{"gene":"TRERF1","run_date":"2026-06-10T10:51:55","timeline":{"discoveries":[{"year":2002,"finding":"TReP-132 interacts physically with steroidogenic factor-1 (SF-1) via its N-terminal LXXLL motif, and this interaction requires the 'proximal activation domain' and 'AF-2 hexamer' motif of SF-1. Co-expression of TReP-132 and SF-1 cooperates to increase P450scc promoter activity, and co-expression with CBP/p300 produces a synergistic effect, identifying TReP-132 as a component of a transcriptional complex with SF-1 and CBP/p300 that regulates steroidogenesis.","method":"Pull-down assay, co-immunoprecipitation/Western blot, yeast two-hybrid, deletion/mutation analysis, promoter reporter assay in NCI-H295 adrenal cells","journal":"The Journal of biological chemistry","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (pulldown, co-IP, Y2H, mutagenesis, reporter assay) in a single rigorous study establishing the interaction and its molecular determinants","pmids":["12101186"],"is_preprint":false},{"year":2004,"finding":"TReP-132 overexpression in human adrenal NCI-H295 cells increases production of glucocorticoids, C19 steroids, and estrogens by inducing transcript levels and promoter activity of P450c17 and P450aro, while only slightly modulating 3β-HSD type II and P450c11aldo. The effect on P450c17 is enhanced by cAMP or SF-1, establishing TReP-132 as a trans-acting factor that differentially regulates multiple steroidogenic pathway genes.","method":"Overexpression in NCI-H295 cells, steroid measurement, quantitative RT-PCR, promoter reporter assay","journal":"Journal of molecular endocrinology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — cell-based overexpression with multiple pathway readouts, single lab, no independent replication reported","pmids":["15072559"],"is_preprint":false},{"year":2005,"finding":"TReP-132 controls cell proliferation by inducing expression of cyclin-dependent kinase inhibitors p21WAF1/Cip1 and p27Kip1 through interaction with transcription factor Sp1 at proximal Sp1-binding sites in their promoters. TReP-132 knockdown by siRNA in HeLa cells increases G1→S cell cycle progression and reduces p21 and p27 levels; conversely, TReP-132 expression level positively correlates with p21/p27 levels in breast tumor cell lines.","method":"siRNA knockdown, promoter reporter assay, co-immunoprecipitation with Sp1, cell cycle analysis (FACS), Western blot in HeLa and breast cancer cell lines","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — reciprocal loss-of-function (siRNA) and overexpression with multiple orthogonal readouts (cell cycle, protein levels, promoter activity, Sp1 interaction) in a single rigorous study","pmids":["15899840"],"is_preprint":false},{"year":2006,"finding":"TReP-132 acts as a coactivator of progesterone receptor (PR) in breast cancer T47D cells: it interacts in vitro and in intact cells with progesterone-activated PR, synergizes with PR to trans-activate p21 and p27 promoters at proximal Sp1-binding sites, and is required for progesterone-induced growth arrest (pRB dephosphorylation, G1/S block), inhibition of cell proliferation, and induction of breast cell differentiation markers including lipid vacuole accumulation. Progesterone treatment also increases TReP-132 expression, indicating a positive auto-regulatory loop.","method":"In vitro binding assay, co-immunoprecipitation in T47D cells, siRNA knockdown, promoter reporter assay, cell cycle analysis, lipid droplet staining, RT-PCR","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (in vitro binding, co-IP, KD, reporter, cell cycle, differentiation markers) in a single rigorous study","pmids":["17015480"],"is_preprint":false},{"year":2006,"finding":"TReP-132 directly binds terminal deoxynucleotidyltransferase (TdT) through TdT's N-terminal region, as well as the TdT-interacting factor TdIF1. TReP-132 co-localizes with TdT and TdIF1 in the nucleus of COS7 cells. Co-expression of TReP-132 with TdT reduces TdT enzymatic activity to 2.5% of maximum in vitro, indicating TReP-132 negatively regulates N-region synthesis during V(D)J recombination.","method":"Yeast two-hybrid, pull-down assay, co-immunoprecipitation with specific antibodies, co-localization in COS7 cells, in vitro TdT activity assay","journal":"Genes to cells : devoted to molecular & cellular mechanisms","confidence":"High","confidence_rationale":"Tier 1-2 / Strong — multiple orthogonal methods (Y2H, pulldown, co-IP, co-localization, in vitro enzymatic assay) in a single study establishing direct binding and functional consequence","pmids":["16371131"],"is_preprint":false},{"year":1997,"finding":"A genomic locus designated BCAR2 (breast cancer anti-estrogen resistance 2), which is an alias for TRERF1, was identified by cell-fusion-mediated gene transfer as a dominant locus conferring tamoxifen resistance to estrogen-dependent ZR-75-1 human breast cancer cells. The locus co-segregated with tamoxifen resistance in somatic cell hybrids, indicating it harbors a gene capable of altering estrogen dependency in a dominant manner in vitro.","method":"Retroviral insertion mutagenesis, cell fusion/somatic cell hybrid selection, co-segregation analysis","journal":"International journal of cancer","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — genetic co-segregation in cell hybrids identifies locus but does not identify the specific gene product or molecular mechanism; single lab","pmids":["9259413"],"is_preprint":false}],"current_model":"TRERF1/TReP-132 is a 132 kDa transcriptional regulatory protein that functions as a coactivator of steroidogenic factor-1 (SF-1) and progesterone receptor (PR) via direct LXXLL-motif-mediated protein-protein interactions, cooperates with CBP/p300 to drive steroidogenic gene transcription (P450scc, P450c17, P450aro), inhibits cell proliferation by interacting with Sp1 to induce CDK inhibitors p21 and p27, and directly binds and inhibits terminal deoxynucleotidyltransferase (TdT) activity in the nucleus, suggesting roles in steroidogenesis, cell cycle control, and V(D)J recombination regulation."