Blackshaw, S. et al. Comprehensive analysis of photoreceptor gene expression and the identification of candidate retinal disease genes. Cell 107(5), 579–589 (2001).
Google Scholar
Arshavsky, V. Y. & Burns, M. E. Photoreceptor signaling: Supporting vision across a wide range of light intensities. J. Biol. Chem. 287(3), 1620–1626 (2012).
Google Scholar
Molday, R. S. & Moritz, O. L. Photoreceptors at a glance. J. Cell Sci. 128(22), 4039–4045 (2015).
Google Scholar
Pearring, J. N. et al. Protein sorting, targeting and trafficking in photoreceptor cells. Prog. Retin. Eye Res. 36, 24–51 (2013).
Google Scholar
Bujakowska, K. M., Liu, Q. & Pierce, E. A. Photoreceptor cilia and retinal ciliopathies. Cold Spring Harb. Perspect. Biol. 9(10), a028274 (2017).
Google Scholar
May-Simera, H., Nagel-Wolfrum, K. & Wolfrum, U. Cilia—The sensory antennae in the eye. Prog. Retin. Eye Res. 60, 144–180 (2017).
Google Scholar
Chen, S. et al. Crx, a novel Otx-like paired-homeodomain protein, binds to and transactivates photoreceptor cell-specific genes. Neuron 19(5), 1017–1030 (1997).
Google Scholar
Furukawa, T., Morrow, E. M. & Cepko, C. L. Crx, a novel otx-like homeobox gene, shows photoreceptor-specific expression and regulates photoreceptor differentiation. Cell 91(4), 531–541 (1997).
Google Scholar
Hennig, A. K., Peng, G. H. & Chen, S. Regulation of photoreceptor gene expression by Crx-associated transcription factor network. Brain Res 1192, 114–133 (2008).
Google Scholar
Swaroop, A., Kim, D. & Forrest, D. Transcriptional regulation of photoreceptor development and homeostasis in the mammalian retina. Nat. Rev. Neurosci. 11(8), 563–576 (2010).
Google Scholar
Swaroop, A. et al. A conserved retina-specific gene encodes a basic motif/leucine zipper domain. Proc. Natl. Acad. Sci. U.S.A. 89(1), 266–270 (1992).
Google Scholar
Furukawa, T. et al. Retinopathy and attenuated circadian entrainment in Crx-deficient mice. Nat. Genet. 23(4), 466–470 (1999).
Google Scholar
Mears, A. J. et al. Nrl is required for rod photoreceptor development. Nat. Genet. 29(4), 447–452 (2001).
Google Scholar
Chen, H. Y. et al. Three-dimensional retinal organoids from mouse pluripotent stem cells mimic in vivo development with enhanced stratification and rod photoreceptor differentiation. Mol. Vis. 22, 1077–1094 (2016).
Google Scholar
Collin, J. et al. CRX expression in pluripotent stem cell-derived photoreceptors marks a transplantable subpopulation of early cones. Stem Cells 37(5), 609–622 (2019).
Google Scholar
Gonzalez-Cordero, A. et al. Recapitulation of human retinal development from human pluripotent stem cells generates transplantable populations of cone photoreceptors. Stem Cell Rep. 9(3), 820–837 (2017).
Google Scholar
Lamba, D. A., Gust, J. & Reh, T. A. Transplantation of human embryonic stem cell-derived photoreceptors restores some visual function in Crx-deficient mice. Cell Stem Cell 4(1), 73–79 (2009).
Google Scholar
Bessant, D. A. et al. A mutation in NRL is associated with autosomal dominant retinitis pigmentosa. Nat. Genet. 21(4), 355–356 (1999).
Google Scholar
Freund, C. L. et al. Cone-rod dystrophy due to mutations in a novel photoreceptor-specific homeobox gene (CRX) essential for maintenance of the photoreceptor. Cell 91(4), 543–553 (1997).
Google Scholar
Kanda, A. et al. Retinopathy mutations in the bZIP protein NRL alter phosphorylation and transcriptional activity. Hum. Mutat. 28(6), 589–598 (2007).
