{"gene":"CYC1","run_date":"2026-06-09T22:57:19","timeline":{"discoveries":[{"year":1983,"finding":"Expression of yeast CYC1 (iso-1-cytochrome c) is transcriptionally regulated by intracellular heme levels via an upstream activation site (UASc) centered ~275 bp upstream of the transcriptional initiation region; substitution of UASc with the GAL10 UAS renders transcription heme-independent, establishing that heme controls transcription initiation per se.","method":"CYC1-lacZ gene fusions, direct mRNA level determination, UAS substitution experiments in yeast","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (reporter fusions, mRNA quantification, UAS substitution), foundational study replicated by subsequent work","pmids":["6301690"],"is_preprint":false},{"year":1984,"finding":"The CYC1 UAS contains two functionally distinct subsites, UAS1 and UAS2: UAS1 mediates most transcription under glucose repression and responds to HAP1 via intracellular heme; UAS2 contributes equally under derepressed conditions and responds to HAP2. A point mutation in UAS2 increases its glucose activity 10–20 fold. Trans-acting mutations hap1-1 and hap2-1 selectively abolish UAS1 or UAS2 activity respectively.","method":"UAS deletion/substitution upstream of LEU2, glucose repression assays, trans-acting regulatory mutant analysis in yeast","journal":"Cell","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic dissection with multiple mutants and reporter substitutions, independently followed up in subsequent papers","pmids":["6319028"],"is_preprint":false},{"year":1987,"finding":"Both HAP2 and HAP3 proteins bind to CYC1 UAS2UP1 in an interdependent manner, forming a single protein-DNA complex (complex C) centered on the sequence TGATTGGT (homologous to the CCAAT box). Binding of either HAP2 or HAP3 is abolished when the complementary HAP gene is mutated, demonstrating that their binding to UAS2 is mutually dependent.","method":"Gel electrophoresis DNA binding assay, mobility-shift with HAP2/HAP3-beta-galactosidase fusions, methylation interference footprinting","journal":"Cell","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — in vitro binding assay with fusion proteins and footprinting, multiple orthogonal methods in one study","pmids":["2826015"],"is_preprint":false},{"year":1987,"finding":"The HAP1 protein directly binds in vitro to UAS1 of CYC1, specifically to region B; binding is stimulated by heme. A second factor, RC2, competes with HAP1 for the same sequence on the same face of the helix. A third factor (RAF) binds region A of UAS1.","method":"Gel electrophoresis DNA binding assay with crudely fractionated yeast extracts, major and minor groove contact analysis","journal":"Cell","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct in vitro binding with fractionated extracts and contact analysis, single lab, partially biochemically defined","pmids":["3030567"],"is_preprint":false},{"year":1985,"finding":"Three of four potential TATA elements in the CYC1 promoter are functional: the −106 TATA promotes initiation at +1, +10, +16; the −52 TATA at +16, +25, +34, +43; and the −22 TATA at +34 and +43. The information determining mRNA initiation sites is partly encoded within the DNA at the initiation site itself, not solely by fixed distance from TATA.","method":"Deletion analysis, introduction of TCGA sequences by site-directed mutagenesis, primer extension/S1 mapping of transcription start sites","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — systematic mutagenesis of multiple TATA elements with direct mapping of transcription start sites, multiple orthogonal approaches","pmids":["3001709"],"is_preprint":false},{"year":1991,"finding":"Two functionally distinct cis-acting elements cooperate in CYC1 mRNA 3′ end formation: (1) an upstream element whose function is enhanced by sequences including TAG...TATGTA and TATATA motifs; and (2) downstream elements that position the poly(A) site. A 38-bp deletion (cyc1-512) abolishing the upstream element reduces CYC1 mRNA to ~10% of normal and produces heterogeneous, elongated, labile transcripts; intragenic revertants restore function by creating new upstream signal sequences.","method":"S1 nuclease mapping, PCR-based 3′ end mapping, site-directed mutagenesis of cyc1-512 revertants","journal":"The EMBO journal","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple mutagenesis approaches with direct RNA end-mapping, replicated across several revertant classes","pmids":["1848175"],"is_preprint":false},{"year":1988,"finding":"Mature 3′ ends of CYC1 mRNA are generated in vitro by an endonucleolytic cleavage activity in yeast whole-cell extracts, followed by polyadenylation; the cleavage is ATP-dependent, accurate (at or near the in vivo poly(A) site), and abolished by mutations that prevent correct 3′ end formation in vivo.","method":"In vitro RNA processing assay using yeast whole-cell extracts with CYC1 precursor mRNA substrates; mutant substrate controls","journal":"Science","confidence":"High","confidence_rationale":"Tier 1 / Strong — biochemical reconstitution of 3′ end processing in vitro with mutant controls establishing sequence requirements","pmids":["2848317"],"is_preprint":false},{"year":1989,"finding":"Transcription of CYC1 terminates near (within ~100 nt of) the poly(A) site in vivo; a 38-bp region required for normal mRNA 3′ end formation is also required for transcription termination, demonstrated by CEN3 plasmid stability assays.","method":"CEN3 plasmid stability assay, insertion of CYC1 3′ sequences to block read-through transcription, nuclear run-on analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional assay (plasmid stability) plus run-on, single lab, two orthogonal approaches","pmids":["2554310"],"is_preprint":false},{"year":1988,"finding":"UAS1 region A and region B of CYC1 both respond individually to HAP1, and a point mutation in region B converts it to a TUF-regulated element; combinatorial analysis shows that HAP1 and TUF act synergistically on the mutant UAS1 to activate transcription.","method":"Point mutagenesis of UAS1 regions, combinatorial reporter assays in yeast","journal":"The EMBO journal","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — targeted mutagenesis with reporter assays, single lab","pmids":["2548856"],"is_preprint":false},{"year":1990,"finding":"Derepression of CYC1 from glucose repression requires both SNF1 and SSN6 gene products; in snf1 mutants CYC1 remains repressed upon shift to derepressing medium; in ssn6 mutants CYC1 is constitutively expressed at high levels even in glucose; SSN6 acts epistatically to SNF1, consistent with SNF1 acting through SSN6.","method":"Genetic epistasis analysis using snf1 and ssn6 single and double mutants, mRNA quantification","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis with defined mutant backgrounds, mRNA measurement, single lab","pmids":["2154683"],"is_preprint":false},{"year":1991,"finding":"Two functional TATA elements at positions −178 (beta-type: ATATATATAT) and −123 (alpha-type: TATATAAAA) are required for normal CYC1 transcription. When the same type occupies both sites, only the upstream element is used; when different types are