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techniques\nSequence database searches were carried out using the BLAST program available through the Bioinformatics Applications at the Rosalind Franklin Centre for Genomics Research [24]. Protein sequences that were highly homologous to the C-terminus of human PAX6 were aligned using CLUSTAL [24]. Secondary structure prediction was performed using the JPRED consensus method [25,26].\n\nYeast two-hybrid constructs\nAll cDNA and amino acid numbering is based on the human PAX6 cDNA and protein reference sequences available from the Human PAX6 Allelic Variant Database web site [27]. Standard PCR and subcloning techniques were used to make three PAX6 cDNA constructs in the pDBLeu expression vector (ProQuest Two-Hybrid System, Invitrogen), which generates a protein fused to the yeast GAL4 DNA binding domain. PAX6PST contains the whole PST domain (amino acids 278–422 of the full-length PAX6 protein). Primers were ST001 (forward) 5'-AAA AGT TCG ACT GCC AGC AAC ACA CCT AGT C-3' and ST005 (R) 5'-TTT TGC GGC TTT TTA CTG TAA TCT TGG CCA GTA TTG-3'. PAX6CTP contains the newly defined C-terminal peptide alone (391–422). Primers were ST004 (F) 5'-AAA AGT CGA CTA CCA CTT CAA CAG GAC TCA TT-3' and ST005 (R). PAX6PST-CT contains the PST domain minus the C-terminal peptide (278–390). This was made by cutting PAX6PST with NdeI and NotI to drop out the C-terminal peptide, and inserting a synthetic linker between the two restriction sites. All fragments generated by PCR or with linkers were sequenced to check that no errors had been introduced.\nA PAX6 PST domain construct containing the mutation 1627A\u003eG (Q422R) was generated in the same way as the PAX6PST construct, but using the reverse PCR primer ST006 5'-TTT TGC GGC CGC TTT TTA CCG TAA TCT TGG CCA GTA TTG AG-3', which contains the mutant nucleotide substitution (underlined).\ncDNA sequences containing the mutations 1615del10 [28] and 1629insT (X423L) [12] were generated by PCR from reverse transcribed RNA (a gift from Dr K Williamson and Prof V van Heyningen). Primers were ST015 (F) 5'-CCC ACA TAT GCA GAC ACA C-3' and ST031 (R) 5'-TTG CGG CCG CAT CCA TCC AGT CTA CAT TGT TC-3'. The PAX6PST construct was cut with NdeI and NotI to release the normal C-terminal peptide, and the mutant sequence was inserted.\n\nYeast two-hybrid library screens\nA mouse brain cDNA library (ProQuest, Invitrogen) was screened with the PAX6PST and PAX6CTP pDBLeu constructs. The library was constructed in the pPC86 vector, which produces proteins fused to the yeast GAL4 activation domain. The system uses three GAL4-activated reporter genes, HIS3, URA3 and lacZ, to identify positive interactions. Reporters are activated when the bait protein fused to the GAL4 DNA binding domain (pDBLeu) interacts with the prey protein fused to the GAL4 activation domain (pPC86), thus reconstituting GAL4 function. HIS3 activation allows growth on plates lacking histidine. Weak URA3 activation suppresses growth on plates containing 5-fluro-orotic acid while strong URA3 activation permits growth on plates lacking uracil. LacZ activation causes X-gal to turn blue in a beta-galactosidase assay. All assays were carried out in parallel with the five ProQuest control yeast strains A-E, which range from non-interactor (A) to strong interactor (E).\nAll procedures were carried out according to the supplier's protocols. Briefly, chemically competent MaV203 yeast cells were co-transformed with the cDNA library and the bait plasmid pDBLeu PAX6CTP or pDBLeu PAX6PST. Transformants (5 × 107) were plated on medium lacking histidine to check for HIS3 activation. HIS3 positives were then assayed for all 3 reporters. The pPC86 prey plasmid was isolated from all HIS3/URA3/LacZ positives and the cDNA insert sequenced. BLAST searches were performed to identify the cDNA insert [24].