{"gene":"POLR1B","run_date":"2026-06-10T06:43:35","timeline":{"discoveries":[{"year":1998,"finding":"Absence of RPA135 (the second-largest subunit of yeast RNA Pol I) triggers a gradual decrease in rDNA repeat number to ~half normal level, and reintroduction of RPA135 restores normal repeat number. This effect requires FOB1 (replication fork blocking protein), placing RNA Pol I/RPA135 as a regulator of rDNA copy number stability via replication fork blockage-stimulated recombination.","method":"Yeast genetic deletion/complementation (rpa135Δ mutants), rDNA copy number analysis, epistasis with fob1Δ","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis with clean deletion and complementation, replicated across multiple genetic backgrounds, mechanistic pathway placement established","pmids":["9869636"],"is_preprint":false},{"year":1991,"finding":"RPA135 was identified as one of at least nine genes (RRN1–RRN9) specifically required for RNA Pol I-dependent 35S rRNA synthesis in S. cerevisiae, established by a genetic screen using a GAL7-driven Pol II rescue system to identify mutants defective in Pol I transcription.","method":"Genetic screen for Pol I transcription mutants using GAL7-hybrid gene suppression system; red/white colony color assay and galactose-dependent growth test","journal":"Proceedings of the National Academy of Sciences of the United States of America","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — clean genetic screen with functional readout (rRNA synthesis), single lab but orthogonal growth and transcription assays","pmids":["1871118"],"is_preprint":false},{"year":1995,"finding":"Yeast cells lacking RNA Pol I activity due to RPA135 gene disruption can survive by switching rDNA transcription to RNA Pol II via a cryptic Pol II promoter overlapping the Pol I promoter in rDNA. This demonstrates that RPA135 (and thus Pol I) is the sole normal source of 25S, 18S, and 5.8S rRNAs, and its loss is viable only through this polymerase switch.","method":"RPA135 gene disruption; RNA analysis of polymerase-specific transcripts; episomal rDNA characterization in petite mutants","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — clean null mutant, RNA analysis confirming polymerase switch, functional rescue demonstrated","pmids":["7739526"],"is_preprint":false},{"year":2003,"finding":"The C-terminal Zn-binding domain of Rpa135 (yeast POLR1B ortholog) is required for recruitment of the largest Pol I subunit Rpa190 into the RNA polymerase I complex. Nonfunctional Rpa135 mutants lacking this domain failed to assemble Pol I. Surprisingly, replacement of all four cysteines with alanines still yielded functional Rpa135, indicating the domain's essential role is structural rather than Zn2+-coordination per se.","method":"Mutagenesis of Zn-binding domain (individual and combinatorial cysteine-to-alanine substitutions); analysis of Pol I complex assembly","journal":"Eukaryotic cell","confidence":"Medium","confidence_rationale":"Tier 1 / Moderate — mutagenesis with functional assembly assay, single lab","pmids":["14555487"],"is_preprint":false},{"year":2007,"finding":"Specific point mutations in RPA135 (rpa135-L656P and rpa135-D395N) are lethal in combination with rpa34Δ or rpa49Δ mutations, placing RPA135 in a functional network with Rpa34 and Rpa49 subunits for Pol I transcription. The lobe domain of Rpa135 and the jaw domain of Rpa190 form a jaw-lobe interface critical for Pol I function.","method":"Yeast genetic epistasis; synthetic lethality analysis of double mutants; growth assays","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — genetic epistasis in yeast, synthetic lethality with multiple alleles, single lab","pmids":["18086878"],"is_preprint":false},{"year":2007,"finding":"Mouse Rpo1-2 (POLR1B ortholog) is essential for pre-implantation development. A gene-trap truncation in exon 14 of Rpo1-2 (removing 312 aa from C-terminus) severely impairs rRNA synthesis, causes nucleolus disruption, and triggers apoptotic cell death by the morula stage in homozygous embryos.","method":"Gene trap insertional mutagenesis in mice; rRNA synthesis assay; histological analysis of embryos; nucleolar structure analysis","journal":"Biochemical and biophysical research communications","confidence":"High","confidence_rationale":"Tier 2 / Strong — in vivo loss-of-function with defined molecular (rRNA synthesis) and cellular (nucleolus disruption, apoptosis) phenotype, mouse model","pmids":["18023416"],"is_preprint":false},{"year":2018,"finding":"RPA135 (POLR1B) is required for BMH-21-mediated degradation of the largest Pol I subunit RPA194. Pol I preinitiation factors and polymerase subunits including RPA135 are necessary components of the conserved transcription elongation checkpoint activated by BMH-21, which directly impairs Pol I transcription elongation causing long-lived polymerase pausing.","method":"Genetic analyses in yeast and human cells; fully reconstituted Pol I transcription assay; small-molecule treatment (BMH-21); subunit dependency analysis","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — reconstituted in vitro transcription assay plus genetic analyses in two organisms, direct mechanistic demonstration of elongation inhibition","pmids":["29642000"],"is_preprint":false},{"year":2019,"finding":"A super-active Pol I mutant allele RPA135-F301S restores normal rRNA synthesis and increases Pol I density on rDNA genes in the absence of Rpa49. The F301S mutation maps to the jaw-lobe interface of Pol I (lobe in Rpa135, jaw in Rpa190/Rpa12), and Pol I bearing this mutation is hyper-active in an in vitro tailed-template transcription assay, proposed to result from a conformational change supporting DNA insertion into the enzyme cleft.","method":"Genetic suppressor screen; rRNA synthesis assay; ChIP (Pol I density on rDNA); in vitro tailed-template transcription assay; structural mapping onto Pol I cryo-EM structure","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution assay plus in vivo genetic and ChIP data, multiple orthogonal methods","pmids":["31136569"],"is_preprint":false},{"year":2019,"finding":"Pathogenic variants in POLR1B cause Treacher Collins syndrome type 4 (TCS4). Knockdown of polr1b in zebrafish induces abnormal craniofacial phenotype mimicking TCS, associated with altered ribosomal gene expression, massive p53-dependent apoptosis in the neuroepithelium, and reduced number of neural crest cell (NCC) derivatives.","method":"Exome sequencing in human patients; zebrafish polr1b morpholino knockdown; craniofacial phenotyping; ribosomal gene expression analysis; apoptosis assay (p53-dependent); NCC derivative quantification","journal":"Genetics in medicine : official journal of the American College of Medical Genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — zebrafish loss-of-function with defined molecular mechanism (p53-dependent apoptosis, rRNA), replicated with human genetic data","pmids":["31649276"],"is_preprint":false},{"year":2020,"finding":"RPA135 (POLR1B) silencing causes alterations in the