Google Scholar
Nishiguchi, K. M. et al. Recessive NRL mutations in patients with clumped pigmentary retinal degeneration and relative preservation of blue cone function. Proc. Natl. Acad. Sci. U.S.A. 101(51), 17819–17824 (2004).
Google Scholar
Swain, P. K. et al. Mutations in the cone-rod homeobox gene are associated with the cone-rod dystrophy photoreceptor degeneration. Neuron 19(6), 1329–1336 (1997).
Google Scholar
Garancher, A. et al. NRL and CRX define photoreceptor identity and reveal subgroup-specific dependencies in medulloblastoma. Cancer Cell 33(3), 435–449 (2018).
Google Scholar
Verbakel, S. K. et al. Non-syndromic retinitis pigmentosa. Prog. Retin. Eye Res. 66, 157–186 (2018).
Google Scholar
Kim, J. W. et al. NRL-regulated transcriptome dynamics of developing rod photoreceptors. Cell Rep. 17(9), 2460–2473 (2016).
Google Scholar
Corbo, J. C. et al. CRX ChIP-seq reveals the cis-regulatory architecture of mouse photoreceptors. Genome Res. 20(11), 1512–1525 (2010).
Google Scholar
Hao, H. et al. Transcriptional regulation of rod photoreceptor homeostasis revealed by in vivo NRL targetome analysis. PLoS Genet. 8(4), e1002649 (2012).
Google Scholar
Brooks, M. J. et al. Next-generation sequencing facilitates quantitative analysis of wild-type and Nrl(-/-) retinal transcriptomes. Mol. Vis. 17, 3034–3054 (2011).
Google Scholar
Kautzmann, M. A. et al. Combinatorial regulation of photoreceptor differentiation factor, neural retina leucine zipper gene NRL, revealed by in vivo promoter analysis. J. Biol. Chem. 286(32), 28247–28255 (2011).
Google Scholar
Mo, A. et al. Epigenomic landscapes of retinal rods and cones. Elife 5, e11613 (2016).
Google Scholar
Peng, G. H. & Chen, S. Active opsin loci adopt intrachromosomal loops that depend on the photoreceptor transcription factor network. Proc. Natl. Acad. Sci. U.S.A. 108(43), 17821–17826 (2011).
Google Scholar
Ruzycki, P. A., Zhang, X. & Chen, S. CRX directs photoreceptor differentiation by accelerating chromatin remodeling at specific target sites. Epigenet. Chromatin 11(1), 42 (2018).
Google Scholar
Lee, J. et al. Quantitative fine-tuning of photoreceptor cis-regulatory elements through affinity modulation of transcription factor binding sites. Gene Ther. 17(11), 1390–1399 (2010).
Google Scholar
Kerppola, T. K. & Curran, T. A conserved region adjacent to the basic domain is required for recognition of an extended DNA binding site by Maf/Nrl family proteins. Oncogene 9(11), 3149–3158 (1994).
Google Scholar
Kerppola, T. K. & Curran, T. Maf and Nrl can bind to AP-1 sites and form heterodimers with Fos and Jun. Oncogene 9(3), 675–684 (1994).
Google Scholar
Mitton, K. P. et al. The leucine zipper of NRL interacts with the CRX homeodomain. A possible mechanism of transcriptional synergy in rhodopsin regulation. J. Biol. Chem. 275(38), 29794–29799 (2000).
Google Scholar
Reks, S. E. et al. Cooperative activation of Xenopus rhodopsin transcription by paired-like transcription factors. BMC Mol. Biol. 15, 4 (2014).
Google Scholar
White, M. A. et al. A simple grammar defines activating and repressing cis-regulatory elements in photoreceptors. Cell Rep. 17(5), 1247–1254 (2016).
Google Scholar
von Alpen, D. et al. Differential dimerization of variants linked to enhanced S-cone sensitivity syndrome (ESCS) located in the NR2E3 ligand-binding domain. Hum. Mutat. 36(6), 599–610 (2015).