at the two sites, both are used equally, suggesting recognition by distinct transcription factors.","method":"Site-directed mutagenesis of TATA elements, rearrangement of TATA element types, transcriptional analysis by primer extension","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — systematic site-directed mutagenesis with all pairwise combinations and direct transcription start site mapping","pmids":["1846668"],"is_preprint":false},{"year":1994,"finding":"TFIID binds to either of the two CYC1 TATA box elements in vivo independently of upstream activating sequences, as shown by high-resolution genomic footprinting; addition of a heat shock element renders the promoter heat-inducible without altering the TATA box footprints. This indicates that TFIID binding is not rate-limiting for CYC1 activation.","method":"High-resolution genomic footprinting (in vivo), site-directed mutagenesis of TATA boxes, heat shock induction assay","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo genomic footprinting plus mutagenesis plus functional induction assay, multiple orthogonal methods","pmids":["7991556"],"is_preprint":false},{"year":2001,"finding":"At the repressed CYC1 promoter (anaerobic + glucose conditions), the core promoter region contains no positioned nucleosomes, and both TFIID and RNA polymerase II are pre-bound in a complex, demonstrating that recruitment of these general transcription factors is not a rate-limiting step in CYC1 activation.","method":"Chromatin mapping, chromatin immunoprecipitation (ChIP) for TFIID and RNA Pol II, nucleosome positioning analysis","journal":"Molecular microbiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — ChIP and chromatin structure analysis, single lab, two orthogonal methods","pmids":["11401707"],"is_preprint":false},{"year":1997,"finding":"NMR analysis of the CYP1(HAP1) DNA-binding domain bound to CYC1 UAS1-B sequences revealed that the zinc cluster recognizes a CGG trinucleotide in the major groove, while the N-terminal basic region (arginyl/lysyl residues) contacts a thymine 5 bp downstream in the minor groove, defining the molecular basis of HAP1 binding specificity to CYC1 UAS1.","method":"NMR spectroscopy of protein–DNA complexes using CYP1(HAP1) DNA-binding domain peptide and CYC1 UAS1-B DNA fragments","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Moderate — NMR structural analysis with defined peptide and DNA fragments, single lab but rigorous structural method","pmids":["9224603"],"is_preprint":false},{"year":1996,"finding":"Degradation of CYC1 mRNA does not require translation: a CYC1 mRNA lacking all AUG triplets is as stable as normal mRNA. Both translatable and AUG-deficient CYC1 mRNAs are degraded 5′→3′ by the same pathway involving Xrn1p (the major 5′→3′ exonuclease), and deadenylation occurs at equivalent rates in both.","method":"AUG-deleted CYC1 alleles, poly(G)18 track insertion to trap degradation intermediates, xrn1Δ strain analysis, mRNA half-life measurements","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — multiple orthogonal genetic and biochemical approaches defining degradation pathway mechanism, single lab","pmids":["8799124"],"is_preprint":false},{"year":2013,"finding":"Mutations in human CYC1 (encoding cytochrome c1, the heme-containing subunit of mitochondrial respiratory chain complex III) cause reduced cytochrome c1 protein levels and reduced complex III activity in patient skeletal muscle and fibroblasts; exogenous expression of wild-type CYC1 in yeast mutants and patient fibroblasts rescues complex III activity, establishing that cytochrome c1 is required for complex III function and mediates electron transfer from the Rieske iron-sulfur protein to cytochrome c.","method":"Patient fibroblast and skeletal muscle biochemical assays, complementation in yeast and patient fibroblasts with wild-type CYC1 expression","journal":"American journal of human genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — complementation rescue in two cellular systems (yeast and human fibroblasts), multiple independent patients, functional complex III activity assay","pmids":["23910460"],"is_preprint":false},{"year":2014,"finding":"CYC1 silencing by shRNA in osteosarcoma cells reduces complex III activity, potentiates TRAIL-induced cytochrome c release and caspase-9 activation, and sensitizes cells to TRAIL-induced apoptosis in vitro and in vivo, placing CYC1/complex III upstream of the mitochondria-dependent (intrinsic) apoptotic pathway.","method":"shRNA knockdown of CYC1 in human osteosarcoma cell lines, complex III activity assay, cytochrome c release assay, caspase-9 activation assay, mouse xenograft model","journal":"Cellular physiology and biochemistry","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — loss-of-function with defined molecular readouts (complex III activity, cytochrome c release, caspase activation), single lab, multiple orthogonal assays","pmids":["25562155"],"is_preprint":false},{"year":1995,"finding":"CYC1 mRNA 3′ end formation in yeast employs redundant, cooperating signals: the strongest signal is TATATA; concomitant mutation of three signals (TTTATA, TATGTT, TATTTA) within and adjacent to the 38-bp region phenocopies the cyc1-512 deletion, establishing that multiple weak signals act together to produce efficient 3′ end formation.","method":"Site-directed mutagenesis of multiple 3′ end-forming signals, CYC1 mRNA level quantification","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic combinatorial mutagenesis with mRNA quantification, single lab","pmids":["7753784"],"is_preprint":false},{"year":1993,"finding":"Three distinct classes of cis-acting elements collaborate in CYC1 mRNA 3′ end formation: (i) upstream elements (TATATA, TAG...TATGTA, TTTTTATA) that enhance efficiency; (ii) downstream positioning elements (TTAAGAAC, AAGAA); and (iii) the actual poly(A) site (after cytidine residues 3′ to the downstream element). Upstream elements affect efficiency, while downstream elements and poly(A) site alterations affect position but not efficiency.","method":"Site-directed mutagenesis combined with analysis of cyc1-512 background, systematic introduction/deletion of signal elements","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic mutagenesis dissecting functional classes of 3′ signals, single lab, multiple mutant combinations","pmids":["8246998"],"is_preprint":false},{"year":1988,"finding":"An 82-bp region spanning the CYC1 mRNA 3′ end formation site is sufficient to direct poly(A) addition and terminate mRNA in an orientation-dependent manner when inserted into a heterologous transcript; in forward orientation the insert causes premature 3′ end formation at the same site as in native CYC1; recessive suppressors defining at least three complementation groups can suppress the insert's effect, implicating multiple trans-acting factors in 3′ end formation.","method":"Cloning of CYC1 3′ fragment into actin-HIS4 fusion gene, RNA blot analysis, 3′ end mapping, genetic suppressor analysis","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — functional heterologous insertion assay plus genetic suppressor screen defining trans-acting components, single