

Supplementary Fig. S2. Apoptosis in Pax6-deficient retina. (A-J) Retinal sections of wild-type (Pax6 fl/fl ) and mutant (Pax6 fl/fl /mrx- Cre) embryos were stained with antibody against cleaved Caspase3 (Cas3) at indicated stages. Retina is indicated with dashed line. (K) Quantification of apoptotic cells determined as proportion of Cas3 + cells versus DAPI + cells in wild-type (wt) and Pax6-deficient (mut) retinae. Error bars indicate s.d. P-values are by Student s t-test.

Supplementary Fig. S3. M-phase cell cycle arrest does not contribute to early proliferation phenotype in Pax6-deficient retina. (A) Sections stained with antibody against phosphorylated histone H3 (PH3) at E10.5, E11.5 and E14.5. (B) Quantification of M-phase cells determined as proportion of PH3+ cells versus DAPI+ cells in wild-type (wt) and Pax6-deficient (mut) retinae (indicated with dashed lines). Error bars indicate s.d. P-values are by Student s t-test. le, lens Supplementary Fig. S4. Expression of bhlhb5, Vc1.1 and Crx in Pax6-deficient retina. (A-D) Confocal images showing bhlhb5 (A,B) and Vc1.1 (HNK-1 epitope) (C,D) immunoreactivity in wild-type (Pax6fl/fl) and Pax6-deficient (Pax6fl/fl/mRx-Cre) retina at E15.5. Arrowheads indicate Vc1.1 immunoreactivity in non-retinal tissue (B,C). (E-H) Crx protein expression assessed using Crx/Otx2 antibody at E11.5 (E, F) and E14.5 (G,H). Dashed lines indicate the position of retina. le, lens; GCL, ganglion cell layer; ONL, outer nuclear layer; RPE, retinal pigmented epithelium. Scale bar: 100 µm.

Supplementary Fig. S5. Pax6 elimination from early RPCs or OV neuroepithelium interferes with optic cup/lens pit morphogenesis. (A-B ) Transversal sections of E10.5 wild-type (Pax6 fl/fl ) and mutant (Pax6 fl/fl /mrx-cre) eyes of littermate embryos stained with DAPI (grey). Forming lens pit is indicated with dashed line. (C-D ) Section of control (Pax6 Sey/fl ) and mutant (Pax6 Sey/fl / mrx-cre) eyes of littermate embryos at E14.5 stained with hematoxylin-eosin. (E-H ) Sections of control (Pax6 fl/fl ) and mutant (Pax6 fl/ fl /EmRx-Cre) eyes stained with antibody against Pax6 at indicated stages. (H ) Expression of EYFP showing area of Cre-mediated deletion visualized using R-EYFP reporter mouse line. OV, optic vesicle; SE, surface ectoderm; le, lens; re, retina. Scale bar: 100 µm.

Supplementary Fig. S6. Wnt/β-catenin inhibitors Sfrp1 and Sfrp2 are downregulated upon OV-specific Pax6 inactivation but Wnt signaling is not responsible for the arrested lens development. (A-F) Sfrp2 (A-C) and Sfrp1 (D-F) mrna expression in control (Pax6 fl and Pax6 Sey/fl ) and mutant (Pax6 Sey/fl /mrx-cre) E11.0 eyes. (G-I) Dkk1 mrna expression at E10.5; eye region indicated with arrowheads. (J,K) Activity of Wnt/β-catenin signaling assessed using a BAT-gal reporter mouse in control (Catnb lox(ex3)/+ ) (J) and retinal mutant (Catnb lox(ex3)/+ /mrx-cre) (K) with activated Wnt/β-catenin pathway in developing neuroretina. Retina is indicated with black dashed line; lens or the corresponding tissue with white dashed line.

Table S1. Primary antibodies and RNA probes Primary antibodies Antibody Host Dilution Source Pax6 Rabbit 1:500 Covance (PRP-278P) Sox2 Goat 1:400 Santa-Cruz (sc-17320) cyclin D1 Mouse 1:500 Santa-Cruz (sc-450) p27 Kip1 Mouse 1:1000 BD Biosciences (610241) p57 Kip2 Goat 1:70 Santa-Cruz (sc-1039) Tuj1 Mouse 1:1500 R&D Systems (MAB1199) cleaved caspase 3 Rabbit 1:300 Cell Signaling (D175) PH3 Rabbit 1:1000 Upstate (06-570) Lef1 Rabbit 1:500 Cell Signaling (C12A5) Pcna Mouse 1:3000 Sigma, P8825 Crx/Otx2 Rabbit 1:500 Kind gift from Dr Craft (Zhu and Craft, 2000) Six3 Rabbit 1:2000 Kind gift from Dr P. Bovolenta (unpublished) Otx2 Rabbit 1:300 R&D Systems (BAF1979) Blimp1 Rat 1:300 Santa-Cruz (sc-47732) Rxrγ Rabbit 1:1500 Santa-Cruz (sc-555) Nr2e3 Rabbit 1:100 Kind gift from Dr S. Chen (Chen et al., 2005) bhlhb5 Goat 1:400 Santa-Cruz (sc-6045) Vc1.1 (HNK-1) Mouse 1:100 Sigma (C6680) Lhx2 Goat 1:1000 Santa-Cruz (sc-19344) Hes1 Rabbit 1:1000 Kind gift from Dr N. Brown (Lee et al., 2005) Chx10 Sheep 1:800 Exalpha (X1180P) Foxe3 Rabbit 1:1000 Kind gift from Dr Carlsson (Blixt et al., 2007) Prox1 Rabbit 1:2000 Chemicon (AB5475) BrdU Rat 1:100 Abcam (AB6326) perk1/2 Rabbit 1:3000 Cell Signaling (9101S) psmad1/5 Rabbit 1:2000 Invitrogen (700047) RNA probes Gene Source Neurod1 p57 Kip2 Rx Trβ2 Crx Atoh7 Kindly provided by Dr Brown (Brown et al., 1998) Math3 Kindly provided by Dr Brown (Farah et al., 2000) Mash1 Kindly provided by Dr Brown (Brown et al., 1998) Bmp4 Kindly provided by Dr Hogan (Jones et al., 1991) Bmp7 Kindly provided by Dr Hogan (Lyons et al., 1995) Ngn2 Kindly provided by Dr J. Rubenstein (Sommer et al., 1996) Sfrp1 Kindly provided by Dr S. Pleasure (Rattner et al., 1997) Sfrp2 Kindly provided by Dr S. Pleasure (Rattner et al., 1997) Dkk1 Kindly provided by Dr S. Krauss (Diep et al., 2004)

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