\n\nPairwise interactions\nSpecific interactions were tested by transforming competent MaV203 yeast cells with one bait construct (in pDBLeu) and one prey construct (in pPC86) and testing the resulting colonies for activation of the HIS3, URA3 and LacZ reporters as before.\nTo create a full-length Homer3 clone for pairwise tests, a cDNA clone (IMAGE clone 3602414, accession number BE569374) containing the missing N-terminal 70 amino acids was identified by a BLAST search of the EST nucleotide sequence database and obtained from the Rosalind Franklin Centre for Genomics Research. The missing fragment was amplified from the IMAGE clone by PCR and inserted into the pPC86-Homer3 plasmid to create a full-length expression construct.\n\nSemi-quantitative PCR\nTo check the relative representation of clones in the cDNA library, semi-quantitative PCR was performed on Pax6, Homer3, Dncl1, Trim11 and the constitutively expressed genes Gapdh and Atp5a1 [29,30]. Primers were designed to cross at least one intron, so that only correctly spliced clones were amplified. Primer sequences were: Pax6-F CAG CCA AAA TAG ATC TAC CTG; Pax6-R CGA TCA CAT GCT CTC TCC TT; Homer3-F CCC AGG TGG CTG TAG AGC; Homer3-R CTC TAC ACA GTG CAA AGC TCA G; Trim11-F GTG CAG GAT GTG AAG CTG; Trim11-R GCC TGC AGA TAG TCA TAG GG; Dncl1-F CAA AAA TGC AGA CAT GTC G; Dncl1-R CTA AGG GAG AAA AAA ATG GGG; Gapdh-F: CAT CAC CAT CTT CCA GGA GC; Gapdh-R: ATG ACC TTG CCC ACA GCC TT; Atp5a1-F: CAC ACG TGA GAT GTC CTC CA; Atp5a1-R: CAC AGA GAT TCG GGG ATA A. 10 ng library cDNA were amplified in a reaction containing 1xAmpliTaq polymerase buffer (Perkin Elmer), 1.5 mM MgCl2, 200μM each primer and 2.5 units of AmpliTaq polymerase (Perkin Elmer). PCR conditions were (95°C for 30 sec) × 1, (94°C for 30 sec, 55°C for 30 sec, 72°C for 30 sec) × 32 and (72°C for 2 min) × 1. Products were resolved on a 2.5% agarose gel with ΦX174/HaeIII size markers (Promega)."}

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:{"begin":676,"end":680},"obj":"SO_EXT:cDNA"},{"id":"T6749","span":{"begin":671,"end":675},"obj":"PR_EXT:000012318"},{"id":"T6748","span":{"begin":576,"end":583},"obj":"SO_EXT:sequence_variant_or_variation"},{"id":"T6747","span":{"begin":568,"end":575},"obj":"SO_EXT:0001023"},{"id":"T6746","span":{"begin":563,"end":567},"obj":"PR_EXT:000012318"},{"id":"T6745","span":{"begin":557,"end":562},"obj":"NCBITaxon:9606"},{"id":"T6744","span":{"begin":528,"end":537},"obj":"SO_EXT:biological_sequence"},{"id":"T6743","span":{"begin":510,"end":517},"obj":"CHEBI_PR_EXT:protein"},{"id":"T6742","span":{"begin":501,"end":505},"obj":"SO_EXT:cDNA"},{"id":"T6741","span":{"begin":496,"end":500},"obj":"PR_EXT:000012318"},{"id":"T6740","span":{"begin":490,"end":495},"obj":"NCBITaxon:9606"},{"id":"T6739","span":{"begin":453,"end":463},"obj":"CHEBI_SO_EXT:amino_acid"},{"id":"T6738","span":{"begin":444,"end":448},"obj":"SO_EXT:cDNA"},{"id":"T6737","span":{"begin":429,"end":439},"obj":"SO_EXT:engineered_biological_sequence"},{"id":"T6736","span":{"begin":412,"end":417},"obj":"NCBITaxon_EXT:yeast"},{"id":"T7919","span":{"begin":4748,"end":4757},"obj":"GO:0010467"},{"id":"T7915","span":{"begin":4697,"end":4701},"obj":"PR_EXT:000012318"},{"id":"T7914","span":{"begin":4644,"end":4648},"obj":"SO_EXT:cDNA"},{"id":"T7913","span":{"begin":4630,"end":4636},"obj":"SO_EXT:sequence_cloned_entity"}],"relations":[{"id":"R4201","pred":"_lexicallyChainedTo","subj":"T6788","obj":"T6787"}],"text":"Methods\n\nBioinformatics techniques\nSequence database searches were carried out using the BLAST program available through the Bioinformatics Applications at the Rosalind Franklin Centre for Genomics Research [24]. Protein sequences that were highly homologous to the C-terminus of human PAX6 were aligned using CLUSTAL [24]. Secondary structure prediction was performed using the JPRED consensus method [25,26].