Affinage

TRERF1

Transcriptional-regulating factor 1 · UniProt Q96PN7

Length
1200 aa
Mass
132.3 kDa
Annotated
2026-04-28
100 papers in source corpus 2 papers cited in narrative 2 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

TRERF1 (TReP-132/BCAR2) is a nuclear transcriptional regulator that directly binds terminal deoxynucleotidyltransferase (TdT) through TdT's N-terminal region and suppresses TdT enzymatic activity to ~2.5% of its maximum, functioning as a negative regulator of N-region nucleotide addition during V(D)J recombination (PMID:16371131). The TRERF1 locus was independently identified as a dominant oncogenic locus (BCAR2) whose retroviral activation confers tamoxifen resistance to estrogen-dependent breast cancer cells (PMID:9259413).

Mechanistic history

Synthesis pass · year-by-year structured walk · 2 steps
  1. 1997 Medium

    Before TRERF1's molecular function was known, retroviral insertion mutagenesis established that activation of this locus (BCAR2) dominantly overrides estrogen dependency in breast cancer cells, revealing it as a potential oncogenic effector of anti-estrogen resistance.

    Evidence Retroviral insertion mutagenesis and somatic cell fusion gene transfer with co-segregation analysis in ZR-75-1 breast cancer cells

    PMID:9259413

    Open questions at the time
    • No molecular characterization of the TRERF1 protein product or its mechanism of action in conferring tamoxifen resistance
    • Single cell line system; generalizability to other breast cancer models not tested
    • Pathway connecting TRERF1 activation to estrogen receptor signaling bypass not defined
  2. 2006 High

    The question of what molecular activity TRERF1 protein performs was answered by showing it directly binds TdT and potently inhibits TdT enzymatic activity, establishing TRERF1 as a negative regulator of template-independent nucleotide addition during V(D)J recombination.

    Evidence Yeast two-hybrid, pull-down, immunoprecipitation, co-localization in COS7 cells, and in vitro TdT activity assay with dsDNA primer

    PMID:16371131

    Open questions at the time
    • Physiological relevance of TdT inhibition not tested in developing lymphocytes or in vivo V(D)J recombination systems
    • Structural basis of the TRERF1–TdT interaction is undefined
    • Whether the transcriptional regulatory activity of TRERF1 is mechanistically linked to its TdT-inhibitory function remains unresolved

Open questions

Synthesis pass · forward-looking unresolved questions
  • The relationship between TRERF1's two described functions — TdT suppression in V(D)J recombination and anti-estrogen resistance in breast cancer — remains mechanistically unconnected, and in vivo validation in both contexts is lacking.
  • No in vivo genetic model (knockout or conditional) to define physiological roles
  • Transcriptional target genes of TRERF1 are not identified
  • Mechanism linking TRERF1 to estrogen receptor signaling or tamoxifen resistance pathway unknown

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0098772 molecular function regulator activity 1
Localization
GO:0005634 nucleus 1
Partners
TDT

Evidence

Reading pass · 2 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2006 TRERF1 (TReP-132) directly binds to terminal deoxynucleotidyltransferase (TdT) through TdT's confined N-terminal region, and co-expression in COS7 cells shows nuclear co-localization; TReP-132 reduces TdT enzymatic activity to ~2.5% of maximum in an in vitro assay using double-stranded DNA with a 3' protrusion as primer, suggesting negative regulation of N-region synthesis during V(D)J recombination. Yeast two-hybrid, pull-down assay, immunoprecipitation with specific antibodies (in vitro and in vivo), co-expression/co-localization in COS7 cells, in vitro TdT activity assay Genes to cells : devoted to molecular & cellular mechanisms High 16371131
1997 The TRERF1 locus (designated BCAR2, breast-cancer-anti-estrogen-resistance locus 2) was identified as a common retroviral integration site that confers tamoxifen resistance to estrogen-dependent ZR-75-1 human breast-cancer cells in a dominant manner, placing it in a pathway that controls estrogen dependency of breast cancer cells. Retroviral insertion mutagenesis, somatic cell fusion gene transfer, co-segregation analysis in 29 somatic-cell hybrid clones International journal of cancer Medium 9259413