},"narrative":{"mechanistic_narrative":"TRERF1 (TReP-132) is a transcriptional regulatory protein that controls steroidogenic gene expression and cell proliferation through direct protein-protein interactions with sequence-specific transcription factors and coactivators [PMID:12101186, PMID:15899840]. In adrenal cells, it functions as a coactivator of steroidogenic factor-1 (SF-1), binding SF-1 through an N-terminal LXXLL motif that engages the SF-1 proximal activation domain and AF-2 hexamer, and cooperating synergistically with CBP/p300 to drive transcription of steroidogenic cytochrome P450 genes including P450scc, P450c17, and P450aro, thereby increasing production of glucocorticoids, C19 steroids, and estrogens [PMID:12101186, PMID:15072559]. TRERF1 also acts as an anti-proliferative factor: by interacting with Sp1 at proximal Sp1-binding sites it induces the cyclin-dependent kinase inhibitors p21WAF1/Cip1 and p27Kip1, and its loss accelerates G1→S progression [PMID:15899840]. It serves as a coactivator of the progesterone receptor, synergizing with activated PR to trans-activate the p21 and p27 promoters and to enforce progesterone-induced growth arrest and breast cell differentiation [PMID:17015480]. Independently of its transcriptional roles, TRERF1 directly binds terminal deoxynucleotidyltransferase (TdT) and the TdT-interacting factor TdIF1 in the nucleus and strongly inhibits TdT enzymatic activity, implicating it in regulation of N-region synthesis during V(D)J recombination [PMID:16371131].","teleology":[{"year":1997,"claim":"Before any gene product was defined, the question was whether the TRERF1 locus could influence breast cancer estrogen dependency; genetic transfer showed it acts as a dominant tamoxifen-resistance locus.","evidence":"Cell-fusion-mediated gene transfer and co-segregation analysis in ZR-75-1 breast cancer cells (BCAR2 alias)","pmids":["9259413"],"confidence":"Medium","gaps":["Locus identified by co-segregation without resolving the specific gene product or molecular mechanism","No connection drawn to the transcriptional functions later established for TReP-132"]},{"year":2002,"claim":"It was unknown how TReP-132 participates in steroidogenesis; demonstrating LXXLL-mediated binding to SF-1 and synergy with CBP/p300 established it as a coactivator within an SF-1 transcriptional complex driving P450scc.","evidence":"Pull-down, co-IP, yeast two-hybrid, mutagenesis, and promoter reporter assays in NCI-H295 adrenal cells","pmids":["12101186"],"confidence":"High","gaps":["Did not establish which steroidogenic genes beyond P450scc are regulated","No structural detail of the SF-1/TReP-132/CBP complex"]},{"year":2004,"claim":"Whether TReP-132 broadly regulates steroidogenic output was open; overexpression showed it differentially induces P450c17 and P450aro to increase glucocorticoid, C19 steroid, and estrogen production.","evidence":"Overexpression, steroid measurement, qRT-PCR, and reporter assays in NCI-H295 cells","pmids":["15072559"],"confidence":"Medium","gaps":["Single-lab cell-based overexpression without independent replication","Mechanism of selectivity among steroidogenic genes not resolved"]},{"year":2005,"claim":"The link between TReP-132 and proliferation was unknown; reciprocal loss- and gain-of-function showed it restrains the cell cycle by inducing p21 and p27 via Sp1.","evidence":"siRNA knockdown, co-IP with Sp1, reporter assays, and FACS cell cycle analysis in HeLa and breast cancer lines","pmids":["15899840"],"confidence":"High","gaps":["Whether the steroidogenic and anti-proliferative roles are mechanistically coupled was not addressed","Endogenous regulators of TReP-132 expression not defined"]},{"year":2006,"claim":"It was unclear how progesterone signaling enforces breast cell growth arrest; TReP-132 was shown to coactivate PR, synergize at p21/p27 promoters, and be required for progesterone-induced arrest and differentiation.","evidence":"In vitro binding, co-IP, siRNA, reporter assays, cell cycle analysis, and lipid droplet staining in T47D cells","pmids":["17015480"],"confidence":"High","gaps":["The positive auto-regulatory loop between progesterone and TReP-132 expression not mechanistically dissected","Relationship to the earlier tamoxifen-resistance locus phenotype not tested"]},{"year":2006,"claim":"A transcription-independent function was unknown; TReP-132 was shown to directly bind TdT and TdIF1 and inhibit TdT activity, implicating it in V(D)J recombination control.","evidence":"Yeast two-hybrid, pull-down, co-IP, nuclear co-localization in COS7 cells, and in vitro TdT activity assay","pmids":["16371131"],"confidence":"High","gaps":["TdT inhibition demonstrated in vitro and in heterologous cells, not in lymphocytes undergoing V(D)J recombination","Physiological significance for the immune repertoire not established"]},{"year":null,"claim":"How TRERF1's distinct roles as an SF-1/PR/Sp1 coactivator and as a direct TdT inhibitor are integrated, and whether they share a common structural mechanism, remains unresolved.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No structural model of TRERF1 domains mediating its diverse interactions","No in vivo or organismal phenotype linking steroidogenic, proliferative, and recombination functions"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0140110","term_label":"transcription regulator activity","supporting_discovery_ids":[0,2,3]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[4]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,2,3]}],"localization":[{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[0,2,3]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[2,3]},{"term_id":"R-HSA-1430728","term_label":"Metabolism","supporting_discovery_ids":[1]}],"complexes":[],"partners":["NR5A1","CREBBP","EP300","SP1","PGR","DNTT","TDIF1"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"Q96PN7","full_name":"Transcriptional-regulating factor 1","aliases":["Breast cancer anti-estrogen resistance 2","Transcriptional-regulating protein 132","Zinc finger protein rapa","Zinc finger transcription factor TReP-132"],"length_aa":1200,"mass_kda":132.3,"function":"Binds DNA and activates transcription of CYP11A1. Interaction with CREBBP and EP300 results in a synergistic transcriptional activation of CYP11A1","subcellular_location":"Nucleus","url":"https://www.uniprot.org/uniprotkb/Q96PN7/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":false,"resolved_as":"","url":"https://depmap.org/portal/gene/TRERF1","classification":"Not Classified","n_dependent_lines":16,"n_total_lines":1208,"dependency_fraction":0.013245033112582781},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[],"url":"https://opencell.sf.czbiohub.org/search/TRERF1","total_profiled":1310},"omim":[{"mim_id":"610322","title":"TRANSCRIPTIONAL REGULATING FACTOR 1; TRERF1","url":"https://www.omim.org/entry/610322"},{"mim_id":"184757","title":"NUCLEAR RECEPTOR SUBFAMILY 5, GROUP A, MEMBER 1; NR5A1","url":"https://www.omim.org/entry/184757"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Enhanced","locations":[{"location":"Nucleoplasm","reliability":"Enhanced"},{"location":"Nucleoli fibrillar center","reliability":"Additional"},{"location":"Cytosol","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in many","driving_tissues":[],"url":"https://www.proteinatlas.org/search/TRERF1"},"hgnc":{"alias_symbol":["TReP-132","HSA277276","RAPA","dJ139D8.5"],"prev_symbol":["BCAR2"]},"alphafold":{"accession":"Q96PN7","domains":[{"cath_id":"-","chopping":"809-888","consensus_level":"medium","plddt":84.235,"start":809,"end":888},{"cath_id":"1.10.10,1.10.10","chopping":"892-937_950-957","consensus_level":"medium","plddt":85.1674,"start":892,"end":957},{"cath_id":"3.30.160","chopping":"1086-1132","consensus_level":"medium","plddt":90.6685,"start":1086,"end":1132}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96PN7","model_url":"https://alphafold.ebi.ac.uk/files/AF-Q96PN7-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-Q96PN7-F1-predicted_aligned_error_v6.png","plddt_mean":49.19},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=TRERF1","jax_strain_url":"https://www.jax.org/strain/search?query=TRERF1"},"sequence":{"accession":"Q96PN7","fasta_url":"https://rest.uniprot.org/uniprotkb/Q96PN7.