{"gene":"SARNP","run_date":"2026-06-10T07:46:29","timeline":{"discoveries":[{"year":2010,"finding":"CIP29 (SARNP) is a component of the human TREX mRNA export complex. UAP56 (DDX39B) mediates an ATP-dependent interaction between the THO complex and both CIP29 and Aly. Using recombinant proteins, UAP56, Aly, and CIP29 form an ATP-dependent trimeric complex in which UAP56 bridges the interaction between CIP29 and Aly. TREX assembly is therefore ATP-dependent.","method":"Proteomic analysis of immunopurified TREX complex; recombinant protein reconstitution in vitro; ATP-dependence assays","journal":"Genes & development","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with recombinant proteins plus proteomic identification, multiple orthogonal methods in a single rigorous study","pmids":["20844015"],"is_preprint":false},{"year":2010,"finding":"A portion of CIP29 (SARNP) localizes to nuclear speckle domains, and its efficient recruitment to mRNA is both splicing- and cap-dependent, consistent with cotranscriptional mRNP assembly.","method":"Subcellular localization imaging; RNA immunoprecipitation with splicing/cap dependency assays","journal":"Genes & development","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct localization experiment with functional context, single lab but two orthogonal methods","pmids":["20844015"],"is_preprint":false},{"year":2006,"finding":"Yeast Tho1 (ortholog of SARNP) is a conserved RNA-binding nuclear protein that binds to transcribed chromatin in a THO-complex- and RNA-dependent manner, and its multicopy expression suppresses mRNA accumulation, export defects, and hyperrecombination of THO mutants (hpr1Δ). The RNA-binding activity resides in the C-terminal half (after the SAP domain).","method":"Genetic epistasis (multicopy suppressor analysis in yeast); chromatin immunoprecipitation; in vitro RNA binding assays","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — genetic epistasis combined with ChIP and in vitro RNA binding, replicated across multiple mutant backgrounds","pmids":["16738307"],"is_preprint":false},{"year":2002,"finding":"CIP29 (SARNP) contains an N-terminal SAP DNA-binding motif and overexpression of CIP29-GFP in HEK293 cells enhances cell cycle progression. Its upregulation by Epo in UT7/Epo cells was associated with cell cycle progression rather than anti-apoptosis.","method":"cDNA cloning; GFP overexpression; cell cycle analysis by flow cytometry","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — overexpression with cell cycle readout, single lab, two complementary approaches","pmids":["11922608"],"is_preprint":false},{"year":2016,"finding":"High-resolution NMR structures of both the N-terminal SAP domain and the C-terminal RNA-binding domain of yeast Tho1 (SARNP ortholog) were determined, confirming domain architecture: the SAP domain at the N-terminus and a distinct C-terminal RNA-binding domain.","method":"High-resolution NMR structure determination","journal":"Acta crystallographica. Section F, Structural biology communications","confidence":"High","confidence_rationale":"Tier 1 / Moderate — atomic-resolution NMR structures of both domains, single lab but rigorous structural method","pmids":["27303905"],"is_preprint":false},{"year":2016,"finding":"KSHV ORF57 interacts with CIP29 (SARNP) and CHTOP. Depletion of CIP29 affects ORF57-mediated viral mRNA processing, indicating CIP29 is recruited to the ORF57-mediated viral ribonucleoprotein particle (vRNP).","method":"Co-immunoprecipitation; siRNA knockdown with viral mRNA processing readout","journal":"The Journal of general virology","confidence":"Medium","confidence_rationale":"Tier 3 / Moderate — Co-IP plus functional knockdown, single lab, two orthogonal methods","pmids":["27189710"],"is_preprint":false},{"year":2017,"finding":"Xenopus Cip29 (SARNP ortholog) is rapidly phosphorylated in response to DNA double-strand breaks in egg extracts, dependent on the ATM kinase activity. A conserved serine residue was identified as the damage-dependent phosphorylation site. However, Cip29 was found NOT required for efficient DNA end-joining in egg extracts.","method":"Xenopus egg extract system; immunoblot for phosphorylation; ATM kinase inhibition; phosphorylation-site identification; DNA end-joining assay","journal":"PloS one","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — direct biochemical phosphorylation mapping with kinase inhibition and site identification, single lab","pmids":["28715428"],"is_preprint":false},{"year":2019,"finding":"SARNP binds UAP56 and Aly within the TREX complex, and its overexpression enhances mRNA splicing while its knockdown suppresses mRNA export. SARNP downregulates E-cadherin expression through interaction with pinin, thereby promoting epithelial-to-mesenchymal transition.","method":"Co-immunoprecipitation; SARNP