lab","pmids":["2839828"],"is_preprint":false},{"year":1995,"finding":"Translation of CYC1 mRNA can only initiate efficiently within a restricted 'initiation region' spanning approximately nucleotide positions −27 to +37 (relative to the AUG). ATG-TAA sequences placed outside this region do not cause mRNA degradation, whereas those inside do (via Upf1-dependent decay). AUG-deficient CYC1 mRNA is stable, confirming that the restricted initiation region, not arbitrary 5′ proximity, determines translation competence.","method":"Introduction of TAA codons, ATG codons, and ATG-TAA sequences at systematic positions along CYC1; polyribosome distribution analysis; mRNA stability measurements in upf1 mutants","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — systematic positional mutagenesis with polysome analysis and NMD mutant controls, single lab","pmids":["7823918"],"is_preprint":false}],"current_model":"Human CYC1 encodes cytochrome c1, the heme-containing subunit of mitochondrial respiratory chain complex III, which mediates electron transfer from the Rieske iron-sulfur protein to cytochrome c; loss-of-function mutations reduce complex III activity and cytochrome c1 stability, cause mitochondrial disease, and sensitize cells to intrinsic apoptosis, while yeast CYC1 (iso-1-cytochrome c) has served as the primary model for dissecting eukaryotic transcriptional regulation—including heme/HAP1-dependent UAS1 activation, HAP2/HAP3 heterodimer binding to UAS2, SNF1/SSN6 glucose derepression, TFIID/RNA Pol II pre-assembly at the repressed core promoter, and the cis-acting signals governing mRNA 3′ end formation and 5′-to-3′ mRNA degradation."},"narrative":{"mechanistic_narrative":"Human CYC1 encodes cytochrome c1, the heme-containing subunit of mitochondrial respiratory chain complex III that mediates electron transfer from the Rieske iron-sulfur protein to cytochrome c; loss-of-function mutations reduce cytochrome c1 protein levels and complex III activity in patient skeletal muscle and fibroblasts, and wild-type CYC1 expression rescues complex III activity in both yeast and patient cells, establishing cytochrome c1 as required for complex III function and causative of a mitochondrial disease [PMID:23910460]. By controlling complex III, CYC1 sits upstream of the intrinsic apoptotic pathway: its silencing diminishes complex III activity and potentiates TRAIL-induced cytochrome c release, caspase-9 activation, and apoptosis [PMID:25562155]. The yeast CYC1 gene (iso-1-cytochrome c) has additionally served as a paradigm for eukaryotic transcriptional and post-transcriptional regulation—its expression is governed by heme through an upstream activation site whose UAS1 and UAS2 subsites respond to HAP1 and to the HAP2/HAP3 CCAAT-binding heterodimer respectively [PMID:6301690, PMID:6319028, PMID:2826015], its promoter is derepressed from glucose repression through SNF1 acting via SSN6 [PMID:2154683], and it has been used to dissect TATA-element selection, TFIID/RNA Pol II pre-assembly at the core promoter, mRNA 3′ end formation, and translation-independent 5′→3′ mRNA decay [PMID:1846668, PMID:11401707, PMID:8246998, PMID:8799124]. These yeast findings describe the model gene used to define general regulatory mechanisms rather than human CYC1 mitochondrial biology.","teleology":[{"year":1983,"claim":"Established that CYC1 expression is set at the level of transcription initiation by intracellular heme, defining heme as the primary regulatory signal acting through a discrete upstream activation site.","evidence":"CYC1-lacZ fusions, mRNA quantification and UAS substitution in yeast","pmids":["6301690"],"confidence":"High","gaps":["Did not identify the trans-acting factors transducing the heme signal","UAS internal architecture not resolved"]},{"year":1984,"claim":"Resolved the UAS into two functionally distinct subsites with separate trans-acting regulators, explaining how heme signaling and glucose state are integrated at one promoter.","evidence":"UAS deletion/substitution upstream of LEU2, glucose repression assays, hap1/hap2 mutant analysis in yeast","pmids":["6319028"],"confidence":"High","gaps":["Did not demonstrate direct factor-DNA binding","Did not define HAP protein composition at UAS2"]},{"year":1987,"claim":"Defined the molecular basis of UAS recognition by showing HAP2 and HAP3 bind UAS2 interdependently as a CCAAT-box heterodimeric complex, and HAP1 binds UAS1 region B in a heme-stimulated manner.","evidence":"Gel-shift with HAP-beta-galactosidase fusions, methylation interference footprinting, and binding with fractionated extracts in yeast","pmids":["2826015","3030567"],"confidence":"Medium","gaps":["RC2 and RAF factors only partially defined biochemically","How heme stimulation alters HAP1 binding not mechanistically resolved"]},{"year":1988,"claim":"Showed that UAS1 regions A and B each respond to HAP1 and can act synergistically with TUF, revealing combinatorial control among activators at a single UAS.","evidence":"Point mutagenesis of UAS1 with combinatorial reporter assays in yeast","pmids":["2548856"],"confidence":"Medium","gaps":["Mechanism of synergy not biochemically defined","Single lab"]},{"year":1990,"claim":"Placed CYC1 glucose derepression within the SNF1/SSN6 regulatory hierarchy, showing SNF1 acts through SSN6 to relieve repression.","evidence":"Genetic epistasis with snf1/ssn6 single and double mutants and mRNA quantification in yeast","pmids":["2154683"],"confidence":"Medium","gaps":["Direct molecular connection between SNF1/SSN6 and the CYC1 promoter not shown","Single lab"]},{"year":1997,"claim":"Provided the structural basis of activator specificity by defining how the HAP1 zinc cluster and basic region contact the CYC1 UAS1-B sequence.","evidence":"NMR of CYP1(HAP1) DNA-binding domain peptide bound to CYC1 UAS1-B DNA","pmids":["9224603"],"confidence":"High","gaps":["Full-length HAP1 and heme-bound state not structurally resolved","Single lab"]},{"year":1994,"claim":"Showed that TFIID binds either CYC1 TATA box in vivo independently of upstream activators, and later that TFIID and RNA Pol II are pre-bound at the repressed core promoter, redefining the rate-limiting step of activation as occurring after general factor recruitment.","evidence":"In vivo genomic footprinting, TATA mutagenesis, heat-shock induction, and ChIP of TFIID/Pol II with nucleosome mapping in yeast","pmids":["7991556","11401707"],"confidence":"Medium","gaps":["The actual rate-limiting activation step not identified","ChIP study single lab"]},{"year":1991,"claim":"Established that distinct TATA element types are recognized by distinct factors and dictate start-site selection, with the initiation site itself encoding positional information.","evidence":"Site-directed TATA mutagenesis, type rearrangement, and primer extension/S1 start-site mapping in yeast","pmids":["3001709","1846668"],"confidence":"High","gaps":["Identity of the distinct TATA-recognizing factors not established"]},{"year":1993,"claim":"Dissected CYC1 mRNA 3′ end formation into cooperating classes of cis-elements (efficiency upstream signals, positioning downstream elements, poly(A) site) acting through multiple redundant weak signals.","evidence":"Systematic