\n\nYeast two-hybrid constructs\nAll cDNA and amino acid numbering is based on the human PAX6 cDNA and protein reference sequences available from the Human PAX6 Allelic Variant Database web site [27]. Standard PCR and subcloning techniques were used to make three PAX6 cDNA constructs in the pDBLeu expression vector (ProQuest Two-Hybrid System, Invitrogen), which generates a protein fused to the yeast GAL4 DNA binding domain. PAX6PST contains the whole PST domain (amino acids 278–422 of the full-length PAX6 protein). Primers were ST001 (forward) 5'-AAA AGT TCG ACT GCC AGC AAC ACA CCT AGT C-3' and ST005 (R) 5'-TTT TGC GGC TTT TTA CTG TAA TCT TGG CCA GTA TTG-3'. PAX6CTP contains the newly defined C-terminal peptide alone (391–422). Primers were ST004 (F) 5'-AAA AGT CGA CTA CCA CTT CAA CAG GAC TCA TT-3' and ST005 (R). PAX6PST-CT contains the PST domain minus the C-terminal peptide (278–390). This was made by cutting PAX6PST with NdeI and NotI to drop out the C-terminal peptide, and inserting a synthetic linker between the two restriction sites. All fragments generated by PCR or with linkers were sequenced to check that no errors had been introduced.\nA PAX6 PST domain construct containing the mutation 1627A\u003eG (Q422R) was generated in the same way as the PAX6PST construct, but using the reverse PCR primer ST006 5'-TTT TGC GGC CGC TTT TTA CCG TAA TCT TGG CCA GTA TTG AG-3', which contains the mutant nucleotide substitution (underlined).\ncDNA sequences containing the mutations 1615del10 [28] and 1629insT (X423L) [12] were generated by PCR from reverse transcribed RNA (a gift from Dr K Williamson and Prof V van Heyningen). Primers were ST015 (F) 5'-CCC ACA TAT GCA GAC ACA C-3' and ST031 (R) 5'-TTG CGG CCG CAT CCA TCC AGT CTA CAT TGT TC-3'. The PAX6PST construct was cut with NdeI and NotI to release the normal C-terminal peptide, and the mutant sequence was inserted.\n\nYeast two-hybrid library screens\nA mouse brain cDNA library (ProQuest, Invitrogen) was screened with the PAX6PST and PAX6CTP pDBLeu constructs. The library was constructed in the pPC86 vector, which produces proteins fused to the yeast GAL4 activation domain. The system uses three GAL4-activated reporter genes, HIS3, URA3 and lacZ, to identify positive interactions. Reporters are activated when the bait protein fused to the GAL4 DNA binding domain (pDBLeu) interacts with the prey protein fused to the GAL4 activation domain (pPC86), thus reconstituting GAL4 function. HIS3 activation allows growth on plates lacking histidine. Weak URA3 activation suppresses growth on plates containing 5-fluro-orotic acid while strong URA3 activation permits growth on plates lacking uracil. LacZ activation causes X-gal to turn blue in a beta-galactosidase assay. All assays were carried out in parallel with the five ProQuest control yeast strains A-E, which range from non-interactor (A) to strong interactor (E).\nAll procedures were carried out according to the supplier's protocols. Briefly, chemically competent MaV203 yeast cells were co-transformed with the cDNA library and the bait plasmid pDBLeu PAX6CTP or pDBLeu PAX6PST. Transformants (5 × 107) were plated on medium lacking histidine to check for HIS3 activation. HIS3 positives were then assayed for all 3 reporters. The pPC86 prey plasmid was isolated from all HIS3/URA3/LacZ positives and the cDNA insert sequenced. BLAST searches were performed to identify the cDNA insert [24].\n\nPairwise interactions\nSpecific interactions were tested by transforming competent MaV203 yeast cells with one bait construct (in pDBLeu) and one prey construct (in pPC86) and testing the resulting colonies for activation of the HIS3, URA3 and LacZ reporters as before.