expression and localization of Pol I subunits RPA194. Despite these alterations, the core Pol I complex between RPA194 and RPA135 remains intact upon RPA12 knockdown, and the transcription of Pol I and its engagement with chromatin remain unaffected when RPA12 is silenced. BMH-21-mediated degradation of RPA194 was found to be independent of RPA12.","method":"siRNA knockdown of RPA12; immunofluorescence (localization); co-immunoprecipitation (complex integrity); chromatin engagement assay; BMH-21 treatment","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal co-IP and localization with functional consequence, single lab, two orthogonal methods","pmids":["37167337"],"is_preprint":false},{"year":2023,"finding":"Homozygous null mutations in Polr1b lead to preimplantation lethality in mice, and Polr1b-/- embryos exhibit defects in nucleolar structure (decreased nucleolar precursor bodies, increased nucleolar volume, single condensed nucleolus), demonstrating that POLR1B/Pol I function and rRNA transcription are required for maintaining nucleolar phase separation properties and integrity during development.","method":"Homozygous null mouse mutants (Polr1b-/-); live imaging and nucleolar structure analysis; pharmacological Pol I inhibition in embryos and hiPSCs; viscosity measurements of granular compartment","journal":"PLoS genetics","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic null + pharmacological inhibition + live imaging with quantitative biophysical readout (viscosity/phase separation), multiple orthogonal approaches","pmids":["37639467"],"is_preprint":false},{"year":2023,"finding":"PAF49 (mammalian orthologue of yeast Rpa34) contains an 'arm' domain that directly interacts with POLR1B (PolR1B). This interaction is required for rDNA transcription; disrupting the PAF49–PolR1B interaction inhibits Pol I transcription in normal and cancer cells, arresting normal cells and killing cancer cells.","method":"Auxin-induced degron system for PAF49 degradation; domain deletion analysis; co-immunoprecipitation; rDNA transcription assay; cell growth/viability assays in normal and cancer cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct binding domain mapping, functional reconstitution-like auxin degron system, multiple orthogonal methods, demonstrated in both normal and cancer cells","pmids":["37356716"],"is_preprint":false},{"year":2023,"finding":"In vitro and in vivo analyses of the A34 family (PAF49/Rpa34) show that the 'arm' of A34 intimately interacts with PolR1B, PolR1A, and PolR1C subunits of Pol I as resolved by cryo-EM, placing this interaction at the structural interface of the Pol I complex.","method":"In silico structural analysis; cryo-EM structure interpretation; domain mapping","journal":"Genes","confidence":"Low","confidence_rationale":"Tier 4 / Weak — primarily computational/structural inference from cryo-EM without functional mutagenesis in this paper","pmids":["39858608"],"is_preprint":false},{"year":2026,"finding":"TCS4-associated mutations R1022C and R1022S in Rpa2 (S. pombe POLR1B ortholog) cause Pol I to abnormally accumulate at the 5' region of rDNA, resulting in defective 35S pre-rRNA biogenesis, impaired cell growth under nutrient-rich conditions, and increased sensitivity to BMH-21. Rpa2 protein levels are unaffected, indicating the mutations impair Pol I elongation/progression rather than subunit stability.","method":"Introduction of TCS4-associated mutations in S. pombe rpa2; ChIP analysis of Pol I distribution on rDNA; pre-rRNA biogenesis analysis; growth assays; BMH-21 sensitivity assay","journal":"FEBS open bio","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct mutagenesis in model organism with ChIP and rRNA analysis, single lab, mechanistic characterization of disease mutations","pmids":["41542823"],"is_preprint":false},{"year":2026,"finding":"The SuperPol mutant RPA135-F301S produces 1.5-fold more rRNA than wild-type Pol I in yeast, linked to reduced premature termination of transcription (PTT). In vitro, SuperPol shows reduced nascent transcript cleavage and more efficient transcript elongation after pauses, at the cost of transcriptional fidelity. SuperPol is resistant to BMH-21 and maintains subunit stability under drug treatment, confirming that PTT is the mechanism by which BMH-21 inhibits wild-type Pol I.","method":"CRAC (cross-linking and analysis of cDNA); in vitro transcription assay; rRNA quantification; BMH-21 treatment; comparison of WT and RPA135-F301S mutant Pol I","journal":"eLife","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution combined with in vivo CRAC and rRNA analysis, multiple orthogonal methods establishing PTT mechanism","pmids":["41677783"],"is_preprint":false},{"year":2014,"finding":"A high-frequency interchromosomal interaction occurs between rDNA intergenic spacer (IGS1) and the intergenic region of the RPA135 locus in S. cerevisiae. A 75-bp sequence within the RPA135-tK(CUU)P intergenic region mediates this interaction, which is dependent on rDNA copy number and Msn2 protein. This interaction stabilizes rDNA repeat number and contributes to nucleolar stability, but does not govern RPA135 transcription.","method":"Quantitative chromosome conformation capture (qCCC); replacement mapping; rDNA copy number analysis; Msn2 deletion epistasis","journal":"Molecular and cellular biology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — quantitative 3C with functional replacement mapping and epistasis, single lab","pmids":["25421713"],"is_preprint":false},{"year":2010,"finding":"POLR1B was identified as a novel c-MYC target gene that is downregulated during granulocyte differentiation in concert with loss of c-MYC, and is reinduced in terminally differentiated granulocytes upon MYC-ER transgene activation. c-MYC coordinately regulates POLR1B and other Pol I factors alongside rDNA chromatin remodeling to control ribosomal RNA gene transcription.","method":"Gene expression arrays; MYC-ER transgene activation in differentiated granulocytes; Pol I loading on rDNA (ChIP); UBF depletion analysis","journal":"Nucleic acids research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — gene expression arrays plus ChIP and functional transgene reactivation, single lab, two orthogonal methods","pmids":["21177653"],"is_preprint":false}],"current_model":"POLR1B (RPA135/Rpa2) is the second-largest structural and catalytic subunit of RNA Polymerase I, essential for rRNA synthesis and ribosome biogenesis; its C-terminal Zn-binding domain recruits the largest subunit RPA190 for Pol I assembly, its jaw-lobe interface (particularly residue F301/equivalent) controls transcription elongation rate and premature termination, it interacts directly with PAF49 (A34 subunit) to support initiation and elongation, it is required for nucleolar phase separation and structural integrity, its loss causes p53-dependent neuroepithelial apoptosis and neural crest cell defects underlying Treacher Collins syndrome type 4, and it is transcriptionally regulated by c-MYC as part of a Pol I regulon controlling ribosome biogenesis."