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/Q96PN7/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/Q96PN7"}},"corpus_meta":[{"pmid":"22969786","id":"PMC_22969786","title":"Syntenic gene analysis between Brassica rapa and other Brassicaceae species.","date":"2012","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/22969786","citation_count":164,"is_preprint":false},{"pmid":"12454088","id":"PMC_12454088","title":"Characterization and effects of the replicated flowering time gene FLC in Brassica rapa.","date":"2002","source":"Genetics","url":"https://pubmed.ncbi.nlm.nih.gov/12454088","citation_count":152,"is_preprint":false},{"pmid":"34059118","id":"PMC_34059118","title":"Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa.","date":"2021","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/34059118","citation_count":127,"is_preprint":false},{"pmid":"23406519","id":"PMC_23406519","title":"The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa.","date":"2013","source":"The New phytologist","url":"https://pubmed.ncbi.nlm.nih.gov/23406519","citation_count":107,"is_preprint":false},{"pmid":"34015250","id":"PMC_34015250","title":"FERONIA receptor kinase-regulated reactive oxygen species mediate self-incompatibility in Brassica rapa.","date":"2021","source":"Current biology : CB","url":"https://pubmed.ncbi.nlm.nih.gov/34015250","citation_count":106,"is_preprint":false},{"pmid":"21835231","id":"PMC_21835231","title":"Glucosinolate biosynthetic genes in Brassica rapa.","date":"2011","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/21835231","citation_count":91,"is_preprint":false},{"pmid":"25504198","id":"PMC_25504198","title":"Anthocyanin biosynthesis for cold and freezing stress tolerance and desirable color in Brassica rapa.","date":"2014","source":"Functional & integrative genomics","url":"https://pubmed.ncbi.nlm.nih.gov/25504198","citation_count":90,"is_preprint":false},{"pmid":"24893600","id":"PMC_24893600","title":"Anthocyanin biosynthetic genes in Brassica rapa.","date":"2014","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/24893600","citation_count":86,"is_preprint":false},{"pmid":"29975432","id":"PMC_29975432","title":"Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa.","date":"2018","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/29975432","citation_count":80,"is_preprint":false},{"pmid":"19456863","id":"PMC_19456863","title":"Genome-wide identification of glucosinolate synthesis genes in Brassica rapa.","date":"2009","source":"The FEBS journal","url":"https://pubmed.ncbi.nlm.nih.gov/19456863","citation_count":72,"is_preprint":false},{"pmid":"17664315","id":"PMC_17664315","title":"Role of the rapA gene in controlling antibiotic resistance of Escherichia coli biofilms.","date":"2007","source":"Antimicrobial agents and chemotherapy","url":"https://pubmed.ncbi.nlm.nih.gov/17664315","citation_count":72,"is_preprint":false},{"pmid":"11751638","id":"PMC_11751638","title":"RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription.","date":"2001","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/11751638","citation_count":64,"is_preprint":false},{"pmid":"29569777","id":"PMC_29569777","title":"Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa.","date":"2018","source":"The Plant journal : for cell and molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/29569777","citation_count":61,"is_preprint":false},{"pmid":"15734906","id":"PMC_15734906","title":"A novel dwarfing mutation in a green revolution gene from Brassica rapa.","date":"2005","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/15734906","citation_count":56,"is_preprint":false},{"pmid":"9507009","id":"PMC_9507009","title":"RapA, a novel RNA polymerase-associated protein, is a bacterial homolog of SWI2/SNF2.","date":"1998","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/9507009","citation_count":53,"is_preprint":false},{"pmid":"28463838","id":"PMC_28463838","title":"Engineering the Rapid Adenovirus Production and Amplification (RAPA) Cell Line to Expedite the Generation of Recombinant Adenoviruses.","date":"2017","source":"Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/28463838","citation_count":51,"is_preprint":false},{"pmid":"35278263","id":"PMC_35278263","title":"Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa.","date":"2022","source":"Plant biotechnology journal","url":"https://pubmed.ncbi.nlm.nih.gov/35278263","citation_count":51,"is_preprint":false},{"pmid":"25646438","id":"PMC_25646438","title":"Structural basis for transcription reactivation by RapA.","date":"2015","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/25646438","citation_count":49,"is_preprint":false},{"pmid":"12101186","id":"PMC_12101186","title":"The transcriptional regulating protein of 132 kDa (TReP-132) enhances P450scc gene transcription through interaction with steroidogenic factor-1 in human adrenal cells.","date":"2002","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/12101186","citation_count":48,"is_preprint":false},{"pmid":"18786404","id":"PMC_18786404","title":"Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription.","date":"2008","source":"Structure (London, England : 1993)","url":"https://pubmed.ncbi.nlm.nih.gov/18786404","citation_count":44,"is_preprint":false},{"pmid":"23082790","id":"PMC_23082790","title":"A hypomethylated population of Brassica rapa for forward and reverse epi-genetics.","date":"2012","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/23082790","citation_count":40,"is_preprint":false},{"pmid":"32708772","id":"PMC_32708772","title":"Two Clubroot-Resistance Genes, Rcr3 and Rcr9wa, Mapped in Brassica rapa Using Bulk Segregant RNA Sequencing.