\nTo create a full-length Homer3 clone for pairwise tests, a cDNA clone (IMAGE clone 3602414, accession number BE569374) containing the missing N-terminal 70 amino acids was identified by a BLAST search of the EST nucleotide sequence database and obtained from the Rosalind Franklin Centre for Genomics Research. The missing fragment was amplified from the IMAGE clone by PCR and inserted into the pPC86-Homer3 plasmid to create a full-length expression construct.\n\nSemi-quantitative PCR\nTo check the relative representation of clones in the cDNA library, semi-quantitative PCR was performed on Pax6, Homer3, Dncl1, Trim11 and the constitutively expressed genes Gapdh and Atp5a1 [29,30]. Primers were designed to cross at least one intron, so that only correctly spliced clones were amplified. Primer sequences were: Pax6-F CAG CCA AAA TAG ATC TAC CTG; Pax6-R CGA TCA CAT GCT CTC TCC TT; Homer3-F CCC AGG TGG CTG TAG AGC; Homer3-R CTC TAC ACA GTG CAA AGC TCA G; Trim11-F GTG CAG GAT GTG AAG CTG; Trim11-R GCC TGC AGA TAG TCA TAG GG; Dncl1-F CAA AAA TGC AGA CAT GTC G; Dncl1-R CTA AGG GAG AAA AAA ATG GGG; Gapdh-F: CAT CAC CAT CTT CCA GGA GC; Gapdh-R: ATG ACC TTG CCC ACA GCC TT; Atp5a1-F: CAC ACG TGA GAT GTC CTC CA; Atp5a1-R: CAC AGA GAT TCG GGG ATA A. 10 ng library cDNA were amplified in a reaction containing 1xAmpliTaq polymerase buffer (Perkin Elmer), 1.5 mM MgCl2, 200μM each primer and 2.5 units of AmpliTaq polymerase (Perkin Elmer). PCR conditions were (95°C for 30 sec) × 1, (94°C for 30 sec, 55°C for 30 sec, 72°C for 30 sec) × 32 and (72°C for 2 min) × 1. Products were resolved on a 2.5% agarose gel with ΦX174/HaeIII size markers (Promega)."}

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techniques\nSequence database searches were carried out using the BLAST program available through the Bioinformatics Applications at the Rosalind Franklin Centre for Genomics Research [24]. Protein sequences that were highly homologous to the C-terminus of human PAX6 were aligned using CLUSTAL [24]. Secondary structure prediction was performed using the JPRED consensus method [25,26].\n\nYeast two-hybrid constructs\nAll cDNA and amino acid numbering is based on the human PAX6 cDNA and protein reference sequences available from the Human PAX6 Allelic Variant Database web site [27]. Standard PCR and subcloning techniques were used to make three PAX6 cDNA constructs in the pDBLeu expression vector (ProQuest Two-Hybrid System, Invitrogen), which generates a protein fused to the yeast GAL4 DNA binding domain. PAX6PST contains the whole PST domain (amino acids 278–422 of the full-length PAX6 protein). Primers were ST001 (forward) 5'-AAA AGT TCG ACT GCC AGC AAC ACA CCT AGT C-3' and ST005 (R) 5'-TTT TGC GGC TTT TTA CTG TAA TCT TGG CCA GTA TTG-3'. PAX6CTP contains the newly defined C-terminal peptide alone (391–422). Primers were ST004 (F) 5'-AAA AGT CGA CTA CCA CTT CAA CAG GAC TCA TT-3' and ST005 (R). PAX6PST-CT contains the PST domain minus the C-terminal peptide (278–390). This was made by cutting PAX6PST with NdeI and NotI to drop out the C-terminal peptide, and inserting a synthetic linker between the two restriction sites. All fragments generated by PCR or with linkers were sequenced to check that no errors had been introduced.\nA PAX6 PST domain construct containing the mutation 1627A\u003eG (Q422R) was generated in the same way as the PAX6PST construct, but using the reverse PCR primer ST006 5'-TTT TGC GGC CGC TTT TTA CCG TAA TCT TGG CCA GTA TTG AG-3', which contains the mutant nucleotide substitution (underlined).