overexpression and shRNA knockdown; mRNA splicing/export assays; in vivo tumor xenograft model","journal":"Journal of cellular physiology","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP plus functional KD/OE with defined molecular readouts, single lab","pmids":["31313837"],"is_preprint":false},{"year":2023,"finding":"Crystal structure of a Tho1/DDX39B/RNA complex reveals that SARNP (Tho1) engages DDX39B through tandem DDX39B-interacting motifs, forming a high-order complex in which human SARNP can simultaneously engage up to five DDX39B molecules. RNA-seq from SARNP knockdown cells showed GC-rich mRNAs are most affected in nuclear export.","method":"X-ray crystallography; biochemical binding assays; RNA-seq from SARNP knockdown cells","journal":"Cell reports","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with functional validation by RNA-seq knockdown, multiple orthogonal methods in a single rigorous study","pmids":["37578863"],"is_preprint":false},{"year":2026,"finding":"The C-terminal domain (CTD) of Tho1 (SARNP ortholog) stimulates the helicase activity of Sub2 (yeast DDX39B/UAP56 homolog) by acting as a rigid scaffold that promotes Sub2 oligomerization on RNA. The Tho1-CTD has two conserved α-helical motifs, each binding one Sub2 molecule, and both motifs are essential for stimulation. This scaffolding/helicase-activation mechanism is conserved in human SARNP.","method":"In vitro helicase activity assays; mutagenesis of α-helical motifs; biochemical oligomerization assays; cross-species functional complementation","journal":"Nucleic acids research","confidence":"High","confidence_rationale":"Tier 1 / Strong — in vitro reconstitution with mutagenesis and cross-species validation, multiple orthogonal methods","pmids":["41543169"],"is_preprint":false}],"current_model":"SARNP (CIP29/THO1) is a conserved component of the TREX mRNA export complex that uses tandem DDX39B-interacting motifs in its C-terminal RNA-binding domain to scaffold multiple DDX39B/UAP56 molecules, stimulating their helicase activity via oligomerization; its association with the THO complex and Aly is bridged by UAP56 in an ATP-dependent manner, enabling cotranscriptional mRNP assembly and nuclear export of GC-rich mRNAs, while its N-terminal SAP domain and ATM-dependent phosphorylation upon DNA damage further link it to nuclear RNA regulation and the DNA damage response."},"narrative":{"mechanistic_narrative":"SARNP (CIP29/THO1) is a conserved RNA-binding component of the TREX mRNA export complex that couples cotranscriptional mRNP assembly to nuclear export [PMID:20844015, PMID:16738307]. Within TREX, an ATP-dependent interaction mediated by UAP56/DDX39B bridges SARNP and Aly, with UAP56 forming a trimeric complex that scaffolds SARNP onto the THO complex [PMID:20844015, PMID:31313837]. SARNP engages DDX39B through tandem DDX39B-interacting motifs in its C-terminal RNA-binding domain, enabling a single SARNP molecule to simultaneously bind up to five DDX39B molecules and stimulate DDX39B/Sub2 helicase activity by acting as a rigid scaffold that promotes its oligomerization on RNA [PMID:37578863, PMID:41543169]. This activity is required for efficient nuclear export of mRNAs, with GC-rich transcripts most dependent on SARNP, and its recruitment to mRNA is splicing- and cap-dependent, consistent with cotranscriptional loading [PMID:20844015, PMID:37578863]. The protein has a bipartite architecture: an N-terminal SAP DNA-binding domain and a distinct C-terminal RNA-binding domain that carries the helicase-stimulating motifs [PMID:27303905, PMID:16738307]. Beyond export, SARNP is phosphorylated on a conserved serine in an ATM-dependent manner upon DNA double-strand breaks, though it is dispensable for DNA end-joining [PMID:28715428], and through interaction with pinin it downregulates E-cadherin to promote epithelial-to-mesenchymal transition [PMID:31313837].","teleology":[{"year":2002,"claim":"Before its RNA-export role was known, the question was what cellular process CIP29 participates in; identifying an N-terminal SAP DNA-binding motif and a cell-cycle-promoting effect gave the first functional foothold.","evidence":"cDNA cloning and GFP overexpression with flow-cytometry cell cycle analysis in HEK293 and UT7/Epo cells","pmids":["11922608"],"confidence":"Medium","gaps":["Overexpression readout does not establish endogenous function","SAP domain DNA-binding activity not biochemically demonstrated","No mechanistic link to mRNA biology yet"]},{"year":2006,"claim":"The yeast ortholog Tho1 was placed in the mRNA biogenesis pathway by showing it binds transcribed chromatin in a THO- and RNA-dependent manner and genetically suppresses THO-mutant export and recombination defects, establishing a conserved RNA-export-linked function.","evidence":"Multicopy