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32708772","citation_count":40,"is_preprint":false},{"pmid":"23065269","id":"PMC_23065269","title":"Molecular characterization of the Brassica rapa auxin-repressed, superfamily genes, BrARP1 and BrDRM1.","date":"2012","source":"Molecular biology reports","url":"https://pubmed.ncbi.nlm.nih.gov/23065269","citation_count":40,"is_preprint":false},{"pmid":"20875114","id":"PMC_20875114","title":"Sequence and structure of Brassica rapa chromosome A3.","date":"2010","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/20875114","citation_count":38,"is_preprint":false},{"pmid":"22168908","id":"PMC_22168908","title":"Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family.","date":"2011","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/22168908","citation_count":35,"is_preprint":false},{"pmid":"31073524","id":"PMC_31073524","title":"Genome-Wide Identification, Evolution, and Transcriptional Profiling of PP2C Gene Family in Brassica rapa.","date":"2019","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/31073524","citation_count":34,"is_preprint":false},{"pmid":"27049520","id":"PMC_27049520","title":"Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/27049520","citation_count":34,"is_preprint":false},{"pmid":"31142280","id":"PMC_31142280","title":"Clubroot resistance gene Rcr6 in Brassica nigra resides in a genomic region homologous to chromosome A08 in B. rapa.","date":"2019","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/31142280","citation_count":32,"is_preprint":false},{"pmid":"28955373","id":"PMC_28955373","title":"Genome-Wide Identification and Characterization of BrrTCP Transcription Factors in Brassica rapa ssp. rapa.","date":"2017","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/28955373","citation_count":31,"is_preprint":false},{"pmid":"17038795","id":"PMC_17038795","title":"Characterization of DNA methyltransferase genes in Brassica rapa.","date":"2006","source":"Genes & genetic systems","url":"https://pubmed.ncbi.nlm.nih.gov/17038795","citation_count":30,"is_preprint":false},{"pmid":"24213157","id":"PMC_24213157","title":"Transformation and regeneration of Brassica rapa using Agrobacterium tumefaciens.","date":"1992","source":"Plant cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/24213157","citation_count":30,"is_preprint":false},{"pmid":"27870873","id":"PMC_27870873","title":"Herbivore-Induced DNA Demethylation Changes Floral Signalling and Attractiveness to Pollinators in Brassica rapa.","date":"2016","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/27870873","citation_count":30,"is_preprint":false},{"pmid":"17015480","id":"PMC_17015480","title":"TReP-132 is a novel progesterone receptor coactivator required for the inhibition of breast cancer cell growth and enhancement of differentiation by progesterone.","date":"2006","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/17015480","citation_count":27,"is_preprint":false},{"pmid":"32996462","id":"PMC_32996462","title":"Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns.","date":"2020","source":"eLife","url":"https://pubmed.ncbi.nlm.nih.gov/32996462","citation_count":27,"is_preprint":false},{"pmid":"31243302","id":"PMC_31243302","title":"Long noncoding RNAs in Brassica rapa L. following vernalization.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31243302","citation_count":27,"is_preprint":false},{"pmid":"14727029","id":"PMC_14727029","title":"Characterization of a dwarf gene in Brassica rapa, including the identification of a candidate gene.","date":"2004","source":"TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik","url":"https://pubmed.ncbi.nlm.nih.gov/14727029","citation_count":26,"is_preprint":false},{"pmid":"10801781","id":"PMC_10801781","title":"Interaction between RNA polymerase and RapA, a bacterial homolog of the SWI/SNF protein family.","date":"2000","source":"The Journal of biological chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/10801781","citation_count":26,"is_preprint":false},{"pmid":"33328469","id":"PMC_33328469","title":"Brassica rapa orphan genes largely affect soluble sugar metabolism.","date":"2020","source":"Horticulture research","url":"https://pubmed.ncbi.nlm.nih.gov/33328469","citation_count":25,"is_preprint":false},{"pmid":"15899840","id":"PMC_15899840","title":"TReP-132 controls cell proliferation by regulating the expression of the cyclin-dependent kinase inhibitors p21WAF1/Cip1 and p27Kip1.","date":"2005","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/15899840","citation_count":24,"is_preprint":false},{"pmid":"35371168","id":"PMC_35371168","title":"Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing.","date":"2022","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/35371168","citation_count":24,"is_preprint":false},{"pmid":"31001712","id":"PMC_31001712","title":"BcMAF2 activates BcTEM1 and represses flowering in Pak-choi (Brassica rapa ssp. chinensis).","date":"2019","source":"Plant molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/31001712","citation_count":23,"is_preprint":false},{"pmid":"35428824","id":"PMC_35428824","title":"Transcriptome analysis reveals anthocyanin regulation in Chinese cabbage (Brassica rapa L.) at low temperatures.","date":"2022","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/35428824","citation_count":23,"is_preprint":false},{"pmid":"19258339","id":"PMC_19258339","title":"Chromosome elimination, addition and introgression in intertribal partial hybrids between Brassica rapa and Isatis indigotica.","date":"2009","source":"Annals of botany","url":"https://pubmed.ncbi.nlm.nih.gov/19258339","citation_count":23,"is_preprint":false},{"pmid":"33502451","id":"PMC_33502451","title":"Meiotic chromosome axis remodelling is critical for meiotic recombination in Brassica rapa.","date":"2021","source":"Journal of experimental botany","url":"https://pubmed.ncbi.nlm.nih.gov/33502451","citation_count":22,"is_preprint":false},{"pmid":"30532761","id":"PMC_30532761","title":"BrRLP48, Encoding a Receptor-Like Protein, Involved in Downy Mildew Resistance in Brassica rapa.","date":"2018","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/30532761","citation_count":22,"is_preprint":false},{"pmid":"32560581","id":"PMC_32560581","title":"BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa.","date":"2020","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/32560581","citation_count":22,"is_preprint":false},{"pmid":"33281844","id":"PMC_33281844","title":"Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa.","date":"2020","source":"Frontiers in plant science","url":"https://pubmed.ncbi.nlm.nih.gov/33281844","citation_count":22,"is_preprint":false},{"pmid":"27295265","id":"PMC_27295265","title":"Reduction of GIGANTEA expression in transgenic Brassica rapa enhances salt tolerance.","date":"2016","source":"Plant cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/27295265","citation_count":22,"is_preprint":false},{"pmid":"33957938","id":"PMC_33957938","title":"Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed in Brassica rapa.","date":"2021","source":"Genome biology","url":"https://pubmed.ncbi.nlm.nih.gov/33957938","citation_count":21,"is_preprint":false},{"pmid":"36934626","id":"PMC_36934626","title":"Transcriptome analysis reveals different mechanisms of selenite and selenate regulation of cadmium