Google Scholar
Roduit, R., Escher, P. & Schorderet, D. F. Mutations in the DNA-binding domain of NR2E3 affect in vivo dimerization and interaction with CRX. PLoS ONE 4(10), e7379 (2009).
Google Scholar
Piehler, J. New methodologies for measuring protein interactions in vivo and in vitro. Curr. Opin. Struct. Biol. 15(1), 4–14 (2005).
Google Scholar
Piston, D. W. & Kremers, G. J. Fluorescent protein FRET: The good, the bad and the ugly. Trends Biochem. Sci. 32(9), 407–414 (2007).
Google Scholar
Day, R. N. & Davidson, M. W. Fluorescent proteins for FRET microscopy: Monitoring protein interactions in living cells. BioEssays 34(5), 341–350 (2012).
Google Scholar
Zeug, A. et al. Quantitative intensity-based FRET approaches—a comparative snapshot. Biophys. J. 103(9), 1821–1827 (2012).
Google Scholar
Banning, C. et al. A flow cytometry-based FRET assay to identify and analyse protein-protein interactions in living cells. PLoS ONE 5(2), e9344 (2010).
Google Scholar
Chan, F. K. et al. Fluorescence resonance energy transfer analysis of cell surface receptor interactions and signaling using spectral variants of the green fluorescent protein. Cytometry 44(4), 361–368 (2001).
Google Scholar
He, L. et al. Flow cytometric measurement of fluorescence (Forster) resonance energy transfer from cyan fluorescent protein to yellow fluorescent protein using single-laser excitation at 458 nm. Cytometry A 53(1), 39–54 (2003).
Google Scholar
He, L. et al. A flow cytometric method to detect protein-protein interaction in living cells by directly visualizing donor fluorophore quenching during CFP–>YFP fluorescence resonance energy transfer (FRET). Cytometry A 55(2), 71–85 (2003).
Google Scholar
He, L. et al. TRAF3 forms heterotrimers with TRAF2 and modulates its ability to mediate NF-{kappa}B activation. J. Biol. Chem. 279(53), 55855–55865 (2004).
Google Scholar
Tron, L. et al. Flow cytometric measurement of fluorescence resonance energy transfer on cell surfaces. Quantitative evaluation of the transfer efficiency on a cell-by-cell basis. Biophys. J. 45(5), 939–946 (1984).
Google Scholar
Vamosi, G. et al. Conformation of the c-Fos/c-Jun complex in vivo: a combined FRET, FCCS, and MD-modeling study. Biophys. J. 94(7), 2859–2868 (2008).
Google Scholar
You, X. et al. Intracellular protein interaction mapping with FRET hybrids. Proc. Natl. Acad. Sci. U.S.A. 103(49), 18458–18463 (2006).
Google Scholar
Wu, X. et al. Prestin-prestin and prestin-GLUT5 interactions in HEK293T cells. Dev. Neurobiol. 67(4), 483–497 (2007).
Google Scholar
Camuzeaux, B. et al. Imaging Erg and Jun transcription factor interaction in living cells using fluorescence resonance energy transfer analyses. Biochem. Biophys. Res. Commun. 332(4), 1107–1114 (2005).
Google Scholar
Youvan, D. C. et al. Calibration of fluorescence resonance energy transfer in microscopy using genetically engineered GFP derivatives on nickel chelating beads. Biotechnol. Alia 3, 1–18 (1997).
Marqusee, S. & Baldwin, R. L. Helix stabilization by Glu-Lys+ salt bridges in short peptides of de novo design. Proc. Natl. Acad. Sci. U.S.A. 84(24), 8898–8902 (1987).
Google Scholar
Kitamura, A., Nakayama, Y. & Kinjo, M. Efficient and dynamic nuclear localization of green fluorescent protein via RNA binding. Biochem. Biophys. Res. Commun. 463(3), 401–406 (2015).
Google Scholar
Berney, C. & Danuser, G. FRET or no FRET: A quantitative comparison. Biophys. J. 84(6), 3992–4010 (2003).