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
1998 Rapamune (RAPA, rapamycin, sirolimus): mechanism of action immunosuppressive effect results from blockade of signal transduction and inhibition of cell cycle progression. Clinical biochemistry 558 9721431
2012 Syntenic gene analysis between Brassica rapa and other Brassicaceae species. Frontiers in plant science 164 22969786
2002 Characterization and effects of the replicated flowering time gene FLC in Brassica rapa. Genetics 152 12454088
2021 Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapa. Genome biology 126 34059118
2013 The dispensable chromosome of Leptosphaeria maculans shelters an effector gene conferring avirulence towards Brassica rapa. The New phytologist 107 23406519
2021 FERONIA receptor kinase-regulated reactive oxygen species mediate self-incompatibility in Brassica rapa. Current biology : CB 102 34015250
2010 A rich TILLING resource for studying gene function in Brassica rapa. BMC plant biology 99 20380715
2018 DNA-Free Genome Editing of Brassica oleracea and B. rapa Protoplasts Using CRISPR-Cas9 Ribonucleoprotein Complexes. Frontiers in plant science 91 30455712
2011 Glucosinolate biosynthetic genes in Brassica rapa. Gene 91 21835231
2014 Anthocyanin biosynthesis for cold and freezing stress tolerance and desirable color in Brassica rapa. Functional & integrative genomics 90 25504198
2014 Anthocyanin biosynthetic genes in Brassica rapa. BMC genomics 86 24893600
2018 Systematic identification of long non-coding RNAs during pollen development and fertilization in Brassica rapa. The Plant journal : for cell and molecular biology 79 29975432
2016 Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa. The New phytologist 76 26871271
2009 Genome-wide identification of glucosinolate synthesis genes in Brassica rapa. The FEBS journal 72 19456863
2014 Physiological, metabolic, and transcriptional effects of biologically-synthesized silver nanoparticles in turnip (Brassica rapa ssp. rapa L.). Protoplasma 64 25471476
2001 RapA, a bacterial homolog of SWI2/SNF2, stimulates RNA polymerase recycling in transcription. Genes & development 64 11751638
2018 Maternal components of RNA-directed DNA methylation are required for seed development in Brassica rapa. The Plant journal : for cell and molecular biology 60 29569777
2014 Identification and characterization of microRNAs in oilseed rape (Brassica napus) responsive to infection with the pathogenic fungus Verticillium longisporum using Brassica AA (Brassica rapa) and CC (Brassica oleracea) as reference genomes. The New phytologist 58 25132374
2005 A novel dwarfing mutation in a green revolution gene from Brassica rapa. Plant physiology 56 15734906
1980 Cloned Cauliflower Mosaic Virus DNA Infects Turnips (Brassica rapa). Science (New York, N.Y.) 54 17830812
1998 RapA, a novel RNA polymerase-associated protein, is a bacterial homolog of SWI2/SNF2. The Journal of biological chemistry 53 9507009
2017 Engineering the Rapid Adenovirus Production and Amplification (RAPA) Cell Line to Expedite the Generation of Recombinant Adenoviruses. Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry, and pharmacology 51 28463838
2022 Transposable element insertion: a hidden major source of domesticated phenotypic variation in Brassica rapa. Plant biotechnology journal 50 35278263
2015 Structural basis for transcription reactivation by RapA. Proceedings of the National Academy of Sciences of the United States of America 49 25646438
2004 RAP--a putative RNA-binding domain. Trends in biochemical sciences 47 15501674
2008 Structure of RapA, a Swi2/Snf2 protein that recycles RNA polymerase during transcription. Structure (London, England : 1993) 44 18786404
2012 Molecular characterization of the Brassica rapa auxin-repressed, superfamily genes, BrARP1 and BrDRM1. Molecular biology reports 40 23065269
2012 A hypomethylated population of Brassica rapa for forward and reverse epi-genetics. BMC plant biology 40 23082790
2020 Two Clubroot-Resistance Genes, Rcr3 and Rcr9wa, Mapped in Brassica rapa Using Bulk Segregant RNA Sequencing. International journal of molecular sciences 39 32708772
2010 Sequence and structure of Brassica rapa chromosome A3. Genome biology 38 20875114
2014 Selenium, putrescine, and cadmium influence health-promoting phytochemicals and molecular-level effects on turnip (Brassica rapa ssp. rapa). Food chemistry 37 25466011
2020 QTL-Seq and Sequence Assembly Rapidly Mapped the Gene BrMYBL2.1 for the Purple Trait in Brassica rapa. Scientific reports 36 32047197
2011 Phylogenetic analysis and classification of the Brassica rapa SET-domain protein family. BMC plant biology 35 22168908
2016 Genome-Wide Analysis and Characterization of Aux/IAA Family Genes in Brassica rapa. PloS one 34 27049520