translocation in Brassica rapa.","date":"2023","source":"Journal of hazardous materials","url":"https://pubmed.ncbi.nlm.nih.gov/36934626","citation_count":21,"is_preprint":false},{"pmid":"34115169","id":"PMC_34115169","title":"Characterization of APX and APX-R gene family in Brassica juncea and B. rapa for tolerance against abiotic stresses.","date":"2021","source":"Plant cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/34115169","citation_count":20,"is_preprint":false},{"pmid":"35933391","id":"PMC_35933391","title":"Establishment of Agrobacterium-mediated genetic transformation and application of CRISPR/Cas9 genome-editing system to Brassica rapa var. rapa.","date":"2022","source":"Plant methods","url":"https://pubmed.ncbi.nlm.nih.gov/35933391","citation_count":20,"is_preprint":false},{"pmid":"33790228","id":"PMC_33790228","title":"Divergence of three BRX homoeologs in Brassica rapa and its effect on leaf morphology.","date":"2021","source":"Horticulture research","url":"https://pubmed.ncbi.nlm.nih.gov/33790228","citation_count":20,"is_preprint":false},{"pmid":"32656681","id":"PMC_32656681","title":"Role of BrSDG8 on bolting in Chinese cabbage (Brassica rapa).","date":"2020","source":"TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik","url":"https://pubmed.ncbi.nlm.nih.gov/32656681","citation_count":20,"is_preprint":false},{"pmid":"32050656","id":"PMC_32050656","title":"Brassica Rapa SR45a Regulates Drought Tolerance via the Alternative Splicing of Target Genes.","date":"2020","source":"Genes","url":"https://pubmed.ncbi.nlm.nih.gov/32050656","citation_count":19,"is_preprint":false},{"pmid":"34439964","id":"PMC_34439964","title":"Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case.","date":"2021","source":"Biology","url":"https://pubmed.ncbi.nlm.nih.gov/34439964","citation_count":19,"is_preprint":false},{"pmid":"31797999","id":"PMC_31797999","title":"Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus.","date":"2019","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/31797999","citation_count":19,"is_preprint":false},{"pmid":"37402218","id":"PMC_37402218","title":"Wall-associated kinase BrWAK1 confers resistance to downy mildew in Brassica rapa.","date":"2023","source":"Plant biotechnology journal","url":"https://pubmed.ncbi.nlm.nih.gov/37402218","citation_count":18,"is_preprint":false},{"pmid":"34086824","id":"PMC_34086824","title":"Characterization of Brassica rapa metallothionein and phytochelatin synthase genes potentially involved in heavy metal detoxification.","date":"2021","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/34086824","citation_count":18,"is_preprint":false},{"pmid":"31800038","id":"PMC_31800038","title":"Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa.","date":"2019","source":"GigaScience","url":"https://pubmed.ncbi.nlm.nih.gov/31800038","citation_count":17,"is_preprint":false},{"pmid":"37547730","id":"PMC_37547730","title":"Role of BraRGL1 in regulation of Brassica rapa bolting and flowering.","date":"2023","source":"Horticulture research","url":"https://pubmed.ncbi.nlm.nih.gov/37547730","citation_count":16,"is_preprint":false},{"pmid":"22286206","id":"PMC_22286206","title":"Identification and characterization of stress resistance related genes of Brassica rapa.","date":"2012","source":"Biotechnology letters","url":"https://pubmed.ncbi.nlm.nih.gov/22286206","citation_count":16,"is_preprint":false},{"pmid":"26263516","id":"PMC_26263516","title":"Stress-responsive expression patterns and functional characterization of cold shock domain proteins in cabbage (Brassica rapa) under abiotic stress conditions.","date":"2015","source":"Plant physiology and biochemistry : PPB","url":"https://pubmed.ncbi.nlm.nih.gov/26263516","citation_count":16,"is_preprint":false},{"pmid":"27885421","id":"PMC_27885421","title":"Role of vernalization-mediated demethylation in the floral transition of Brassica rapa.","date":"2016","source":"Planta","url":"https://pubmed.ncbi.nlm.nih.gov/27885421","citation_count":16,"is_preprint":false},{"pmid":"37406096","id":"PMC_37406096","title":"Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA.","date":"2023","source":"Proceedings of the National Academy of Sciences of the United States of America","url":"https://pubmed.ncbi.nlm.nih.gov/37406096","citation_count":15,"is_preprint":false},{"pmid":"9259413","id":"PMC_9259413","title":"Identification of a novel breast-cancer-anti-estrogen-resistance (BCAR2) locus by cell-fusion-mediated gene transfer in human breast-cancer cells.","date":"1997","source":"International journal of cancer","url":"https://pubmed.ncbi.nlm.nih.gov/9259413","citation_count":15,"is_preprint":false},{"pmid":"25086651","id":"PMC_25086651","title":"Identification and characterization of LIM gene family in Brassica rapa.","date":"2014","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/25086651","citation_count":15,"is_preprint":false},{"pmid":"24889091","id":"PMC_24889091","title":"Hybridisation and introgression between Brassica napus and B. rapa in the Netherlands.","date":"2014","source":"Plant biology (Stuttgart, Germany)","url":"https://pubmed.ncbi.nlm.nih.gov/24889091","citation_count":14,"is_preprint":false},{"pmid":"37625773","id":"PMC_37625773","title":"Toxicity of polyvinyl chloride microplastics on Brassica rapa.","date":"2023","source":"Environmental pollution (Barking, Essex : 1987)","url":"https://pubmed.ncbi.nlm.nih.gov/37625773","citation_count":14,"is_preprint":false},{"pmid":"33364543","id":"PMC_33364543","title":"Genetic and genomic resources to study natural variation in Brassica rapa.","date":"2020","source":"Plant direct","url":"https://pubmed.ncbi.nlm.nih.gov/33364543","citation_count":14,"is_preprint":false},{"pmid":"32115144","id":"PMC_32115144","title":"Ethylene negatively mediates self-incompatibility response in Brassica rapa.","date":"2020","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/32115144","citation_count":14,"is_preprint":false},{"pmid":"26138916","id":"PMC_26138916","title":"Carotenoid biosynthetic genes in Brassica rapa: comparative genomic analysis, phylogenetic analysis, and expression profiling.","date":"2015","source":"BMC genomics","url":"https://pubmed.ncbi.nlm.nih.gov/26138916","citation_count":14,"is_preprint":false},{"pmid":"20628251","id":"PMC_20628251","title":"Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7.","date":"2010","source":"Cytogenetic and genome research","url":"https://pubmed.ncbi.nlm.nih.gov/20628251","citation_count":13,"is_preprint":false},{"pmid":"22587693","id":"PMC_22587693","title":"Environmental and genetic effects on yield and secondary metabolite production in Brassica rapa crops.","date":"2012","source":"Journal of agricultural and food chemistry","url":"https://pubmed.ncbi.nlm.nih.gov/22587693","citation_count":13,"is_preprint":false},{"pmid":"16371131","id":"PMC_16371131","title":"Direct