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Tab A: Fig 1a. Clock gene per1b expression in medaka 6–4 wild type (WT) and mutant (KO) cell lines. Fig 1b. Clock gene per2a expression in medaka 6–4 wild type (WT) and mutant (KO) cell lines. Fig 1c. Clock gene per3 expression in medaka 6–4 wild type (WT) and mutant (KO) cell lines. Fig 1d. Clock gene per1b expression in medaka explanted wild type (iCab) and 6–4phr mutant (6–4 KO) fish fin clips. Fig 1e. Clock gene per2a expression in medaka explanted wild type (iCab) and 6–4phr mutant (6–4 KO) fish fin clips. Fig 1f. Clock gene per3 expression in medaka explanted wild type (iCab) and 6–4phr mutant (6–4 KO) fish fin clips. Fig 1g. In vivo luciferase assay of medaka 6–4 WT and KO cell lines transfected with a luciferase reporter carrying the zebrafish clock-regulated per1b promoter. Fig 1h. In vitro luciferase assay of medaka 6–4 WT and KO cells transfected with a luciferase reporter construct containing 15 tandemly repeated copies of the D-box sequence derived from the zebrafish cry1aa gene promoter (D-boxcry1aaLuc) and exposed to visible light or maintained in constant darkness. Tab B: Fig 2a. In vitro luciferase assay of zebrafish PAC-2 cells co-transfected with an E-box luciferase reporter construct containing 4 tandemly multimerized copies of the E-box sequence derived from the zebrafish per1b gene promoter (4xE-box (-7)) and expression vectors for zebrafish Clock1a and Bmal1a, 6–4phr, CPDphr and Cry1aa. Fig 2b. In vitro luciferase assay of mammalian 3T3 cells co-transfected with an E-box luciferase reporter construct containing 4 tandemly multimerized copies of the E-box sequence derived from the zebrafish per1b gene promoter (4xE-box (-7)) and expression vectors for zebrafish Clock1a and Bmal1a, 6–4phr, CPDphr and Cry1aa. Fig 2c. In vitro luciferase assay of zebrafish PAC-2 cells co-transfected with a D-box reporter construct containing 15 tandemly multimerized copies of the D-box sequence derived from the zebrafish cry1aa gene promoter (D-boxcry1aaLuc) together with expression vectors for the six PAR factors, specifically Tefa, Tefb, Dbpa, Dbpb, Hlfa and Hlfb as well as zebrafish 6–4phr. Fig 2d. In vitro luciferase assay of zebrafish PAC-2 cells co-transfected with a D-box reporter construct containing 15 tandemly multimerized copies of the D-box sequence derived from the zebrafish cry1aa gene promoter (D-boxcry1aaLuc) together with expression vectors for the six E4bp4/nfil3 factors as well as zebrafish 6–4phr. Fig 2e. In vitro luciferase assay of zebrafish PAC-2 cells co-transfected with the D-boxcry1aaLuc reporter construct and expression vector for zebrafish Tefb together with the titration of expression vector for 6–4phr. Fig 2f. In vitro luciferase assay of mammalian 3T3 cells co-transfected with the D-boxcry1aaLuc reporter construct and expression vector for zebrafish Tefb together with the titration of expression vector for 6–4phr. Fig 2g. In vitro luciferase assay of medaka 6–4 WT and KO cell lines co-transfected with the D-boxcry1aaLuc reporter construct and the expression vector for zebrafish Tefb. Fig 2h. In vitro luciferase assay of zebrafish PAC-2 cells co-transfected with the D-boxcry1aaLuc reporter construct and expression vector for zebrafish Tefb together with the titration of expression vector for Cry3. Fig 2i. In vitro luciferase assay of zebrafish PAC-2 cells co-transfected with the D-boxcry1aaLuc reporter construct and expression vector for zebrafish Tefb together with the titration of expression vector for Cry1aa. Fig 2j. In vitro luciferase assay of zebrafish PAC-2 cells co-transfected with the D-boxcry1aaLuc reporter construct and expression vector for zebrafish Tefb together with the titration of expression vector for CPDphr. Tab C: Fig 3a. NanoLuc Binary Technology (NanoBiT) assay to test the physical interaction between zebrafish Clock1a and 6–4phr. Fig 3b. NanoLuc Binary Technology (NanoBiT) assay to test the physical interaction between zebrafish Bmal1a and 6–4phr. Fig 3e. NanoLuc Binary Technology (NanoBiT) assay to test the physical interaction between zebrafish Tefb and 6–4phr. Tab D: Fig 4b. NanoBiT assays testing which domains of 6–4phr mediate the interactions with the Clock1a proteins. Fig 4c. NanoBiT assays testing which domains of 6–4phr mediate the interactions with the Bmal1a proteins. Fig 4d. NanoBiT assays testing which domains of 6–4phr mediate the interactions with the Tefb proteins. Tab E: Fig 5a. NanoBiT assay to test the effect of 6–4phr on Clock1a-Bmal1a heterodimerization. Fig 5d. NanoBiT assay to test the domains of Clock1a responsible for the interaction with 6–4phr. Fig 5e. NanoBiT assay to test the domains of Bmal1a responsible for the interaction with 6–4phr. Tab F: - S1a Fig. Clock gene per1b expression in medaka CPD wild type (WT) and mutant (KO) cell lines. S1b Fig. Clock gene per2a expression in medaka CPD wild type (WT) and mutant (KO) cell lines. S1c Fig. Clock gene per3 expression in medaka CPD wild type (WT) and mutant (KO) cell lines. S1d Fig. Clock gene per1b expression in medaka DASH wild type (WT) and mutant (KO) cell lines. S1e Fig. Clock gene per2a expression in medaka DASH wild type (WT) and mutant (KO) cell lines. S1f Fig. Clock gene per3 expression in medaka DASH wild type (WT) and mutant (KO) cell lines. Tab G: S2a Fig. Western blotting analysis of NanoBiT-tagged expression constructs, including clock1a, bmal1a and 6–4phr. S2b Fig. Western blotting analysis of NanoBiT-tagged expression constructs, including clock1a, bmal1a and tefb. S2c Fig. Western blotting analysis of NanoBiT-tagged bmal1a expression construct. S2d Fig. NanoBiT assay in zebrafish PAC-2 cells to test the heterodimerization of N terminally, SmBiT-tagged Clock1a and C terminally, LgBiT-tagged Bmal1a. S2g Fig. NanoBiT assay in zebrafish PAC-2 cells to test the homodimerization of C terminally, LgBiT and SmBiT tagged Tefb. Tab H: S3a Fig. Western blotting of LgBiT- or SmBiT-tagged 6–4phr deletions to test the expression in zebrafish PAC-2 cells. S3b Fig. Western blotting of LgBiT- or SmBiT-tagged 6–4phr deletions to test the expression in zebrafish PAC-2 cells. S3c Fig. Western blotting of LgBiT- or SmBiT-tagged Clock1a deletions to test the expression in zebrafish PAC-2 cells. S3d Fig. Western blotting of LgBiT- or SmBiT-tagged Clock1a deletions to test the expression in zebrafish PAC-2 cells. S3e Fig. Western blotting of LgBiT- or SmBiT-tagged Bmal1a deletions to test the expression in zebrafish PAC-2 cells. S3f Fig. Western blotting of LgBiT- or SmBiT-tagged Bmal1a deletions to test the expression in zebrafish PAC-2 cells. S3g Fig. Western blotting of LgBiT- or SmBiT-tagged Bmal1a deletions to test the expression in zebrafish PAC-2 cells. (XLSX)