site-directed mutagenesis of 3′ signals, revertant analysis, RNA end-mapping, and heterologous insertion with suppressor genetics in yeast","pmids":["1848175","8246998","7753784","2839828"],"confidence":"Medium","gaps":["Trans-acting 3′ processing machinery only inferred from suppressor groups","Individual factor assignments not made"]},{"year":1988,"claim":"Demonstrated biochemical reconstitution of CYC1 mature 3′ end formation by ATP-dependent endonucleolytic cleavage followed by polyadenylation, and linked the 3′ signal to transcription termination.","evidence":"In vitro RNA processing in yeast whole-cell extracts with mutant substrate controls; CEN3 plasmid stability and nuclear run-on for termination","pmids":["2848317","2554310"],"confidence":"Medium","gaps":["Cleavage/polyadenylation enzymes not purified or identified","Coupling mechanism between processing and termination not defined"]},{"year":1996,"claim":"Defined CYC1 mRNA decay as translation-independent 5′→3′ degradation by Xrn1p, and mapped a restricted translation initiation region that governs both translation competence and NMD susceptibility.","evidence":"AUG-deleted alleles, poly(G) intermediate trapping, xrn1Δ and upf1 mutants, polysome and half-life analysis in yeast","pmids":["8799124","7823918"],"confidence":"Medium","gaps":["Decapping and deadenylation enzymes not directly assayed here","Single lab"]},{"year":2013,"claim":"Connected human CYC1 to disease by showing that mutations reduce cytochrome c1 levels and complex III activity, with complementation rescue establishing cytochrome c1 as essential for complex III electron transfer.","evidence":"Patient muscle/fibroblast biochemistry and complementation rescue in yeast and patient fibroblasts","pmids":["23910460"],"confidence":"High","gaps":["Structural basis of mutation-induced destabilization not resolved","Assembly steps of complex III incorporation not detailed"]},{"year":2014,"claim":"Placed human CYC1/complex III upstream of intrinsic apoptosis by showing knockdown sensitizes cells to TRAIL-induced cytochrome c release and caspase-9 activation.","evidence":"shRNA knockdown in osteosarcoma cells with complex III, cytochrome c release, caspase-9 assays and xenograft model","pmids":["25562155"],"confidence":"Medium","gaps":["Direct molecular link between complex III activity and apoptotic priming not defined","Single lab"]},{"year":null,"claim":"How human cytochrome c1 is assembled into complex III, how its heme is incorporated, and how complex III status mechanistically tunes apoptotic sensitivity remain unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of human cytochrome c1 in the corpus","Heme attachment machinery not characterized here","Quantitative link between complex III output and apoptotic threshold unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0016491","term_label":"oxidoreductase activity","supporting_discovery_ids":[15]}],"localization":[{"term_id":"GO:0005739","term_label":"mitochondrion","supporting_discovery_ids":[15]}],"pathway":[{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[15]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[16]}],"complexes":["mitochondrial respiratory chain complex III"],"partners":["RIESKE IRON-SULFUR PROTEIN","CYTOCHROME C"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P08574","full_name":"Cytochrome c1, heme protein, mitochondrial","aliases":["Complex III subunit 4","Complex III subunit IV","Cytochrome b-c1 complex subunit 4","Ubiquinol-cytochrome-c reductase complex cytochrome c1 subunit","Cytochrome c-1"],"length_aa":325,"mass_kda":35.4,"function":"Component of the ubiquinol-cytochrome c oxidoreductase, a multisubunit transmembrane complex that is part of the mitochondrial electron transport chain which drives oxidative phosphorylation. The respiratory chain contains 3 multisubunit complexes succinate dehydrogenase (complex II, CII), ubiquinol-cytochrome c oxidoreductase (cytochrome b-c1 complex, complex III, CIII) and cytochrome c oxidase (complex IV, CIV), that cooperate to transfer electrons derived from NADH and succinate to molecular oxygen, creating an electrochemical gradient over the inner membrane that drives transmembrane transport and the ATP synthase. The cytochrome b-c1 complex catalyzes electron transfer from ubiquinol to cytochrome c, linking this redox reaction to translocation of protons across the mitochondrial inner membrane, with protons being carried across the membrane as hydrogens on the quinol. In the process called Q cycle, 2 protons are consumed from the matrix, 4 protons are released into the intermembrane space and 2 electrons are passed to cytochrome c. Cytochrome c1 is a catalytic core subunit containing a c-type heme. It transfers electrons from the [2Fe-2S] iron-sulfur cluster of the Rieske protein to cytochrome c","subcellular_location":"Mitochondrion inner membrane","url":"https://www.uniprot.org/uniprotkb/P08574/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/CYC1","classification":"Common Essential","n_dependent_lines":737,"n_total_lines":1208,"dependency_fraction":0.6100993377483444},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/CYC1","total_profiled":1310},"omim":[{"mim_id":"615453","title":"MITOCHONDRIAL COMPLEX III DEFICIENCY, NUCLEAR TYPE 6; MC3DN6","url":"https://www.omim.org/entry/615453"},{"mim_id":"613844","title":"UBIQUINOL-CYTOCHROME C REDUCTASE HINGE PROTEIN; UQCRH","url":"https://www.omim.org/entry/613844"},{"mim_id":"610843","title":"UBIQUINOL-CYTOCHROME C REDUCTASE, COMPLEX III SUBUNIT X; UQCR10","url":"https://www.omim.org/entry/610843"},{"mim_id":"300056","title":"HOLOCYTOCHROME C SYNTHASE; HCCS","url":"https://www.omim.org/entry/300056"},{"mim_id":"191329","title":"UBIQUINOL-CYTOCHROME c REDUCTASE CORE PROTEIN II; UQCRC2","url":"https://www.omim.org/entry/191329"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Mitochondria","reliability":"Approved"},{"location":"Equatorial segment","reliability":"Additional"}],"tissue_specificity":"Tissue enhanced","tissue_distribution":"Detected in all","driving_tissues":[{"tissue":"skeletal muscle","ntpm":684.3},{"tissue":"tongue","ntpm":676.8}],"url":"https://www.proteinatlas.org/search/CYC1"},"hgnc":{"alias_symbol":["UQCR4"],"prev_symbol":[]},"alphafold":{"accession":"P08574","domains":[{"cath_id":"1.10.760.10","chopping":"108-281","consensus_level":"medium","plddt":96.6856,"start":108,"end":281}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P08574","model_url":"https://alphafold.ebi.ac.uk/files/AF-P08574-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P08574-F1-predicted_aligned_error_v6.png","plddt_mean":84.94},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=CYC1","jax_strain_url":"https://www.jax.org/strain/search?query=CYC1"},"sequence":{"accession":"P08574","fasta_url":"https://rest.uniprot.org/uniprotkb/P08574.