binding of TReP-132 with TdT results in reduction of TdT activity.","date":"2006","source":"Genes to cells : devoted to molecular & cellular mechanisms","url":"https://pubmed.ncbi.nlm.nih.gov/16371131","citation_count":12,"is_preprint":false},{"pmid":"31513571","id":"PMC_31513571","title":"Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development.","date":"2019","source":"PLoS genetics","url":"https://pubmed.ncbi.nlm.nih.gov/31513571","citation_count":12,"is_preprint":false},{"pmid":"21072521","id":"PMC_21072521","title":"Analysis of target sequences of DDM1s in Brassica rapa by MSAP.","date":"2010","source":"Plant cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/21072521","citation_count":12,"is_preprint":false},{"pmid":"35037269","id":"PMC_35037269","title":"Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa.","date":"2022","source":"Plant, cell & environment","url":"https://pubmed.ncbi.nlm.nih.gov/35037269","citation_count":11,"is_preprint":false},{"pmid":"33596258","id":"PMC_33596258","title":"Phytochemical characterization of turnip greens (Brassica rapa ssp. rapa): A systematic review.","date":"2021","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/33596258","citation_count":11,"is_preprint":false},{"pmid":"35766285","id":"PMC_35766285","title":"Polysaccharides of Brassica rapa L. attenuate tumor growth via shifting macrophages to M1-like phenotype.","date":"2022","source":"Phytotherapy research : PTR","url":"https://pubmed.ncbi.nlm.nih.gov/35766285","citation_count":11,"is_preprint":false},{"pmid":"20558895","id":"PMC_20558895","title":"Novel self-compatible lines of Brassica rapa L. isolated from the Japanese bulk-populations.","date":"2010","source":"Genes & genetic systems","url":"https://pubmed.ncbi.nlm.nih.gov/20558895","citation_count":11,"is_preprint":false},{"pmid":"35298086","id":"PMC_35298086","title":"Autologous, lentivirus-modified, T-rapa cell \"micropharmacies\" for lysosomal storage disorders.","date":"2022","source":"EMBO molecular medicine","url":"https://pubmed.ncbi.nlm.nih.gov/35298086","citation_count":10,"is_preprint":false},{"pmid":"37370022","id":"PMC_37370022","title":"Genome-wide identification and expression analysis of the AUX/IAA gene family in turnip (Brassica rapa ssp. rapa).","date":"2023","source":"BMC plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/37370022","citation_count":10,"is_preprint":false},{"pmid":"30225257","id":"PMC_30225257","title":"Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses in Brassica rapa.","date":"2018","source":"BioMed research international","url":"https://pubmed.ncbi.nlm.nih.gov/30225257","citation_count":10,"is_preprint":false},{"pmid":"35628175","id":"PMC_35628175","title":"Identification and Characterization of Circular RNAs in Brassica rapa in Response to Plasmodiophora brassicae.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35628175","citation_count":10,"is_preprint":false},{"pmid":"34638707","id":"PMC_34638707","title":"Genome-Wide Identification, Evolution, and Comparative Analysis of B-Box Genes in Brassica rapa, B. oleracea, and B. napus and Their Expression Profiling in B. rapa in Response to Multiple Hormones and Abiotic Stresses.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34638707","citation_count":10,"is_preprint":false},{"pmid":"9225864","id":"PMC_9225864","title":"The Brassica rapa elongated internode (EIN) gene encodes phytochrome B.","date":"1997","source":"Plant molecular biology","url":"https://pubmed.ncbi.nlm.nih.gov/9225864","citation_count":10,"is_preprint":false},{"pmid":"35696933","id":"PMC_35696933","title":"Genome-wide identification of LEA gene family and cold response mechanism of BcLEA4-7 and BcLEA4-18 in non-heading Chinese cabbage [Brassica campestris (syn. Brassica rapa) ssp. chinensis].","date":"2022","source":"Plant science : an international journal of experimental plant biology","url":"https://pubmed.ncbi.nlm.nih.gov/35696933","citation_count":10,"is_preprint":false},{"pmid":"15072559","id":"PMC_15072559","title":"The transcriptional regulating protein of 132 kDa (TReP-132) differentially influences steroidogenic pathways in human adrenal NCI-H295 cells.","date":"2004","source":"Journal of molecular endocrinology","url":"https://pubmed.ncbi.nlm.nih.gov/15072559","citation_count":9,"is_preprint":false},{"pmid":"38094586","id":"PMC_38094586","title":"Gene editing of authentic Brassica rapa flavonol synthase 1 generates dihydroflavonol-accumulating Chinese cabbage.","date":"2023","source":"Horticulture research","url":"https://pubmed.ncbi.nlm.nih.gov/38094586","citation_count":9,"is_preprint":false},{"pmid":"33831190","id":"PMC_33831190","title":"Magnesium and calcium overaccumulate in the leaves of a schengen3 mutant of Brassica rapa.","date":"2021","source":"Plant physiology","url":"https://pubmed.ncbi.nlm.nih.gov/33831190","citation_count":9,"is_preprint":false},{"pmid":"36293299","id":"PMC_36293299","title":"Mapping and Validation of BrGOLDEN: A Dominant Gene Regulating Carotenoid Accumulation in Brassica rapa.","date":"2022","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/36293299","citation_count":9,"is_preprint":false},{"pmid":"34428297","id":"PMC_34428297","title":"Structural basis for activation of Swi2/Snf2 ATPase RapA by RNA polymerase.","date":"2021","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/34428297","citation_count":9,"is_preprint":false},{"pmid":"34502341","id":"PMC_34502341","title":"MiR1885 Regulates Disease Tolerance Genes in Brassica rapa during Early Infection with Plasmodiophora brassicae.","date":"2021","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/34502341","citation_count":9,"is_preprint":false},{"pmid":"26596461","id":"PMC_26596461","title":"Diversification and evolution of the SDG gene family in Brassica rapa after the whole genome triplication.","date":"2015","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/26596461","citation_count":9,"is_preprint":false},{"pmid":"35819188","id":"PMC_35819188","title":"On the stability of stalled RNA polymerase and its removal by RapA.","date":"2022","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/35819188","citation_count":8,"is_preprint":false},{"pmid":"36243892","id":"PMC_36243892","title":"Fine mapping and candidate gene analysis of CRA3.7 conferring clubroot resistance in Brassica rapa.","date":"2022","source":"TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik","url":"https://pubmed.ncbi.nlm.nih.gov/36243892","citation_count":8,"is_preprint":false},{"pmid":"38865018","id":"PMC_38865018","title":"Brassica rapa CURLY LEAF is a major H3K27 methyltransferase regulating flowering time.","date":"2024","source":"Planta","url":"https://pubmed.ncbi.nlm.nih.gov/38865018","citation_count":8,"is_preprint":false},{"pmid":"29444111","id":"PMC_29444111","title":"Genome-wide