2019 Genome-Wide Identification, Evolution, and Transcriptional Profiling of PP2C Gene Family in Brassica rapa. BioMed research international 33 31073524
2019 Clubroot resistance gene Rcr6 in Brassica nigra resides in a genomic region homologous to chromosome A08 in B. rapa. BMC plant biology 31 31142280
2017 Genome-Wide Identification and Characterization of BrrTCP Transcription Factors in Brassica rapa ssp. rapa. Frontiers in plant science 31 28955373
2006 A family of auxin conjugate hydrolases from Brassica rapa: characterization and expression during clubroot disease. The New phytologist 30 16771990
2006 Characterization of DNA methyltransferase genes in Brassica rapa. Genes & genetic systems 30 17038795
1992 Transformation and regeneration of Brassica rapa using Agrobacterium tumefaciens. Plant cell reports 30 24213157
2016 Herbivore-Induced DNA Demethylation Changes Floral Signalling and Attractiveness to Pollinators in Brassica rapa. PloS one 29 27870873
2020 Expansion of the circadian transcriptome in Brassica rapa and genome-wide diversification of paralog expression patterns. eLife 27 32996462
2019 Long noncoding RNAs in Brassica rapa L. following vernalization. Scientific reports 27 31243302
2004 Characterization of a dwarf gene in Brassica rapa, including the identification of a candidate gene. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 26 14727029
2014 Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing. G3 (Bethesda, Md.) 25 25122667
2007 Molecular cloning of Brassica rapa nitrilases and their expression during clubroot development. Molecular plant pathology 25 20507526
2022 Improved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing. Frontiers in plant science 24 35371168
2022 Transcriptome analysis reveals anthocyanin regulation in Chinese cabbage (Brassica rapa L.) at low temperatures. Scientific reports 23 35428824
2019 BcMAF2 activates BcTEM1 and represses flowering in Pak-choi (Brassica rapa ssp. chinensis). Plant molecular biology 23 31001712
2020 BrmiR828 Targets BrPAP1, BrMYB82, and BrTAS4 Involved in the Light Induced Anthocyanin Biosynthetic Pathway in Brassica rapa. International journal of molecular sciences 22 32560581
2023 BrMYB108 confers resistance to Verticillium wilt by activating ROS generation in Brassica rapa. Cell reports 21 37552600
2021 Meiotic chromosome axis remodelling is critical for meiotic recombination in Brassica rapa. Journal of experimental botany 21 33502451
2020 Genome Size Variation and Comparative Genomics Reveal Intraspecific Diversity in Brassica rapa. Frontiers in plant science 21 33281844
2018 BrRLP48, Encoding a Receptor-Like Protein, Involved in Downy Mildew Resistance in Brassica rapa. Frontiers in plant science 21 30532761
2016 Reduction of GIGANTEA expression in transgenic Brassica rapa enhances salt tolerance. Plant cell reports 21 27295265
2023 Transcriptome analysis reveals different mechanisms of selenite and selenate regulation of cadmium translocation in Brassica rapa. Journal of hazardous materials 20 36934626
2021 Divergence of three BRX homoeologs in Brassica rapa and its effect on leaf morphology. Horticulture research 20 33790228
2021 Embryo CHH hypermethylation is mediated by RdDM and is autonomously directed in Brassica rapa. Genome biology 20 33957938
2012 Genomic and transcriptomic alterations following hybridisation and genome doubling in trigenomic allohexaploid Brassica carinata × Brassica rapa. Plant biology (Stuttgart, Germany) 20 22309095
2022 Establishment of Agrobacterium-mediated genetic transformation and application of CRISPR/Cas9 genome-editing system to Brassica rapa var. rapa. Plant methods 19 35933391
2021 Sequencing and Chromosome-Scale Assembly of Plant Genomes, Brassica rapa as a Use Case. Biology 19 34439964
2014 The role of small RNAs in wide hybridisation and allopolyploidisation between Brassica rapa and Brassica nigra. BMC plant biology 19 25326708
2013 Genome-wide characterization of the Pectate Lyase-like (PLL) genes in Brassica rapa. Molecular genetics and genomics : MGG 19 23999922
2021 Characterization of Brassica rapa metallothionein and phytochelatin synthase genes potentially involved in heavy metal detoxification. PloS one 18 34086824
2020 Role of BrSDG8 on bolting in Chinese cabbage (Brassica rapa). TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 18 32656681
2019 Integration of metabolome and transcriptome reveals flavonoid accumulation in the intergeneric hybrid between Brassica rapa and Raphanus sativus. Scientific reports 18 31797999
2023 Wall-associated kinase BrWAK1 confers resistance to downy mildew in Brassica rapa. Plant biotechnology journal 17 37402218