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P08574/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P08574"}},"corpus_meta":[{"pmid":"6301690","id":"PMC_6301690","title":"Heme regulates transcription of the CYC1 gene of S. cerevisiae via an upstream activation site.","date":"1983","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/6301690","citation_count":566,"is_preprint":false},{"pmid":"6760197","id":"PMC_6760197","title":"A GAL10-CYC1 hybrid yeast promoter identifies the GAL4 regulatory region as an upstream site.","date":"1982","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/6760197","citation_count":519,"is_preprint":false},{"pmid":"6319028","id":"PMC_6319028","title":"Distinctly regulated tandem upstream activation sites mediate catabolite repression of the CYC1 gene of S. cerevisiae.","date":"1984","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/6319028","citation_count":407,"is_preprint":false},{"pmid":"3001709","id":"PMC_3001709","title":"Each of three \"TATA elements\" specifies a subset of the transcription initiation sites at the CYC-1 promoter of Saccharomyces cerevisiae.","date":"1985","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/3001709","citation_count":308,"is_preprint":false},{"pmid":"2826015","id":"PMC_2826015","title":"Yeast HAP2 and HAP3 activators both bind to the CYC1 upstream activation site, UAS2, in an interdependent manner.","date":"1987","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/2826015","citation_count":211,"is_preprint":false},{"pmid":"3030567","id":"PMC_3030567","title":"Yeast HAP1 activator competes with the factor RC2 for binding to the upstream activation site UAS1 of the CYC1 gene.","date":"1987","source":"Cell","url":"https://pubmed.ncbi.nlm.nih.gov/3030567","citation_count":196,"is_preprint":false},{"pmid":"6096863","id":"PMC_6096863","title":"Upstream activation sites of the CYC1 gene of Saccharomyces cerevisiae are active when inverted but not when placed downstream of the \"TATA box\".","date":"1984","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/6096863","citation_count":173,"is_preprint":false},{"pmid":"2982161","id":"PMC_2982161","title":"A synthetic HIS4 regulatory element confers general amino acid control on the cytochrome c gene (CYC1) of yeast.","date":"1985","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/2982161","citation_count":123,"is_preprint":false},{"pmid":"185210","id":"PMC_185210","title":"Yeast cytochrome c messenger RNA. 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transcription initiation per se.\",\n      \"method\": \"CYC1-lacZ gene fusions, direct mRNA level determination, UAS substitution experiments in yeast\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (reporter fusions, mRNA quantification, UAS substitution), foundational study replicated by subsequent work\",\n      \"pmids\": [\"6301690\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1984,\n      \"finding\": \"The CYC1 UAS contains two functionally distinct subsites, UAS1 and UAS2: UAS1 mediates most transcription under glucose repression and responds to HAP1 via intracellular heme; UAS2 contributes equally under derepressed conditions and responds to HAP2. A point mutation in UAS2 increases its glucose activity 10–20 fold. Trans-acting mutations hap1-1 and hap2-1 selectively abolish UAS1 or UAS2 activity respectively.\",\n      \"method\": \"UAS deletion/substitution upstream of LEU2, glucose repression assays, trans-acting regulatory mutant analysis in yeast\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic dissection with multiple mutants and reporter substitutions, independently followed up in subsequent papers\",\n      \"pmids\": [\"6319028\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1987,\n      \"finding\": \"Both HAP2 and HAP3 proteins bind to CYC1 UAS2UP1 in an interdependent manner, forming a single protein-DNA complex (complex C) centered on the sequence TGATTGGT (homologous to the CCAAT box). Binding of either HAP2 or HAP3 is abolished when the complementary HAP gene is mutated, demonstrating that their binding to UAS2 is mutually dependent.\",\n      \"method\": \"Gel electrophoresis DNA binding assay, mobility-shift with HAP2/HAP3-beta-galactosidase fusions, methylation interference footprinting\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — in vitro binding assay with fusion proteins and footprinting, multiple orthogonal methods in one study\",\n      \"pmids\": [\"2826015\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1987,\n      \"finding\": \"The HAP1 protein directly binds in vitro to UAS1 of CYC1, specifically to region B; binding is stimulated by heme. A second factor, RC2, competes with HAP1 for the same sequence on the same face of the helix. A third factor (RAF) binds region A of UAS1.\",\n      \"method\": \"Gel electrophoresis DNA binding assay with crudely fractionated yeast extracts, major and minor groove contact analysis\",\n      \"journal\": \"Cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct in vitro binding with fractionated extracts and contact analysis, single lab, partially biochemically defined\",\n      \"pmids\": [\"3030567\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1985,\n      \"finding\": \"Three of four potential TATA elements in the CYC1 promoter are functional: the −106 TATA promotes initiation at +1, +10, +16; the −52 TATA at +16, +25, +34, +43; and the −22 TATA at +34 and +43. The information determining mRNA initiation sites is partly encoded within the DNA at the initiation site itself, not solely by fixed distance from TATA.\",\n      \"method\": \"Deletion analysis, introduction of TCGA sequences by site-directed mutagenesis, primer extension/S1 mapping of transcription start sites\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — systematic mutagenesis of multiple TATA elements with direct mapping of transcription start sites, multiple orthogonal approaches\",\n      \"pmids\": [\"3001709\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"Two functionally distinct cis-acting elements cooperate in CYC1 mRNA 3′ end formation: (1) an upstream element whose function is enhanced by sequences including TAG...TATGTA and TATATA motifs; and (2) downstream elements that position the poly(A) site. A 38-bp deletion (cyc1-512) abolishing the upstream element reduces CYC1 mRNA to ~10% of normal and produces heterogeneous, elongated, labile transcripts; intragenic revertants restore function by creating new upstream signal sequences.\",\n      \"method\": \"S1 nuclease mapping, PCR-based 3′ end mapping, site-directed mutagenesis of cyc1-512 revertants\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple mutagenesis approaches with direct RNA end-mapping, replicated across several revertant classes\",\n      \"pmids\": [\"1848175\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"Mature 3′ ends of CYC1 mRNA are generated in vitro by an endonucleolytic cleavage activity in yeast whole-cell extracts, followed by polyadenylation; the cleavage is ATP-dependent, accurate (at or near the in vivo poly(A) site), and abolished by mutations that prevent correct 3′ end formation in vivo.