Google Scholar
Lakowicz, J. R. Principles of Fluorescence Spectroscopy 3rd edn, 954 (Springer, 2006).
Google Scholar
Erickson, M. G., Moon, D. L. & Yue, D. T. DsRed as a potential FRET partner with CFP and GFP. Biophys. J. 85(1), 599–611 (2003).
Google Scholar
Butz, E. S. et al. Quantifying macromolecular interactions in living cells using FRET two-hybrid assays. Nat. Protoc. 11(12), 2470–2498 (2016).
Google Scholar
Arai, R. et al. Design of the linkers which effectively separate domains of a bifunctional fusion protein. Protein Eng. 14(8), 529–532 (2001).
Google Scholar
Arai, R. et al. Conformations of variably linked chimeric proteins evaluated by synchrotron X-ray small-angle scattering. Proteins 57(4), 829–838 (2004).
Google Scholar
Wriggers, W., Chakravarty, S. & Jennings, P. A. Control of protein functional dynamics by peptide linkers. Biopolymers 80(6), 736–746 (2005).
Google Scholar
Tramier, M. et al. Sensitivity of CFP/YFP and GFP/mCherry pairs to donor photobleaching on FRET determination by fluorescence lifetime imaging microscopy in living cells. Microsc. Res. Tech. 69(11), 933–939 (2006).
Google Scholar
Albertazzi, L. et al. Quantitative FRET analysis with the EGFP-mCherry fluorescent protein pair. Photochem. Photobiol. 85(1), 287–297 (2009).
Google Scholar
Akrap, N., Seidel, T. & Barisas, B. G. Forster distances for fluorescence resonant energy transfer between mCherry and other visible fluorescent proteins. Anal. Biochem. 402(1), 105–106 (2010).
Google Scholar
Amiri, H., Schultz, G. & Schaefer, M. FRET-based analysis of TRPC subunit stoichiometry. Cell Calcium 33(5–6), 463–470 (2003).
Google Scholar
Malm, M. et al. Evolution from adherent to suspension: Systems biology of HEK293 cell line development. Sci. Rep. 10(1), 18996 (2020).
Google Scholar
Lu, X. et al. A novel DNA binding mechanism for maf basic region-leucine zipper factors inferred from a MafA-DNA complex structure and binding specificities. Biochemistry 51(48), 9706–9717 (2012).
Google Scholar
Ormo, M. et al. Crystal structure of the Aequorea victoria green fluorescent protein. Science 273(5280), 1392–1395 (1996).
Google Scholar
Wilson, D. et al. Cooperative dimerization of paired class homeo domains on DNA. Genes Dev. 7(11), 2120–2134 (1993).
Google Scholar
Wilson, D. S. et al. High resolution crystal structure of a paired (Pax) class cooperative homeodomain dimer on DNA. Cell 82(5), 709–719 (1995).
Google Scholar
Sheng, G. et al. Modular organization of Pax/homeodomain proteins in transcriptional regulation. Biol. Chem. 378(8), 863–872 (1997).
Google Scholar
Wilson, D. S. & Desplan, C. Structural basis of Hox specificity. Nat. Struct. Biol. 6(4), 297–300 (1999).
Google Scholar
Roy, R., Hohng, S. & Ha, T. A practical guide to single-molecule FRET. Nat. Methods 5(6), 507–516 (2008).
Google Scholar
Lerner, E. et al. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. Elife 10, e60416 (2021).
Google Scholar
Xia, Z. & Liu, Y. Reliable and global measurement of fluorescence resonance energy transfer using fluorescence microscopes. Biophys. J. 81(4), 2395–2402 (2001).
Google Scholar
Higuchi, R., Krummel, B. & Saiki, R. K. A general method of in vitro preparation and specific mutagenesis of DNA fragments: Study of protein and DNA interactions. Nucleic Acids Res. 16(15), 7351–7367 (1988).
Google Scholar
Braman, J., Papworth, C. & Greener, A. Site-directed mutagenesis using double-stranded plasmid DNA templates. Methods Mol. Biol. 57, 31–44 (1996).
Google Scholar