2019 Genome-wide analysis of the H3K27me3 epigenome and transcriptome in Brassica rapa. GigaScience 17 31800038
2023 Role of BraRGL1 in regulation of Brassica rapa bolting and flowering. Horticulture research 16 37547730
2016 Role of vernalization-mediated demethylation in the floral transition of Brassica rapa. Planta 16 27885421
2015 Stress-responsive expression patterns and functional characterization of cold shock domain proteins in cabbage (Brassica rapa) under abiotic stress conditions. Plant physiology and biochemistry : PPB 16 26263516
2012 Identification and characterization of stress resistance related genes of Brassica rapa. Biotechnology letters 16 22286206
2023 Recycling of bacterial RNA polymerase by the Swi2/Snf2 ATPase RapA. Proceedings of the National Academy of Sciences of the United States of America 15 37406096
2019 Microfluidic preparation of PLGA microspheres as cell carriers with sustainable Rapa release. Journal of biomaterials science. Polymer edition 15 30935290
2014 Identification and characterization of LIM gene family in Brassica rapa. BMC genomics 15 25086651
1997 Identification of a novel breast-cancer-anti-estrogen-resistance (BCAR2) locus by cell-fusion-mediated gene transfer in human breast-cancer cells. International journal of cancer 15 9259413
2023 Toxicity of polyvinyl chloride microplastics on Brassica rapa. Environmental pollution (Barking, Essex : 1987) 14 37625773
2021 Comparative Transcriptome Analysis of Early- and Late-Bolting Traits in Chinese Cabbage (Brassica rapa). Frontiers in genetics 14 33747036
2020 Ethylene negatively mediates self-incompatibility response in Brassica rapa. Biochemical and biophysical research communications 14 32115144
2020 Genetic and genomic resources to study natural variation in Brassica rapa. Plant direct 14 33364543
2015 Carotenoid biosynthetic genes in Brassica rapa: comparative genomic analysis, phylogenetic analysis, and expression profiling. BMC genomics 14 26138916
2013 Inferring the Brassica rapa Interactome Using Protein-Protein Interaction Data from Arabidopsis thaliana. Frontiers in plant science 14 23293649
2008 Genetically monomorphic invasive populations of the rapa whelk, Rapana venosa. Molecular ecology 14 19238707
2012 Environmental and genetic effects on yield and secondary metabolite production in Brassica rapa crops. Journal of agricultural and food chemistry 13 22587693
2010 Integration of genetic, physical, and cytogenetic maps for Brassica rapa chromosome A7. Cytogenetic and genome research 13 20628251
2023 Brassica rapa orphan gene BR1 delays flowering time in Arabidopsis. Frontiers in plant science 12 36909380
2022 Genome-Wide Identification of C2H2 ZFPs and Functional Analysis of BRZAT12 under Low-Temperature Stress in Winter Rapeseed (Brassica rapa). International journal of molecular sciences 12 36293086
2020 Revealing biomass heterosis in the allodiploid xBrassicoraphanus, a hybrid between Brassica rapa and Raphanus sativus, through integrated transcriptome and metabolites analysis. BMC plant biology 12 32493222
2019 Integrating transcriptomic network reconstruction and eQTL analyses reveals mechanistic connections between genomic architecture and Brassica rapa development. PLoS genetics 12 31513571
2018 Genetic dissection of flowering time in Brassica rapa responses to temperature and photoperiod. Plant science : an international journal of experimental plant biology 12 30823988
2014 Hybridisation and introgression between Brassica napus and B. rapa in the Netherlands. Plant biology (Stuttgart, Germany) 12 24889091
2013 Phylogenetic Analysis of Brassica rapa MATH-Domain Proteins. Current genomics 12 24179444
2006 Direct binding of TReP-132 with TdT results in reduction of TdT activity. Genes to cells : devoted to molecular & cellular mechanisms 12 16371131
2022 Conserved and distinct roles of H3K27me3 demethylases regulating flowering time in Brassica rapa. Plant, cell & environment 11 35037269
2022 Polysaccharides of Brassica rapa L. attenuate tumor growth via shifting macrophages to M1-like phenotype. Phytotherapy research : PTR 11 35766285
2021 Phytochemical characterization of turnip greens (Brassica rapa ssp. rapa): A systematic review. PloS one 11 33596258
2017 Molecular characterization of an AtPYL1-like protein, BrPYL1, as a putative ABA receptor in Brassica rapa. Biochemical and biophysical research communications 11 28450111
2010 Novel self-compatible lines of Brassica rapa L. isolated from the Japanese bulk-populations. Genes & genetic systems 11 20558895
2006 Competition affects gene flow from oilseed rape (female symbol) to Brassica rapa (male symbol). Heredity 11 16508664
2022 Autologous, lentivirus-modified, T-rapa cell "micropharmacies" for lysosomal storage disorders. EMBO molecular medicine 10 35298086