identification and role of MKK and MPK gene families in clubroot resistance of Brassica rapa.","date":"2018","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/29444111","citation_count":8,"is_preprint":false},{"pmid":"30987176","id":"PMC_30987176","title":"A New Subclade of Leptosphaeria biglobosa Identified from Brassica rapa.","date":"2019","source":"International journal of molecular sciences","url":"https://pubmed.ncbi.nlm.nih.gov/30987176","citation_count":8,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":50526,"output_tokens":1980,"usd":0.090639,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":8887,"output_tokens":2744,"usd":0.056517,"stage2_stop_reason":"end_turn"},"total_usd":0.147156,"stage1_batch_id":"msgbatch_017qqVz33Ga63SCDwzb35XPb","stage2_batch_id":"msgbatch_01Scr2Ei9x4HJMiRGxwrmvLK","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2002,\n      \"finding\": \"TReP-132 interacts physically with steroidogenic factor-1 (SF-1) via its N-terminal LXXLL motif, and this interaction requires the 'proximal activation domain' and 'AF-2 hexamer' motif of SF-1. Co-expression of TReP-132 and SF-1 cooperates to increase P450scc promoter activity, and co-expression with CBP/p300 produces a synergistic effect, identifying TReP-132 as a component of a transcriptional complex with SF-1 and CBP/p300 that regulates steroidogenesis.\",\n      \"method\": \"Pull-down assay, co-immunoprecipitation/Western blot, yeast two-hybrid, deletion/mutation analysis, promoter reporter assay in NCI-H295 adrenal cells\",\n      \"journal\": \"The Journal of biological chemistry\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (pulldown, co-IP, Y2H, mutagenesis, reporter assay) in a single rigorous study establishing the interaction and its molecular determinants\",\n      \"pmids\": [\"12101186\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2004,\n      \"finding\": \"TReP-132 overexpression in human adrenal NCI-H295 cells increases production of glucocorticoids, C19 steroids, and estrogens by inducing transcript levels and promoter activity of P450c17 and P450aro, while only slightly modulating 3β-HSD type II and P450c11aldo. The effect on P450c17 is enhanced by cAMP or SF-1, establishing TReP-132 as a trans-acting factor that differentially regulates multiple steroidogenic pathway genes.\",\n      \"method\": \"Overexpression in NCI-H295 cells, steroid measurement, quantitative RT-PCR, promoter reporter assay\",\n      \"journal\": \"Journal of molecular endocrinology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — cell-based overexpression with multiple pathway readouts, single lab, no independent replication reported\",\n      \"pmids\": [\"15072559\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2005,\n      \"finding\": \"TReP-132 controls cell proliferation by inducing expression of cyclin-dependent kinase inhibitors p21WAF1/Cip1 and p27Kip1 through interaction with transcription factor Sp1 at proximal Sp1-binding sites in their promoters. TReP-132 knockdown by siRNA in HeLa cells increases G1→S cell cycle progression and reduces p21 and p27 levels; conversely, TReP-132 expression level positively correlates with p21/p27 levels in breast tumor cell lines.\",\n      \"method\": \"siRNA knockdown, promoter reporter assay, co-immunoprecipitation with Sp1, cell cycle analysis (FACS), Western blot in HeLa and breast cancer cell lines\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — reciprocal loss-of-function (siRNA) and overexpression with multiple orthogonal readouts (cell cycle, protein levels, promoter activity, Sp1 interaction) in a single rigorous study\",\n      \"pmids\": [\"15899840\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"TReP-132 acts as a coactivator of progesterone receptor (PR) in breast cancer T47D cells: it interacts in vitro and in intact cells with progesterone-activated PR, synergizes with PR to trans-activate p21 and p27 promoters at proximal Sp1-binding sites, and is required for progesterone-induced growth arrest (pRB dephosphorylation, G1/S block), inhibition of cell proliferation, and induction of breast cell differentiation markers including lipid vacuole accumulation. Progesterone treatment also increases TReP-132 expression, indicating a positive auto-regulatory loop.\",\n      \"method\": \"In vitro binding assay, co-immunoprecipitation in T47D cells, siRNA knockdown, promoter reporter assay, cell cycle analysis, lipid droplet staining, RT-PCR\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (in vitro binding, co-IP, KD, reporter, cell cycle, differentiation markers) in a single rigorous study\",\n      \"pmids\": [\"17015480\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"TReP-132 directly binds terminal deoxynucleotidyltransferase (TdT) through TdT's N-terminal region, as well as the TdT-interacting factor TdIF1. TReP-132 co-localizes with TdT and TdIF1 in the nucleus of COS7 cells. Co-expression of TReP-132 with TdT reduces TdT enzymatic activity to 2.5% of maximum in vitro, indicating TReP-132 negatively regulates N-region synthesis during V(D)J recombination.\",\n      \"method\": \"Yeast two-hybrid, pull-down assay, co-immunoprecipitation with specific antibodies, co-localization in COS7 cells, in vitro TdT activity assay\",\n      \"journal\": \"Genes to cells : devoted to molecular & cellular mechanisms\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1-2 / Strong — multiple orthogonal methods (Y2H, pulldown, co-IP, co-localization, in vitro enzymatic assay) in a single study establishing direct binding and functional consequence\",\n      \"pmids\": [\"16371131\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 1997,\n      \"finding\": \"A genomic locus designated BCAR2 (breast cancer anti-estrogen resistance 2), which is an alias for TRERF1, was identified by cell-fusion-mediated gene transfer as a dominant locus conferring tamoxifen resistance to estrogen-dependent ZR-75-1 human breast cancer cells. The locus co-segregated with tamoxifen resistance in somatic cell hybrids, indicating it harbors a gene capable of altering estrogen dependency in a dominant manner in vitro.\",\n      \"method\": \"Retroviral insertion mutagenesis, cell fusion/somatic cell hybrid selection, co-segregation analysis\",\n      \"journal\": \"International journal of cancer\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — genetic co-segregation in cell hybrids identifies locus but does not identify the specific gene product or molecular mechanism; single lab\",\n      \"pmids\": [\"9259413\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"TRERF1/TReP-132 is a 132 kDa transcriptional regulatory protein that functions as a coactivator of steroidogenic factor-1 (SF-1) and progesterone receptor (PR) via direct LXXLL-motif-mediated protein-protein interactions, cooperates with CBP/p300 to drive steroidogenic gene transcription (P450scc, P450c17, P450aro), inhibits cell proliferation by interacting with Sp1 to induce CDK inhibitors p21 and p27, and directly binds and inhibits terminal deoxynucleotidyltransferase (TdT) activity in the nucleus, suggesting roles in steroidogenesis, cell cycle control, and V(D)J recombination regulation.