},"narrative":{"mechanistic_narrative":"POLR1B (yeast RPA135/Rpa2) is the second-largest catalytic subunit of RNA polymerase I and is the essential, normally sole source of rRNA synthesis required for ribosome biogenesis [PMID:7739526]. Its C-terminal Zn-binding domain serves a structural role in recruiting the largest subunit RPA190/Rpa190 to assemble the Pol I complex [PMID:14555487], and it forms a core complex with RPA194 that remains intact independently of the peripheral RPA12 subunit [PMID:37167337]. POLR1B sits at a jaw-lobe structural interface (lobe in RPA135, jaw in RPA190/RPA12) that governs transcription elongation: the gain-of-function RPA135-F301S allele yields a hyperactive \"SuperPol\" that reduces premature transcription termination and increases rRNA output at the cost of fidelity, and this same property confers resistance to the elongation inhibitor BMH-21 — establishing premature termination as the mechanism of BMH-21 action and POLR1B as a controller of elongation rate [PMID:31136569, PMID:41677783]. POLR1B also functions through direct interaction with the PAF49/A34 subunit, whose 'arm' domain binds POLR1B to support rDNA transcription [PMID:37356716]. Loss of POLR1B function disrupts rRNA synthesis, collapses nucleolar phase-separation and structural integrity, and causes preimplantation lethality in mice [PMID:18023416, PMID:37639467]. Pathogenic POLR1B variants cause Treacher Collins syndrome type 4, acting via p53-dependent apoptosis in the neuroepithelium and depletion of neural crest cell derivatives [PMID:31649276]; disease-associated residue substitutions impair Pol I elongation/progression along rDNA rather than subunit stability [PMID:41542823]. At the regulatory level, POLR1B is a c-MYC target gene coordinately controlled with other Pol I factors to set ribosomal RNA gene transcription [PMID:21177653].","teleology":[{"year":1991,"claim":"Established that POLR1B (RPA135) is genetically required for Pol I-dependent rRNA synthesis, defining it as a member of the dedicated rRNA transcription machinery.","evidence":"Genetic screen for Pol I transcription mutants using a GAL7-hybrid rescue system in S. cerevisiae","pmids":["1871118"],"confidence":"Medium","gaps":["Did not define the biochemical role of RPA135 within Pol I","No structural or interaction data"]},{"year":1995,"claim":"Demonstrated that Pol I (via RPA135) is the normal sole source of 25S/18S/5.8S rRNAs, with loss survivable only through a cryptic Pol II promoter switch.","evidence":"RPA135 gene disruption and polymerase-specific transcript analysis in yeast petite mutants","pmids":["7739526"],"confidence":"High","gaps":["Did not address mechanism of subunit catalytic contribution","Polymerase switch is non-physiological rescue"]},{"year":1998,"claim":"Linked RPA135/Pol I to genomic stability of the rDNA array, showing it regulates rDNA copy number via FOB1-dependent replication fork blockage.","evidence":"Yeast deletion/complementation, rDNA copy number analysis, fob1 epistasis","pmids":["9869636"],"confidence":"High","gaps":["Mechanistic link between transcription and recombination not fully resolved","Not tested in metazoans"]},{"year":2003,"claim":"Identified the structural basis of Pol I assembly: the RPA135 C-terminal Zn-binding domain recruits the largest subunit RPA190, a role that is structural rather than dependent on Zn coordination.","evidence":"Cysteine-to-alanine mutagenesis and Pol I complex assembly analysis in yeast","pmids":["14555487"],"confidence":"Medium","gaps":["Single-lab mutagenesis without structural confirmation at the time","Atomic-level interface not resolved"]},{"year":2007,"claim":"Placed RPA135 in a functional network with Rpa34/Rpa49 and defined the jaw-lobe interface as critical for Pol I function.","evidence":"Synthetic lethality analysis of rpa135 point mutants with rpa34/rpa49 deletions in yeast","pmids":["18086878"],"confidence":"Medium","gaps":["Genetic interaction did not establish direct physical contacts","Functional consequence of jaw-lobe interface not biochemically tested"]},{"year":2007,"claim":"Showed the metazoan POLR1B ortholog is essential for early development, with truncation impairing rRNA synthesis, disrupting the nucleolus, and triggering apoptosis.","evidence":"Gene-trap truncation in mouse Rpo1-2 with rRNA synthesis, nucleolar, and embryo histology assays","pmids":["18023416"],"confidence":"High","gaps":["Truncation rather than clean null","Mechanism connecting nucleolar disruption to apoptosis not defined"]},{"year":2018,"claim":"Established that POLR1B and Pol I subunits are required for the conserved elongation checkpoint that drives BMH-21-mediated degradation of RPA194.","evidence":"Genetic analyses in yeast and human cells plus reconstituted Pol I transcription assay with BMH-21","pmids":["29642000"],"confidence":"High","gaps":["Precise molecular trigger of the checkpoint not defined","Role of POLR1B residues in pausing not yet mapped"]},{"year":2019,"claim":"Defined POLR1B residue F301 at the jaw-lobe interface as a controller of Pol I activity, with F301S producing hyperactive polymerase via a conformational change favoring DNA cleft insertion.","evidence":"Suppressor screen, ChIP, in vitro tailed-template transcription, and cryo-EM structural mapping in yeast","pmids":["31136569"],"confidence":"High","gaps":["Mechanism of increased activity inferred rather than directly visualized","Did not yet link to termination control"]},{"year":2019,"claim":"Demonstrated that POLR1B is a Treacher Collins syndrome type 4 gene, acting through ribosomal gene dysregulation, p53-dependent neuroepithelial apoptosis, and neural crest depletion.","evidence":"Human exome sequencing plus zebrafish polr1b morpholino knockdown with craniofacial, apoptosis, and NCC phenotyping","pmids":["31649276"],"confidence":"High","gaps":["Morpholino-based knockdown rather than stable genetic model","Variant-specific molecular effects not resolved here"]},{"year":2020,"claim":"Showed the RPA194-POLR1B core complex remains intact independently of the peripheral RPA12 subunit, distinguishing core from accessory subunit dependencies.","evidence":"RPA12 siRNA knockdown with co-IP, immunofluorescence, and chromatin engagement assays in human cells","pmids":["37167337"],"confidence":"Medium","gaps":["Single-lab study","Did not test reciprocal effects of POLR1B loss on RPA194 stability"]},{"year":2023,"claim":"Mapped a direct physical interaction between the PAF49/A34 'arm' domain and POLR1B that is required for rDNA transcription and selectively lethal to cancer cells when disrupted.","evidence":"Auxin-induced degron, domain deletion, co-IP, and transcription/viability assays in normal and cancer cells","pmids":["37356716"],"confidence":"High","gaps":["Structural detail of the interface not resolved in this work","Basis of cancer-cell selectivity not fully defined"]},{"year":2023,"claim":"Provided structural placement of the A34 arm at the POLR1B/PolR1A/PolR1C interface within the Pol I