\",\n      \"method\": \"In vitro RNA processing assay using yeast whole-cell extracts with CYC1 precursor mRNA substrates; mutant substrate controls\",\n      \"journal\": \"Science\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — biochemical reconstitution of 3′ end processing in vitro with mutant controls establishing sequence requirements\",\n      \"pmids\": [\"2848317\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1989,\n      \"finding\": \"Transcription of CYC1 terminates near (within ~100 nt of) the poly(A) site in vivo; a 38-bp region required for normal mRNA 3′ end formation is also required for transcription termination, demonstrated by CEN3 plasmid stability assays.\",\n      \"method\": \"CEN3 plasmid stability assay, insertion of CYC1 3′ sequences to block read-through transcription, nuclear run-on analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional assay (plasmid stability) plus run-on, single lab, two orthogonal approaches\",\n      \"pmids\": [\"2554310\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"UAS1 region A and region B of CYC1 both respond individually to HAP1, and a point mutation in region B converts it to a TUF-regulated element; combinatorial analysis shows that HAP1 and TUF act synergistically on the mutant UAS1 to activate transcription.\",\n      \"method\": \"Point mutagenesis of UAS1 regions, combinatorial reporter assays in yeast\",\n      \"journal\": \"The EMBO journal\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — targeted mutagenesis with reporter assays, single lab\",\n      \"pmids\": [\"2548856\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1990,\n      \"finding\": \"Derepression of CYC1 from glucose repression requires both SNF1 and SSN6 gene products; in snf1 mutants CYC1 remains repressed upon shift to derepressing medium; in ssn6 mutants CYC1 is constitutively expressed at high levels even in glucose; SSN6 acts epistatically to SNF1, consistent with SNF1 acting through SSN6.\",\n      \"method\": \"Genetic epistasis analysis using snf1 and ssn6 single and double mutants, mRNA quantification\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis with defined mutant backgrounds, mRNA measurement, single lab\",\n      \"pmids\": [\"2154683\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"Two functional TATA elements at positions −178 (beta-type: ATATATATAT) and −123 (alpha-type: TATATAAAA) are required for normal CYC1 transcription. When the same type occupies both sites, only the upstream element is used; when different types are at the two sites, both are used equally, suggesting recognition by distinct transcription factors.\",\n      \"method\": \"Site-directed mutagenesis of TATA elements, rearrangement of TATA element types, transcriptional analysis by primer extension\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — systematic site-directed mutagenesis with all pairwise combinations and direct transcription start site mapping\",\n      \"pmids\": [\"1846668\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1994,\n      \"finding\": \"TFIID binds to either of the two CYC1 TATA box elements in vivo independently of upstream activating sequences, as shown by high-resolution genomic footprinting; addition of a heat shock element renders the promoter heat-inducible without altering the TATA box footprints. This indicates that TFIID binding is not rate-limiting for CYC1 activation.\",\n      \"method\": \"High-resolution genomic footprinting (in vivo), site-directed mutagenesis of TATA boxes, heat shock induction assay\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo genomic footprinting plus mutagenesis plus functional induction assay, multiple orthogonal methods\",\n      \"pmids\": [\"7991556\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2001,\n      \"finding\": \"At the repressed CYC1 promoter (anaerobic + glucose conditions), the core promoter region contains no positioned nucleosomes, and both TFIID and RNA polymerase II are pre-bound in a complex, demonstrating that recruitment of these general transcription factors is not a rate-limiting step in CYC1 activation.\",\n      \"method\": \"Chromatin mapping, chromatin immunoprecipitation (ChIP) for TFIID and RNA Pol II, nucleosome positioning analysis\",\n      \"journal\": \"Molecular microbiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — ChIP and chromatin structure analysis, single lab, two orthogonal methods\",\n      \"pmids\": [\"11401707\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"NMR analysis of the CYP1(HAP1) DNA-binding domain bound to CYC1 UAS1-B sequences revealed that the zinc cluster recognizes a CGG trinucleotide in the major groove, while the N-terminal basic region (arginyl/lysyl residues) contacts a thymine 5 bp downstream in the minor groove, defining the molecular basis of HAP1 binding specificity to CYC1 UAS1.\",\n      \"method\": \"NMR spectroscopy of protein–DNA complexes using CYP1(HAP1) DNA-binding domain peptide and CYC1 UAS1-B DNA fragments\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — NMR structural analysis with defined peptide and DNA fragments, single lab but rigorous structural method\",\n      \"pmids\": [\"9224603\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1996,\n      \"finding\": \"Degradation of CYC1 mRNA does not require translation: a CYC1 mRNA lacking all AUG triplets is as stable as normal mRNA. Both translatable and AUG-deficient CYC1 mRNAs are degraded 5′→3′ by the same pathway involving Xrn1p (the major 5′→3′ exonuclease), and deadenylation occurs at equivalent rates in both.\",\n      \"method\": \"AUG-deleted CYC1 alleles, poly(G)18 track insertion to trap degradation intermediates, xrn1Δ strain analysis, mRNA half-life measurements\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — multiple orthogonal genetic and biochemical approaches defining degradation pathway mechanism, single lab\",\n      \"pmids\": [\"8799124\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2013,\n      \"finding\": \"Mutations in human CYC1 (encoding cytochrome c1, the heme-containing subunit of mitochondrial respiratory chain complex III) cause reduced cytochrome c1 protein levels and reduced complex III activity in patient skeletal muscle and fibroblasts; exogenous expression of wild-type CYC1 in yeast mutants and patient fibroblasts rescues complex III activity, establishing that cytochrome c1 is required for complex III function and mediates electron transfer from the Rieske iron-sulfur protein to cytochrome c.\",\n      \"method\": \"Patient fibroblast and skeletal muscle biochemical assays, complementation in yeast and patient fibroblasts with wild-type CYC1 expression\",\n      \"journal\": \"American journal of human genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — complementation rescue in two cellular systems (yeast and human fibroblasts), multiple independent patients, functional complex III activity assay\",\n      \"pmids\": [\"23910460\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"CYC1 silencing by shRNA in osteosarcoma cells reduces complex III activity, potentiates TRAIL-induced cytochrome c release and caspase-9 activation, and sensitizes cells to TRAIL-induced apoptosis in vitro and in vivo, placing CYC1/complex III upstream of the mitochondria-dependent (intrinsic) apoptotic pathway.