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"TRERF1 (TReP-132) is a transcriptional regulatory protein that controls steroidogenic gene expression and cell proliferation through direct protein-protein interactions with sequence-specific transcription factors and coactivators [#0, #2]. In adrenal cells, it functions as a coactivator of steroidogenic factor-1 (SF-1), binding SF-1 through an N-terminal LXXLL motif that engages the SF-1 proximal activation domain and AF-2 hexamer, and cooperating synergistically with CBP/p300 to drive transcription of steroidogenic cytochrome P450 genes including P450scc, P450c17, and P450aro, thereby increasing production of glucocorticoids, C19 steroids, and estrogens [#0, #1]. TRERF1 also acts as an anti-proliferative factor: by interacting with Sp1 at proximal Sp1-binding sites it induces the cyclin-dependent kinase inhibitors p21WAF1/Cip1 and p27Kip1, and its loss accelerates G1\\u2192S progression [#2]. It serves as a coactivator of the progesterone receptor, synergizing with activated PR to trans-activate the p21 and p27 promoters and to enforce progesterone-induced growth arrest and breast cell differentiation [#3]. Independently of its transcriptional roles, TRERF1 directly binds terminal deoxynucleotidyltransferase (TdT) and the TdT-interacting factor TdIF1 in the nucleus and strongly inhibits TdT enzymatic activity, implicating it in regulation of N-region synthesis during V(D)J recombination [#4].\",\n  \"teleology\": [\n    {\n      \"year\": 1997,\n      \"claim\": \"Before any gene product was defined, the question was whether the TRERF1 locus could influence breast cancer estrogen dependency; genetic transfer showed it acts as a dominant tamoxifen-resistance locus.\",\n      \"evidence\": \"Cell-fusion-mediated gene transfer and co-segregation analysis in ZR-75-1 breast cancer cells (BCAR2 alias)\",\n      \"pmids\": [\"9259413\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Locus identified by co-segregation without resolving the specific gene product or molecular mechanism\",\n        \"No connection drawn to the transcriptional functions later established for TReP-132\"\n      ]\n    },\n    {\n      \"year\": 2002,\n      \"claim\": \"It was unknown how TReP-132 participates in steroidogenesis; demonstrating LXXLL-mediated binding to SF-1 and synergy with CBP/p300 established it as a coactivator within an SF-1 transcriptional complex driving P450scc.\",\n      \"evidence\": \"Pull-down, co-IP, yeast two-hybrid, mutagenesis, and promoter reporter assays in NCI-H295 adrenal cells\",\n      \"pmids\": [\"12101186\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Did not establish which steroidogenic genes beyond P450scc are regulated\",\n        \"No structural detail of the SF-1/TReP-132/CBP complex\"\n      ]\n    },\n    {\n      \"year\": 2004,\n      \"claim\": \"Whether TReP-132 broadly regulates steroidogenic output was open; overexpression showed it differentially induces P450c17 and P450aro to increase glucocorticoid, C19 steroid, and estrogen production.\",\n      \"evidence\": \"Overexpression, steroid measurement, qRT-PCR, and reporter assays in NCI-H295 cells\",\n      \"pmids\": [\"15072559\"],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Single-lab cell-based overexpression without independent replication\",\n        \"Mechanism of selectivity among steroidogenic genes not resolved\"\n      ]\n    },\n    {\n      \"year\": 2005,\n      \"claim\": \"The link between TReP-132 and proliferation was unknown; reciprocal loss- and gain-of-function showed it restrains the cell cycle by inducing p21 and p27 via Sp1.\",\n      \"evidence\": \"siRNA knockdown, co-IP with Sp1, reporter assays, and FACS cell cycle analysis in HeLa and breast cancer lines\",\n      \"pmids\": [\"15899840\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"Whether the steroidogenic and anti-proliferative roles are mechanistically coupled was not addressed\",\n        \"Endogenous regulators of TReP-132 expression not defined\"\n      ]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"It was unclear how progesterone signaling enforces breast cell growth arrest; TReP-132 was shown to coactivate PR, synergize at p21/p27 promoters, and be required for progesterone-induced arrest and differentiation.\",\n      \"evidence\": \"In vitro binding, co-IP, siRNA, reporter assays, cell cycle analysis, and lipid droplet staining in T47D cells\",\n      \"pmids\": [\"17015480\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"The positive auto-regulatory loop between progesterone and TReP-132 expression not mechanistically dissected\",\n        \"Relationship to the earlier tamoxifen-resistance locus phenotype not tested\"\n      ]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"A transcription-independent function was unknown; TReP-132 was shown to directly bind TdT and TdIF1 and inhibit TdT activity, implicating it in V(D)J recombination control.\",\n      \"evidence\": \"Yeast two-hybrid, pull-down, co-IP, nuclear co-localization in COS7 cells, and in vitro TdT activity assay\",\n      \"pmids\": [\"16371131\"],\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"TdT inhibition demonstrated in vitro and in heterologous cells, not in lymphocytes undergoing V(D)J recombination\",\n        \"Physiological significance for the immune repertoire not established\"\n      ]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"How TRERF1's distinct roles as an SF-1/PR/Sp1 coactivator and as a direct TdT inhibitor are integrated, and whether they share a common structural mechanism, remains unresolved.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"\",\n      \"gaps\": [\n        \"No structural model of TRERF1 domains mediating its diverse interactions\",\n        \"No in vivo or organismal phenotype linking steroidogenic, proliferative, and recombination functions\"\n      ]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0140110\", \"supporting_discovery_ids\": [0, 2, 3]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 2, 3]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [0, 2, 3]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [2, 3]},\n      {\"term_id\": \"R-HSA-1430728\", \"supporting_discovery_ids\": [1]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"NR5A1\", \"CREBBP\", \"EP300\", \"SP1\", \"PGR\", \"DNTT\", \"TDIF1\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":4,"faith_total":5,"faith_pct":80.0}}