complex.","evidence":"In silico structural analysis and cryo-EM interpretation","pmids":["39858608"],"confidence":"Low","gaps":["Primarily computational/structural inference without functional mutagenesis in this paper","Interface contacts not biochemically validated here"]},{"year":2023,"claim":"Established that POLR1B/Pol I activity and rRNA transcription are required to maintain nucleolar phase-separation properties and integrity in development.","evidence":"Polr1b-/- mouse null, pharmacological Pol I inhibition, live imaging, and viscosity measurements","pmids":["37639467"],"confidence":"High","gaps":["Molecular link between rRNA output and phase behavior not fully dissected","Specific POLR1B contribution versus general Pol I activity not separable"]},{"year":2026,"claim":"Defined the mechanism of TCS4 disease mutations: substitutions at Rpa2 R1022 cause abnormal 5' Pol I accumulation and defective pre-rRNA biogenesis by impairing elongation/progression rather than subunit stability.","evidence":"TCS4-mutation knock-in in S. pombe rpa2 with ChIP, pre-rRNA, growth, and BMH-21 sensitivity assays","pmids":["41542823"],"confidence":"Medium","gaps":["Modeled in fission yeast rather than human cells","Single-lab characterization"]},{"year":2026,"claim":"Unified the elongation phenotypes by showing the POLR1B-F301S SuperPol reduces premature transcription termination to boost rRNA output and confers BMH-21 resistance, establishing premature termination as the BMH-21 inhibition mechanism.","evidence":"CRAC, in vitro transcription, rRNA quantification, and BMH-21 treatment comparing WT and RPA135-F301S Pol I","pmids":["41677783"],"confidence":"High","gaps":["Fidelity trade-off mechanism not fully characterized","Relevance to mammalian POLR1B termination control inferred"]},{"year":null,"claim":"How transcriptional regulators such as c-MYC and the upstream signals controlling POLR1B expression integrate with its elongation-rate and nucleolar phase-separation functions in human tissues remains undefined.","evidence":"No direct experimental evidence in the available corpus","pmids":[],"confidence":"Low","gaps":["No structural model of human POLR1B-containing Pol I in the corpus","Tissue-specific regulation linking MYC control to disease phenotype not established","Mechanism connecting elongation defects to neural-crest-specific p53 apoptosis unresolved"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140098","term_label":"catalytic activity, acting on RNA","supporting_discovery_ids":[2,6,7,14]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[7,13]},{"term_id":"GO:0005198","term_label":"structural molecule activity","supporting_discovery_ids":[3,9,11]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[5,10]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[9]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[1,2,11]},{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[2,5,14]},{"term_id":"R-HSA-1643685","term_label":"Disease","supporting_discovery_ids":[8,13]}],"complexes":["RNA polymerase I"],"partners":["RPA194","RPA190","PAF49","RPA12","POLR1A","POLR1C"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q9H9Y6","full_name":"DNA-directed RNA polymerase I subunit RPA2","aliases":["DNA-directed RNA polymerase I 135 kDa polypeptide","RPA135"],"length_aa":1135,"mass_kda":128.2,"function":"Catalytic core component of RNA polymerase I (Pol I), a DNA-dependent RNA polymerase which synthesizes ribosomal RNA precursors using the four ribonucleoside triphosphates as substrates. Transcribes 47S pre-rRNAs from multicopy rRNA gene clusters, giving rise to 5.8S, 18S and 28S ribosomal RNAs (PubMed:11250903, PubMed:11283244, PubMed:16858408, PubMed:34671025, PubMed:34887565, PubMed:36271492). Pol I-mediated transcription cycle proceeds through transcription initiation, transcription elongation and transcription termination stages. During transcription initiation, Pol I pre-initiation complex (PIC) is recruited by the selectivity factor 1 (SL1/TIF-IB) complex bound to the core promoter that precedes an rDNA repeat unit. The PIC assembly bends the promoter favoring the formation of the transcription bubble and promoter escape. Once the polymerase has escaped from the promoter it enters the elongation phase during which RNA is actively polymerized, based on complementarity with the template DNA strand. Highly processive, assembles in structures referred to as 'Miller trees' where many elongating Pol I complexes queue and transcribe the same rDNA coding regions. At terminator sequences downstream of the rDNA gene, PTRF interacts with Pol I and halts Pol I transcription leading to the release of the RNA transcript and polymerase from the DNA (PubMed:11250903, PubMed:11283244, PubMed:16858408, PubMed:34671025, PubMed:34887565, PubMed:36271492). Forms Pol I active center together with the largest subunit POLR1A/RPA1. Appends one nucleotide at a time to the 3' end of the nascent RNA, with POLR1A/RPA1 contributing a Mg(2+)-coordinating DxDGD motif, and POLR1B/RPA2 participating in the coordination of a second Mg(2+) ion and providing lysine residues believed to facilitate Watson-Crick base pairing between the incoming nucleotide and the template base. Typically, Mg(2+) ions direct a 5' nucleoside triphosphate to form a phosphodiester bond with the 3' hydroxyl of the preceding nucleotide of the nascent RNA, with the elimination of pyrophosphate. Has proofreading activity: Pauses and backtracks to allow the cleavage of a missincorporated nucleotide via POLR1H/RPA12. High Pol I processivity is associated with decreased transcription fidelity (By similarity) (PubMed:11250903, PubMed:11283244, PubMed:16809778, PubMed:16858408, PubMed:34671025, PubMed:34887565, PubMed:36271492)","subcellular_location":"Nucleus, nucleolus; Chromosome","url":"https://www.uniprot.org/uniprotkb/Q9H9Y6/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/POLR1B","classification":"Common Essential","n_dependent_lines":1194,"n_total_lines":1208,"dependency_fraction":0.9884105960264901},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000125630","cell_line_id":"CID000841","localizations":[{"compartment":"nucleolus_fc_dfc","grade":3}],"interactors":[{"gene":"POLR2K","stoichiometry":10.0},{"gene":"POLR1E","stoichiometry":10.0},{"gene":"POLR1C","stoichiometry":10.0},{"gene":"POLR1A","stoichiometry":10.0},{"gene":"POLR2E","stoichiometry":10.0},{"gene":"POLR1D","stoichiometry":4.0},{"gene":"CD3EAP","stoichiometry":4.0},{"gene":"POLR2F","stoichiometry":4.0},{"gene":"POLR2H","stoichiometry":4.0},{"gene":"FKBP5","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/target/CID000841","total_profiled":1310},"omim":[{"mim_id":"621031","title":"POLYMERASE I, RNA, SUBUNIT E; POLR1E","url":"https://www.omim.org/entry/621031"},{"mim_id":"618939","title":"TREACHER COLLINS SYNDROME 4; TCS4","url":"https://www.omim.org/entry/618939"},{"mim_id":"616404","title":"POLYMERASE I, RNA, SUBUNIT A; POLR1A","url":"https://www.omim.org/entry/616404"},{"mim_id":"615366","title":"NUCLEOLAR PROTEIN 