\",\n      \"method\": \"shRNA knockdown of CYC1 in human osteosarcoma cell lines, complex III activity assay, cytochrome c release assay, caspase-9 activation assay, mouse xenograft model\",\n      \"journal\": \"Cellular physiology and biochemistry\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — loss-of-function with defined molecular readouts (complex III activity, cytochrome c release, caspase activation), single lab, multiple orthogonal assays\",\n      \"pmids\": [\"25562155\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"CYC1 mRNA 3′ end formation in yeast employs redundant, cooperating signals: the strongest signal is TATATA; concomitant mutation of three signals (TTTATA, TATGTT, TATTTA) within and adjacent to the 38-bp region phenocopies the cyc1-512 deletion, establishing that multiple weak signals act together to produce efficient 3′ end formation.\",\n      \"method\": \"Site-directed mutagenesis of multiple 3′ end-forming signals, CYC1 mRNA level quantification\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic combinatorial mutagenesis with mRNA quantification, single lab\",\n      \"pmids\": [\"7753784\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1993,\n      \"finding\": \"Three distinct classes of cis-acting elements collaborate in CYC1 mRNA 3′ end formation: (i) upstream elements (TATATA, TAG...TATGTA, TTTTTATA) that enhance efficiency; (ii) downstream positioning elements (TTAAGAAC, AAGAA); and (iii) the actual poly(A) site (after cytidine residues 3′ to the downstream element). Upstream elements affect efficiency, while downstream elements and poly(A) site alterations affect position but not efficiency.\",\n      \"method\": \"Site-directed mutagenesis combined with analysis of cyc1-512 background, systematic introduction/deletion of signal elements\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic mutagenesis dissecting functional classes of 3′ signals, single lab, multiple mutant combinations\",\n      \"pmids\": [\"8246998\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1988,\n      \"finding\": \"An 82-bp region spanning the CYC1 mRNA 3′ end formation site is sufficient to direct poly(A) addition and terminate mRNA in an orientation-dependent manner when inserted into a heterologous transcript; in forward orientation the insert causes premature 3′ end formation at the same site as in native CYC1; recessive suppressors defining at least three complementation groups can suppress the insert's effect, implicating multiple trans-acting factors in 3′ end formation.\",\n      \"method\": \"Cloning of CYC1 3′ fragment into actin-HIS4 fusion gene, RNA blot analysis, 3′ end mapping, genetic suppressor analysis\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — functional heterologous insertion assay plus genetic suppressor screen defining trans-acting components, single lab\",\n      \"pmids\": [\"2839828\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Translation of CYC1 mRNA can only initiate efficiently within a restricted 'initiation region' spanning approximately nucleotide positions −27 to +37 (relative to the AUG). ATG-TAA sequences placed outside this region do not cause mRNA degradation, whereas those inside do (via Upf1-dependent decay). AUG-deficient CYC1 mRNA is stable, confirming that the restricted initiation region, not arbitrary 5′ proximity, determines translation competence.\",\n      \"method\": \"Introduction of TAA codons, ATG codons, and ATG-TAA sequences at systematic positions along CYC1; polyribosome distribution analysis; mRNA stability measurements in upf1 mutants\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — systematic positional mutagenesis with polysome analysis and NMD mutant controls, single lab\",\n      \"pmids\": [\"7823918\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"Human CYC1 encodes cytochrome c1, the heme-containing subunit of mitochondrial respiratory chain complex III, which mediates electron transfer from the Rieske iron-sulfur protein to cytochrome c; loss-of-function mutations reduce complex III activity and cytochrome c1 stability, cause mitochondrial disease, and sensitize cells to intrinsic apoptosis, while yeast CYC1 (iso-1-cytochrome c) has served as the primary model for dissecting eukaryotic transcriptional regulation—including heme/HAP1-dependent UAS1 activation, HAP2/HAP3 heterodimer binding to UAS2, SNF1/SSN6 glucose derepression, TFIID/RNA Pol II pre-assembly at the repressed core promoter, and the cis-acting signals governing mRNA 3′ end formation and 5′-to-3′ mRNA degradation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"Human CYC1 encodes cytochrome c1, the heme-containing subunit of mitochondrial respiratory chain complex III that mediates electron transfer from the Rieske iron-sulfur protein to cytochrome c; loss-of-function mutations reduce cytochrome c1 protein levels and complex III activity in patient skeletal muscle and fibroblasts, and wild-type CYC1 expression rescues complex III activity in both yeast and patient cells, establishing cytochrome c1 as required for complex III function and causative of a mitochondrial disease [#15]. By controlling complex III, CYC1 sits upstream of the intrinsic apoptotic pathway: its silencing diminishes complex III activity and potentiates TRAIL-induced cytochrome c release, caspase-9 activation, and apoptosis [#16]. The yeast CYC1 gene (iso-1-cytochrome c) has additionally served as a paradigm for eukaryotic transcriptional and post-transcriptional regulation\\u2014its expression is governed by heme through an upstream activation site whose UAS1 and UAS2 subsites respond to HAP1 and to the HAP2/HAP3 CCAAT-binding heterodimer respectively [#0, #1, #2], its promoter is derepressed from glucose repression through SNF1 acting via SSN6 [#9], and it has been used to dissect TATA-element selection, TFIID/RNA Pol II pre-assembly at the core promoter, mRNA 3\\u2032 end formation, and translation-independent 5\\u2032\\u21923\\u2032 mRNA decay [#10, #12, #18, #14]. These yeast findings describe the model gene used to define general regulatory mechanisms rather than human CYC1 mitochondrial biology.\",\n  \"teleology\": [\n    {\n      \"year\": 1983,\n      \"claim\": \"Established that CYC1 expression is set at the level of transcription initiation by intracellular heme, defining heme as the primary regulatory signal acting through a discrete upstream activation site.\",\n      \"evidence\": \"CYC1-lacZ fusions, mRNA quantification and UAS substitution in yeast\",\n      \"pmids\": [\"6301690\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not identify the trans-acting factors transducing the heme signal\", \"UAS internal architecture not resolved\"]\n    },\n    {\n      \"year\": 1984,\n      \"claim\": \"Resolved the UAS into two functionally distinct subsites with separate trans-acting regulators, explaining how heme signaling and glucose state are integrated at one promoter.\",\n      \"evidence\": \"UAS deletion/substitution upstream of LEU2, glucose repression assays, hap1/hap2 mutant analysis in yeast\",\n      \"pmids\": [\"6319028\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not demonstrate direct factor-DNA binding\", \"Did not define HAP protein composition at UAS2\"]\n    },\n    {\n      \"year\": 1987,\n      \"claim\": \"Defined the molecular basis of UAS recognition by showing HAP2 and HAP3 bind UAS2 interdependently as a CCAAT-box heterodimeric complex, and HAP1 binds UAS1 region B in a heme-stimulated manner.