\ncDNA sequences containing the mutations 1615del10 [28] and 1629insT (X423L) [12] were generated by PCR from reverse transcribed RNA (a gift from Dr K Williamson and Prof V van Heyningen). Primers were ST015 (F) 5'-CCC ACA TAT GCA GAC ACA C-3' and ST031 (R) 5'-TTG CGG CCG CAT CCA TCC AGT CTA CAT TGT TC-3'. The PAX6PST construct was cut with NdeI and NotI to release the normal C-terminal peptide, and the mutant sequence was inserted.\n\nYeast two-hybrid library screens\nA mouse brain cDNA library (ProQuest, Invitrogen) was screened with the PAX6PST and PAX6CTP pDBLeu constructs. The library was constructed in the pPC86 vector, which produces proteins fused to the yeast GAL4 activation domain. The system uses three GAL4-activated reporter genes, HIS3, URA3 and lacZ, to identify positive interactions. Reporters are activated when the bait protein fused to the GAL4 DNA binding domain (pDBLeu) interacts with the prey protein fused to the GAL4 activation domain (pPC86), thus reconstituting GAL4 function. HIS3 activation allows growth on plates lacking histidine. Weak URA3 activation suppresses growth on plates containing 5-fluro-orotic acid while strong URA3 activation permits growth on plates lacking uracil. LacZ activation causes X-gal to turn blue in a beta-galactosidase assay. All assays were carried out in parallel with the five ProQuest control yeast strains A-E, which range from non-interactor (A) to strong interactor (E).\nAll procedures were carried out according to the supplier's protocols. Briefly, chemically competent MaV203 yeast cells were co-transformed with the cDNA library and the bait plasmid pDBLeu PAX6CTP or pDBLeu PAX6PST. Transformants (5 × 107) were plated on medium lacking histidine to check for HIS3 activation. HIS3 positives were then assayed for all 3 reporters. The pPC86 prey plasmid was isolated from all HIS3/URA3/LacZ positives and the cDNA insert sequenced. BLAST searches were performed to identify the cDNA insert [24].\n\nPairwise interactions\nSpecific interactions were tested by transforming competent MaV203 yeast cells with one bait construct (in pDBLeu) and one prey construct (in pPC86) and testing the resulting colonies for activation of the HIS3, URA3 and LacZ reporters as before.\nTo create a full-length Homer3 clone for pairwise tests, a cDNA clone (IMAGE clone 3602414, accession number BE569374) containing the missing N-terminal 70 amino acids was identified by a BLAST search of the EST nucleotide sequence database and obtained from the Rosalind Franklin Centre for Genomics Research. The missing fragment was amplified from the IMAGE clone by PCR and inserted into the pPC86-Homer3 plasmid to create a full-length expression construct.\n\nSemi-quantitative PCR\nTo check the relative representation of clones in the cDNA library, semi-quantitative PCR was performed on Pax6, Homer3, Dncl1, Trim11 and the constitutively expressed genes Gapdh and Atp5a1 [29,30]. Primers were designed to cross at least one intron, so that only correctly spliced clones were amplified. Primer sequences were: Pax6-F CAG CCA AAA TAG ATC TAC CTG; Pax6-R CGA TCA CAT GCT CTC TCC TT; Homer3-F CCC AGG TGG CTG TAG AGC; Homer3-R CTC TAC ACA GTG CAA AGC TCA G; Trim11-F GTG CAG GAT GTG AAG CTG; Trim11-R GCC TGC AGA TAG TCA TAG GG; Dncl1-F CAA AAA TGC AGA CAT GTC G; Dncl1-R CTA AGG GAG AAA AAA ATG GGG; Gapdh-F: CAT CAC CAT CTT CCA GGA GC; Gapdh-R: ATG ACC TTG CCC ACA GCC TT; Atp5a1-F: CAC ACG TGA GAT GTC CTC CA; Atp5a1-R: CAC AGA GAT TCG GGG ATA A. 10 ng library cDNA were amplified in a reaction containing 1xAmpliTaq polymerase buffer (Perkin Elmer), 1.5 mM MgCl2, 200μM each primer and 2.5 units of AmpliTaq polymerase (Perkin Elmer). PCR conditions were (95°C for 30 sec) × 1, (94°C for 30 sec, 55°C for 30 sec, 72°C for 30 sec) × 32 and (72°C for 2 min) × 1. Products were resolved on a 2.5% agarose gel with ΦX174/HaeIII size markers (Promega)."}