11; NOL11","url":"https://www.omim.org/entry/615366"},{"mim_id":"614405","title":"DEAH-BOX HELICASE 33; DHX33","url":"https://www.omim.org/entry/614405"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nucleoli fibrillar center","reliability":"Supported"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/POLR1B"},"hgnc":{"alias_symbol":["Rpo1-2","FLJ21921","FLJ10816","RPA2","RPA135"],"prev_symbol":[]},"alphafold":{"accession":"Q9H9Y6","domains":[{"cath_id":"3.90.1110.10","chopping":"203-364","consensus_level":"medium","plddt":94.1846,"start":203,"end":364},{"cath_id":"2.40.270.10","chopping":"675-771_880-1003","consensus_level":"medium","plddt":95.1862,"start":675,"end":1003},{"cath_id":"2.40.50.150","chopping":"777-875","consensus_level":"high","plddt":87.1259,"start":777,"end":875},{"cath_id":"3.90.1800.10","chopping":"1066-1135","consensus_level":"medium","plddt":87.3921,"start":1066,"end":1135}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9Y6","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9Y6-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q9H9Y6-F1-predicted_aligned_error_v6.png","plddt_mean":92.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=POLR1B","jax_strain_url":"https://www.jax.org/strain/search?query=POLR1B"},"sequence":{"accession":"Q9H9Y6","fasta_url":"https://rest.uniprot.org/uniprotkb/Q9H9Y6.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q9H9Y6/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q9H9Y6"}},"corpus_meta":[{"pmid":"9869636","id":"PMC_9869636","title":"Expansion and contraction of ribosomal DNA repeats in Saccharomyces cerevisiae: requirement of replication fork blocking (Fob1) protein and the role of RNA polymerase I.","date":"1998","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/9869636","citation_count":339,"is_preprint":false},{"pmid":"1871118","id":"PMC_1871118","title":"An approach for isolation of mutants defective in 35S ribosomal RNA synthesis in Saccharomyces cerevisiae.","date":"1991","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/1871118","citation_count":82,"is_preprint":false},{"pmid":"21177653","id":"PMC_21177653","title":"c-MYC coordinately regulates ribosomal gene chromatin remodeling and Pol I availability during granulocyte differentiation.","date":"2010","source":"Nucleic acids 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This effect requires FOB1 (replication fork blocking protein), placing RNA Pol I/RPA135 as a regulator of rDNA copy number stability via replication fork blockage-stimulated recombination.\",\n      \"method\": \"Yeast genetic deletion/complementation (rpa135Δ mutants), rDNA copy number analysis, epistasis with fob1Δ\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis with clean deletion and complementation, replicated across multiple genetic backgrounds, mechanistic pathway placement established\",\n      \"pmids\": [\"9869636\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1991,\n      \"finding\": \"RPA135 was identified as one of at least nine genes (RRN1–RRN9) specifically required for RNA Pol I-dependent 35S rRNA synthesis in S. cerevisiae, established by a genetic screen using a GAL7-driven Pol II rescue system to identify mutants defective in Pol I transcription.\",\n      \"method\": \"Genetic screen for Pol I transcription mutants using GAL7-hybrid gene suppression system; red/white colony color assay and galactose-dependent growth test\",\n      \"journal\": \"Proceedings of the National Academy of Sciences of the United States of America\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — clean genetic screen with functional readout (rRNA synthesis), single lab but orthogonal growth and transcription assays\",\n      \"pmids\": [\"1871118\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1995,\n      \"finding\": \"Yeast cells lacking RNA Pol I activity due to RPA135 gene disruption can survive by switching rDNA transcription to RNA Pol II via a cryptic Pol II promoter overlapping the Pol I promoter in rDNA. This demonstrates that RPA135 (and thus Pol I) is the sole normal source of 25S, 18S, and 5.8S rRNAs, and its loss is viable only through this polymerase switch.\",\n      \"method\": \"RPA135 gene disruption; RNA analysis of polymerase-specific transcripts; episomal rDNA characterization in petite mutants\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — clean null mutant, RNA analysis confirming polymerase switch, functional rescue demonstrated\",\n      \"pmids\": [\"7739526\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2003,\n      \"finding\": \"The C-terminal Zn-binding domain of Rpa135 (yeast POLR1B ortholog) is required for recruitment of the largest Pol I subunit Rpa190 into the RNA polymerase I complex. Nonfunctional Rpa135 mutants lacking this domain failed to assemble Pol I. Surprisingly, replacement of all four cysteines with alanines still yielded functional Rpa135, indicating the domain's essential role is structural rather than Zn2+-coordination per se.\",\n      \"method\": \"Mutagenesis of Zn-binding domain (individual and combinatorial cysteine-to-alanine substitutions); analysis of Pol I complex assembly\",\n      \"journal\": \"Eukaryotic cell\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — mutagenesis with functional assembly assay, single lab\",\n      \"pmids\": [\"14555487\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Specific point mutations in RPA135 (rpa135-L656P and rpa135-D395N) are lethal in combination with rpa34Δ or rpa49Δ mutations, placing RPA135 in a functional network with Rpa34 and Rpa49 subunits for Pol I transcription. The lobe domain of Rpa135 and the jaw domain of Rpa190 form a jaw-lobe interface critical for Pol I function.\",\n      \"method\": \"Yeast genetic epistasis; synthetic lethality analysis of double mutants; growth assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — genetic epistasis in yeast, synthetic lethality with multiple alleles, single lab\",\n      \"pmids\": [\"18086878\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2007,\n      \"finding\": \"Mouse Rpo1-2 (POLR1B ortholog) is essential for pre-implantation development. A gene-trap truncation in exon 14 of Rpo1-2 (removing 312 aa from C-terminus) severely impairs rRNA synthesis, causes nucleolus disruption, and triggers apoptotic cell death by the morula stage in homozygous embryos.\",\n      \"method\": \"Gene trap insertional mutagenesis in mice; rRNA synthesis assay; histological analysis of embryos; nucleolar structure analysis\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — in vivo loss-of-function with defined molecular (rRNA synthesis) and cellular (nucleolus disruption, apoptosis) phenotype, mouse model\",\n      \"pmids\": [\"18023416\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2018,\n      \"finding\": \"RPA135 (POLR1B) is required for BMH-21-mediated degradation of the largest Pol I subunit RPA194. Pol I preinitiation factors and polymerase subunits including RPA135 are necessary components of the conserved transcription elongation checkpoint activated by BMH-21, which directly impairs Pol I transcription elongation causing long-lived polymerase pausing.