\",\n      \"evidence\": \"Gel-shift with HAP-beta-galactosidase fusions, methylation interference footprinting, and binding with fractionated extracts in yeast\",\n      \"pmids\": [\"2826015\", \"3030567\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"RC2 and RAF factors only partially defined biochemically\", \"How heme stimulation alters HAP1 binding not mechanistically resolved\"]\n    },\n    {\n      \"year\": 1988,\n      \"claim\": \"Showed that UAS1 regions A and B each respond to HAP1 and can act synergistically with TUF, revealing combinatorial control among activators at a single UAS.\",\n      \"evidence\": \"Point mutagenesis of UAS1 with combinatorial reporter assays in yeast\",\n      \"pmids\": [\"2548856\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of synergy not biochemically defined\", \"Single lab\"]\n    },\n    {\n      \"year\": 1990,\n      \"claim\": \"Placed CYC1 glucose derepression within the SNF1/SSN6 regulatory hierarchy, showing SNF1 acts through SSN6 to relieve repression.\",\n      \"evidence\": \"Genetic epistasis with snf1/ssn6 single and double mutants and mRNA quantification in yeast\",\n      \"pmids\": [\"2154683\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular connection between SNF1/SSN6 and the CYC1 promoter not shown\", \"Single lab\"]\n    },\n    {\n      \"year\": 1997,\n      \"claim\": \"Provided the structural basis of activator specificity by defining how the HAP1 zinc cluster and basic region contact the CYC1 UAS1-B sequence.\",\n      \"evidence\": \"NMR of CYP1(HAP1) DNA-binding domain peptide bound to CYC1 UAS1-B DNA\",\n      \"pmids\": [\"9224603\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Full-length HAP1 and heme-bound state not structurally resolved\", \"Single lab\"]\n    },\n    {\n      \"year\": 1994,\n      \"claim\": \"Showed that TFIID binds either CYC1 TATA box in vivo independently of upstream activators, and later that TFIID and RNA Pol II are pre-bound at the repressed core promoter, redefining the rate-limiting step of activation as occurring after general factor recruitment.\",\n      \"evidence\": \"In vivo genomic footprinting, TATA mutagenesis, heat-shock induction, and ChIP of TFIID/Pol II with nucleosome mapping in yeast\",\n      \"pmids\": [\"7991556\", \"11401707\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"The actual rate-limiting activation step not identified\", \"ChIP study single lab\"]\n    },\n    {\n      \"year\": 1991,\n      \"claim\": \"Established that distinct TATA element types are recognized by distinct factors and dictate start-site selection, with the initiation site itself encoding positional information.\",\n      \"evidence\": \"Site-directed TATA mutagenesis, type rearrangement, and primer extension/S1 start-site mapping in yeast\",\n      \"pmids\": [\"3001709\", \"1846668\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Identity of the distinct TATA-recognizing factors not established\"]\n    },\n    {\n      \"year\": 1993,\n      \"claim\": \"Dissected CYC1 mRNA 3\\u2032 end formation into cooperating classes of cis-elements (efficiency upstream signals, positioning downstream elements, poly(A) site) acting through multiple redundant weak signals.\",\n      \"evidence\": \"Systematic site-directed mutagenesis of 3\\u2032 signals, revertant analysis, RNA end-mapping, and heterologous insertion with suppressor genetics in yeast\",\n      \"pmids\": [\"1848175\", \"8246998\", \"7753784\", \"2839828\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Trans-acting 3\\u2032 processing machinery only inferred from suppressor groups\", \"Individual factor assignments not made\"]\n    },\n    {\n      \"year\": 1988,\n      \"claim\": \"Demonstrated biochemical reconstitution of CYC1 mature 3\\u2032 end formation by ATP-dependent endonucleolytic cleavage followed by polyadenylation, and linked the 3\\u2032 signal to transcription termination.\",\n      \"evidence\": \"In vitro RNA processing in yeast whole-cell extracts with mutant substrate controls; CEN3 plasmid stability and nuclear run-on for termination\",\n      \"pmids\": [\"2848317\", \"2554310\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Cleavage/polyadenylation enzymes not purified or identified\", \"Coupling mechanism between processing and termination not defined\"]\n    },\n    {\n      \"year\": 1996,\n      \"claim\": \"Defined CYC1 mRNA decay as translation-independent 5\\u2032\\u21923\\u2032 degradation by Xrn1p, and mapped a restricted translation initiation region that governs both translation competence and NMD susceptibility.\",\n      \"evidence\": \"AUG-deleted alleles, poly(G) intermediate trapping, xrn1\\u0394 and upf1 mutants, polysome and half-life analysis in yeast\",\n      \"pmids\": [\"8799124\", \"7823918\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Decapping and deadenylation enzymes not directly assayed here\", \"Single lab\"]\n    },\n    {\n      \"year\": 2013,\n      \"claim\": \"Connected human CYC1 to disease by showing that mutations reduce cytochrome c1 levels and complex III activity, with complementation rescue establishing cytochrome c1 as essential for complex III electron transfer.\",\n      \"evidence\": \"Patient muscle/fibroblast biochemistry and complementation rescue in yeast and patient fibroblasts\",\n      \"pmids\": [\"23910460\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of mutation-induced destabilization not resolved\", \"Assembly steps of complex III incorporation not detailed\"]\n    },\n    {\n      \"year\": 2014,\n      \"claim\": \"Placed human CYC1/complex III upstream of intrinsic apoptosis by showing knockdown sensitizes cells to TRAIL-induced cytochrome c release and caspase-9 activation.\",\n      \"evidence\": \"shRNA knockdown in osteosarcoma cells with complex III, cytochrome c release, caspase-9 assays and xenograft model\",\n      \"pmids\": [\"25562155\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Direct molecular link between complex III activity and apoptotic priming not defined\", \"Single lab\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How human cytochrome c1 is assembled into complex III, how its heme is incorporated, and how complex III status mechanistically tunes apoptotic sensitivity remain unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No structural model of human cytochrome c1 in the corpus\", \"Heme attachment machinery not characterized here\", \"Quantitative link between complex III output and apoptotic threshold unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0016491\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005739\", \"supporting_discovery_ids\": [15]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [15]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [16]}\n    ],\n    \"complexes\": [\"mitochondrial respiratory chain complex III\"],\n    \"partners\": [\"Rieske iron-sulfur protein\", \"cytochrome c\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":3,"faith_total":3,"faith_pct":100.0}}