\",\n      \"method\": \"Genetic analyses in yeast and human cells; fully reconstituted Pol I transcription assay; small-molecule treatment (BMH-21); subunit dependency analysis\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — reconstituted in vitro transcription assay plus genetic analyses in two organisms, direct mechanistic demonstration of elongation inhibition\",\n      \"pmids\": [\"29642000\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"A super-active Pol I mutant allele RPA135-F301S restores normal rRNA synthesis and increases Pol I density on rDNA genes in the absence of Rpa49. The F301S mutation maps to the jaw-lobe interface of Pol I (lobe in Rpa135, jaw in Rpa190/Rpa12), and Pol I bearing this mutation is hyper-active in an in vitro tailed-template transcription assay, proposed to result from a conformational change supporting DNA insertion into the enzyme cleft.\",\n      \"method\": \"Genetic suppressor screen; rRNA synthesis assay; ChIP (Pol I density on rDNA); in vitro tailed-template transcription assay; structural mapping onto Pol I cryo-EM structure\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution assay plus in vivo genetic and ChIP data, multiple orthogonal methods\",\n      \"pmids\": [\"31136569\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"Pathogenic variants in POLR1B cause Treacher Collins syndrome type 4 (TCS4). Knockdown of polr1b in zebrafish induces abnormal craniofacial phenotype mimicking TCS, associated with altered ribosomal gene expression, massive p53-dependent apoptosis in the neuroepithelium, and reduced number of neural crest cell (NCC) derivatives.\",\n      \"method\": \"Exome sequencing in human patients; zebrafish polr1b morpholino knockdown; craniofacial phenotyping; ribosomal gene expression analysis; apoptosis assay (p53-dependent); NCC derivative quantification\",\n      \"journal\": \"Genetics in medicine : official journal of the American College of Medical Genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — zebrafish loss-of-function with defined molecular mechanism (p53-dependent apoptosis, rRNA), replicated with human genetic data\",\n      \"pmids\": [\"31649276\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2020,\n      \"finding\": \"RPA135 (POLR1B) silencing causes alterations in the expression and localization of Pol I subunits RPA194. Despite these alterations, the core Pol I complex between RPA194 and RPA135 remains intact upon RPA12 knockdown, and the transcription of Pol I and its engagement with chromatin remain unaffected when RPA12 is silenced. BMH-21-mediated degradation of RPA194 was found to be independent of RPA12.\",\n      \"method\": \"siRNA knockdown of RPA12; immunofluorescence (localization); co-immunoprecipitation (complex integrity); chromatin engagement assay; BMH-21 treatment\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal co-IP and localization with functional consequence, single lab, two orthogonal methods\",\n      \"pmids\": [\"37167337\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Homozygous null mutations in Polr1b lead to preimplantation lethality in mice, and Polr1b-/- embryos exhibit defects in nucleolar structure (decreased nucleolar precursor bodies, increased nucleolar volume, single condensed nucleolus), demonstrating that POLR1B/Pol I function and rRNA transcription are required for maintaining nucleolar phase separation properties and integrity during development.\",\n      \"method\": \"Homozygous null mouse mutants (Polr1b-/-); live imaging and nucleolar structure analysis; pharmacological Pol I inhibition in embryos and hiPSCs; viscosity measurements of granular compartment\",\n      \"journal\": \"PLoS genetics\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic null + pharmacological inhibition + live imaging with quantitative biophysical readout (viscosity/phase separation), multiple orthogonal approaches\",\n      \"pmids\": [\"37639467\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"PAF49 (mammalian orthologue of yeast Rpa34) contains an 'arm' domain that directly interacts with POLR1B (PolR1B). This interaction is required for rDNA transcription; disrupting the PAF49–PolR1B interaction inhibits Pol I transcription in normal and cancer cells, arresting normal cells and killing cancer cells.\",\n      \"method\": \"Auxin-induced degron system for PAF49 degradation; domain deletion analysis; co-immunoprecipitation; rDNA transcription assay; cell growth/viability assays in normal and cancer cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct binding domain mapping, functional reconstitution-like auxin degron system, multiple orthogonal methods, demonstrated in both normal and cancer cells\",\n      \"pmids\": [\"37356716\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"In vitro and in vivo analyses of the A34 family (PAF49/Rpa34) show that the 'arm' of A34 intimately interacts with PolR1B, PolR1A, and PolR1C subunits of Pol I as resolved by cryo-EM, placing this interaction at the structural interface of the Pol I complex.\",\n      \"method\": \"In silico structural analysis; cryo-EM structure interpretation; domain mapping\",\n      \"journal\": \"Genes\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 4 / Weak — primarily computational/structural inference from cryo-EM without functional mutagenesis in this paper\",\n      \"pmids\": [\"39858608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"TCS4-associated mutations R1022C and R1022S in Rpa2 (S. pombe POLR1B ortholog) cause Pol I to abnormally accumulate at the 5' region of rDNA, resulting in defective 35S pre-rRNA biogenesis, impaired cell growth under nutrient-rich conditions, and increased sensitivity to BMH-21. Rpa2 protein levels are unaffected, indicating the mutations impair Pol I elongation/progression rather than subunit stability.\",\n      \"method\": \"Introduction of TCS4-associated mutations in S. pombe rpa2; ChIP analysis of Pol I distribution on rDNA; pre-rRNA biogenesis analysis; growth assays; BMH-21 sensitivity assay\",\n      \"journal\": \"FEBS open bio\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct mutagenesis in model organism with ChIP and rRNA analysis, single lab, mechanistic characterization of disease mutations\",\n      \"pmids\": [\"41542823\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The SuperPol mutant RPA135-F301S produces 1.5-fold more rRNA than wild-type Pol I in yeast, linked to reduced premature termination of transcription (PTT). In vitro, SuperPol shows reduced nascent transcript cleavage and more efficient transcript elongation after pauses, at the cost of transcriptional fidelity. SuperPol is resistant to BMH-21 and maintains subunit stability under drug treatment, confirming that PTT is the mechanism by which BMH-21 inhibits wild-type Pol I.\",\n      \"method\": \"CRAC (cross-linking and analysis of cDNA); in vitro transcription assay; rRNA quantification; BMH-21 treatment; comparison of WT and RPA135-F301S mutant Pol I\",\n      \"journal\": \"eLife\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution combined with in vivo CRAC and rRNA analysis, multiple orthogonal methods establishing PTT mechanism\",\n      \"pmids\": [\"41677783\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2014,\n      \"finding\": \"A high-frequency interchromosomal interaction occurs between rDNA intergenic spacer (IGS1) and the intergenic region of the RPA135 locus in S. cerevisiae. A 75-bp sequence within the RPA135-tK(CUU)P intergenic region mediates this interaction, which is dependent on rDNA copy number and Msn2 protein. This interaction stabilizes rDNA repeat number and contributes to nucleolar stability, but does not govern RPA135 transcription.\",\n      \"method\": \"Quantitative chromosome conformation capture (qCCC); replacement mapping; rDNA copy number analysis; Msn2 deletion epistasis\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — quantitative 3C with functional replacement mapping and epistasis, single lab\",\n      \"pmids\": [\"25421713\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"POLR1B was identified as a novel c-MYC target gene that is downregulated during granulocyte differentiation in concert with loss of c-MYC, and is reinduced in terminally differentiated granulocytes upon MYC-ER transgene activation. c-MYC coordinately regulates POLR1B and other Pol I factors alongside rDNA chromatin remodeling to control ribosomal RNA gene transcription.\",\n      \"method\": \"Gene expression arrays; MYC-ER transgene activation in differentiated granulocytes; Pol I loading on rDNA (ChIP); UBF depletion analysis\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — gene expression arrays plus ChIP and functional transgene reactivation, single lab, two orthogonal methods\",\n      \"pmids\": [\"21177653\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"POLR1B (RPA135/Rpa2) is the second-largest structural and catalytic subunit of RNA Polymerase I, essential for rRNA synthesis and ribosome biogenesis; its C-terminal Zn-binding domain recruits the largest subunit RPA190 for Pol I assembly, its jaw-lobe interface (particularly residue F301/equivalent) controls transcription elongation rate and premature termination, it interacts directly with PAF49 (A34 subunit) to support initiation and elongation, it is required for nucleolar phase separation and structural integrity, its loss causes p53-dependent neuroepithelial apoptosis and neural crest cell defects underlying Treacher Collins syndrome type 4, and it is transcriptionally regulated by c-MYC as part of a Pol I regulon controlling ribosome biogenesis.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"POLR1B (yeast RPA135/Rpa2) is the second-largest catalytic subunit of RNA polymerase I and is the essential, normally sole source of rRNA synthesis required for ribosome biogenesis [#2]. Its C-terminal Zn-binding domain serves a structural role in recruiting the largest subunit RPA190/Rpa190 to assemble the Pol I complex [#3], and it forms a core complex with RPA194 that remains intact independently of the peripheral RPA12 subunit [#9]. POLR1B sits at a jaw-lobe structural interface (lobe in RPA135, jaw in RPA190/RPA12) that governs transcription elongation: the gain-of-function RPA135-F301S allele yields a hyperactive \\\"SuperPol\\\" that reduces premature transcription termination and increases rRNA output at the cost of fidelity, and this same property confers resistance to the elongation inhibitor BMH-21 — establishing premature termination as the mechanism of BMH-21 action and POLR1B as a controller of elongation rate [#7, #14]. POLR1B also functions through direct interaction with the PAF49/A34 subunit, whose 'arm' domain binds POLR1B to support rDNA transcription [#11]. Loss of POLR1B function disrupts rRNA synthesis, collapses nucleolar phase-separation and structural integrity, and causes preimplantation lethality in mice [#5, #10]. Pathogenic POLR1B variants cause Treacher Collins syndrome type 4, acting via p53-dependent apoptosis in the neuroepithelium and depletion of neural crest cell derivatives [#8]; disease-associated residue substitutions impair Pol I elongation/progression along rDNA rather than subunit stability [#13]. At the regulatory level, POLR1B is a c-MYC target gene coordinately controlled with other Pol I factors to set ribosomal RNA gene transcription [#16].\",\n  \"teleology\": [\n    {\n      \"year\": 1991,\n      \"claim\": \"Established that POLR1B (RPA135) is genetically required for Pol I-dependent rRNA synthesis, defining it as a member of the dedicated rRNA transcription machinery.\",\n      \"evidence\": \"Genetic screen for Pol I transcription mutants using a GAL7-hybrid rescue system in S. cerevisiae\",\n      \"pmids\": [\"1871118\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Did not define the biochemical role of RPA135 within Pol I\", \"No structural or interaction data\"]\n    },\n    {\n      \"year\": 1995,\n      \"claim\": \"Demonstrated that Pol I (via RPA135) is the normal sole source of 25S/18S/5.8S rRNAs, with loss survivable only through a cryptic Pol II promoter switch.\",\n      \"evidence\": \"RPA135 gene disruption and polymerase-specific transcript analysis in yeast petite mutants\",\n      \"pmids\": [\"7739526\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not address mechanism of subunit catalytic contribution\", \"Polymerase switch is non-physiological rescue\"]\n    },\n    {\n      \"year\": 1998,\n      \"claim\": \"Linked RPA135/Pol I to genomic stability of the rDNA array, showing it regulates rDNA copy number via FOB1-dependent replication fork blockage.\",\n      \"evidence\": \"Yeast deletion/complementation, rDNA copy number analysis, fob1 epistasis\",\n      \"pmids\": [\"9869636\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanistic link between transcription and recombination not fully resolved\", \"Not tested in metazoans\"]\n    },\n    {\n      \"year\": 2003,\n      \"claim\": \"Identified the structural basis of Pol I assembly: the RPA135 C-terminal Zn-binding domain recruits the largest subunit RPA190, a role that is structural rather than dependent on Zn coordination.\",\n      \"evidence\": \"Cysteine-to-alanine mutagenesis and Pol I complex assembly analysis in yeast\",\n      \"pmids\": [\"14555487\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab mutagenesis without structural confirmation at the time\", \"Atomic-level interface not resolved\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Placed RPA135 in a functional network with Rpa34/Rpa49 and defined the jaw-lobe interface as critical for Pol I function.\",\n      \"evidence\": \"Synthetic lethality analysis of rpa135 point mutants with rpa34/rpa49 deletions in yeast\",\n      \"pmids\": [\"18086878\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Genetic interaction did not establish direct physical contacts\", \"Functional consequence of jaw-lobe interface not biochemically tested\"]\n    },\n    {\n      \"year\": 2007,\n      \"claim\": \"Showed the metazoan POLR1B ortholog is essential for early development, with truncation impairing rRNA synthesis, disrupting the nucleolus, and triggering apoptosis.\",\n      \"evidence\": \"Gene-trap truncation in mouse Rpo1-2 with rRNA synthesis, nucleolar, and embryo histology assays\",\n      \"pmids\": [\"18023416\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Truncation rather than clean null\", \"Mechanism connecting nucleolar disruption to apoptosis not defined\"]\n    },\n    {\n      \"year\": 2018,\n      \"claim\": \"Established that POLR1B and Pol I subunits are required for the conserved elongation checkpoint that drives BMH-21-mediated degradation of RPA194.\",\n      \"evidence\": \"Genetic analyses in yeast and human cells plus reconstituted Pol I transcription assay with BMH-21\",\n      \"pmids\": [\"29642000\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Precise molecular trigger of the checkpoint not defined\", \"Role of POLR1B residues in pausing not yet mapped\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Defined POLR1B residue F301 at the jaw-lobe interface as a controller of Pol I activity, with F301S producing hyperactive polymerase via a conformational change favoring DNA cleft insertion.\",\n      \"evidence\": \"Suppressor screen, ChIP, in vitro tailed-template transcription, and cryo-EM structural mapping in yeast\",\n      \"pmids\": [\"31136569\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Mechanism of increased activity inferred rather than directly visualized\", \"Did not yet link to termination control\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"Demonstrated that POLR1B is a Treacher Collins syndrome type 4 gene, acting through ribosomal gene dysregulation, p53-dependent neuroepithelial apoptosis, and neural crest depletion.\",\n      \"evidence\": \"Human exome sequencing plus zebrafish polr1b morpholino knockdown with craniofacial, apoptosis, and NCC phenotyping\",\n      \"pmids\": [\"31649276\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Morpholino-based knockdown rather than stable genetic model\", \"Variant-specific molecular effects not resolved here\"]\n    },\n    {\n      \"year\": 2020,\n      \"claim\": \"Showed the RPA194-POLR1B core complex remains intact independently of the peripheral RPA12 subunit, distinguishing core from accessory subunit dependencies.\",\n      \"evidence\": \"RPA12 siRNA knockdown with co-IP, immunofluorescence, and chromatin engagement assays in human cells\",\n      \"pmids\": [\"37167337\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Single-lab study\", \"Did not test reciprocal effects of POLR1B loss on RPA194 stability\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Mapped a direct physical interaction between the PAF49/A34 'arm' domain and POLR1B that is required for rDNA transcription and selectively lethal to cancer cells when disrupted.\",\n      \"evidence\": \"Auxin-induced degron, domain deletion, co-IP, and transcription/viability assays in normal and cancer cells\",\n      \"pmids\": [\"37356716\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural detail of the interface not resolved in this work\", \"Basis of cancer-cell selectivity not fully defined\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Provided structural placement of the A34 arm at the POLR1B/PolR1A/PolR1C interface within the Pol I complex.\",\n      \"evidence\": \"In silico structural analysis and cryo-EM interpretation\",\n      \"pmids\": [\"39858608\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Primarily computational/structural inference without functional mutagenesis in this paper\", \"Interface contacts not biochemically validated here\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Established that POLR1B/Pol I activity and rRNA transcription are required to maintain nucleolar phase-separation properties and integrity in development.\",\n      \"evidence\": \"Polr1b-/- mouse null, pharmacological Pol I inhibition, live imaging, and viscosity measurements\",\n      \"pmids\": [\"37639467\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Molecular link between rRNA output and phase behavior not fully dissected\", \"Specific POLR1B contribution versus general Pol I activity not separable\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Defined the mechanism of TCS4 disease mutations: substitutions at Rpa2 R1022 cause abnormal 5' Pol I accumulation and defective pre-rRNA biogenesis by impairing elongation/progression rather than subunit stability.\",\n      \"evidence\": \"TCS4-mutation knock-in in S. pombe rpa2 with ChIP, pre-rRNA, growth, and BMH-21 sensitivity assays\",\n      \"pmids\": [\"41542823\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Modeled in fission yeast rather than human cells\", \"Single-lab characterization\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"Unified the elongation phenotypes by showing the POLR1B-F301S SuperPol reduces premature transcription termination to boost rRNA output and confers BMH-21 resistance, establishing premature termination as the BMH-21 inhibition mechanism.\",\n      \"evidence\": \"CRAC, in vitro transcription, rRNA quantification, and BMH-21 treatment comparing WT and RPA135-F301S Pol I\",\n      \"pmids\": [\"41677783\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Fidelity trade-off mechanism not fully characterized\", \"Relevance to mammalian POLR1B termination control inferred\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How transcriptional regulators such as c-MYC and the upstream signals controlling POLR1B expression integrate with its elongation-rate and nucleolar phase-separation functions in human tissues remains undefined.\",\n      \"evidence\": \"No direct experimental evidence in the available corpus\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No structural model of human POLR1B-containing Pol I in the corpus\", \"Tissue-specific regulation linking MYC control to disease phenotype not established\", \"Mechanism connecting elongation defects to neural-crest-specific p53 apoptosis unresolved\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140098\", \"supporting_discovery_ids\": [2, 6, 7, 14]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [7, 13]},\n      {\"term_id\": \"GO:0005198\", \"supporting_discovery_ids\": [3, 9, 11]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [5, 10]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [9]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [1, 2, 11]},\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [2, 5, 14]},\n      {\"term_id\": \"R-HSA-1643685\", \"supporting_discovery_ids\": [8, 13]}\n    ],\n    \"complexes\": [\"RNA polymerase I\"],\n    \"partners\": [\"RPA194\", \"RPA190\", \"PAF49\", \"RPA12\", \"POLR1A\", \"POLR1C\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":7,"faith_pct":85.71428571428571}}