suppressor genetics in hpr1Δ yeast, ChIP, and in vitro RNA binding localizing activity to the C-terminal half","pmids":["16738307"],"confidence":"High","gaps":["Direct partners within THO/TREX not biochemically defined","Conservation to human protein assumed, not shown here"]},{"year":2010,"claim":"The architecture of human TREX was resolved by showing UAP56 bridges CIP29 and Aly into an ATP-dependent trimeric complex, defining how SARNP is incorporated and that assembly requires ATP.","evidence":"Proteomics of immunopurified TREX plus recombinant protein reconstitution and ATP-dependence assays; localization to nuclear speckles with splicing/cap-dependent RNA recruitment","pmids":["20844015"],"confidence":"High","gaps":["Structural basis of the bridging interaction unknown","Functional consequence of SARNP within TREX for export not directly tested"]},{"year":2016,"claim":"Two structural and functional questions were addressed: the domain architecture of the protein was defined atomically, and a viral context for SARNP recruitment was identified.","evidence":"NMR structures of the yeast Tho1 SAP and C-terminal RNA-binding domains; Co-IP and siRNA knockdown showing CIP29 in the KSHV ORF57 vRNP","pmids":["27303905","27189710"],"confidence":"High","gaps":["NMR structures lack RNA or partner-bound complexes","How ORF57 redirects SARNP to viral mRNAs not mechanistically defined"]},{"year":2017,"claim":"Whether SARNP participates in the DNA damage response was tested, revealing ATM-dependent phosphorylation on a conserved serine but no requirement for end-joining, narrowing its DDR role to a regulated modification of uncertain output.","evidence":"Xenopus egg extract DSB system with ATM inhibition, phospho-site mapping, and DNA end-joining assays","pmids":["28715428"],"confidence":"Medium","gaps":["Functional consequence of the phosphorylation unknown","Whether phosphorylation modulates mRNA export untested"]},{"year":2019,"claim":"The functional output of human SARNP in mRNA metabolism and disease was tied together: it binds UAP56 and Aly, promotes splicing and export, and drives EMT by repressing E-cadherin via pinin.","evidence":"Reciprocal Co-IP, overexpression and shRNA knockdown with splicing/export assays, and a tumor xenograft model","pmids":["31313837"],"confidence":"Medium","gaps":["Mechanism linking export function to E-cadherin repression unclear","Single-lab functional data without structural detail"]},{"year":2023,"claim":"The molecular logic of SARNP–DDX39B engagement was solved structurally, showing tandem DDX39B-interacting motifs let one SARNP bind up to five DDX39B molecules, with GC-rich mRNAs most export-dependent on SARNP.","evidence":"X-ray crystallography of a Tho1/DDX39B/RNA complex, biochemical binding assays, and RNA-seq from SARNP knockdown cells","pmids":["37578863"],"confidence":"High","gaps":["Why GC-rich mRNAs are preferentially affected not resolved","In vivo stoichiometry of the high-order complex unknown"]},{"year":2026,"claim":"The enzymatic purpose of the scaffolding was established: the Tho1/SARNP C-terminal domain stimulates DDX39B/Sub2 helicase activity by promoting its oligomerization on RNA through two essential conserved α-helical motifs.","evidence":"In vitro helicase and oligomerization assays, α-helical motif mutagenesis, and cross-species functional complementation","pmids":["41543169"],"confidence":"High","gaps":["How helicase stimulation translates to directional mRNP packaging in cells untested","Regulation of this activity (e.g. by phosphorylation) unknown"]},{"year":null,"claim":"It remains unknown how SARNP's DNA-damage phosphorylation and its EMT/E-cadherin functions mechanistically connect to its core TREX helicase-scaffolding role.","evidence":"","pmids":[],"confidence":"Medium","gaps":["No unifying model linking DDR phosphorylation to export activity","SAP domain function in vivo undefined","Selectivity for GC-rich transcripts unexplained"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[2,8]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[9]},{"term_id":"GO:0060090","term_label":"molecular adaptor activity","supporting_discovery_ids":[0,8]},{"term_id":"GO:0003677","term_label":"DNA binding","supporting_discovery_ids":[3,4]}],"localization":[{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[1]},{"term_id":"GO:0005634","term_label":"nucleus","supporting_discovery_ids":[1,2]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,8]},{"term_id":"R-HSA-74160","term_label":"Gene expression (Transcription)","supporting_discovery_ids":[2,7]}],"complexes":["TREX complex"],"partners":["DDX39B","ALYREF","PNN"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"P82979","full_name":"SAP domain-containing ribonucleoprotein","aliases":["Cytokine-induced protein of 29 kDa","Nuclear protein Hcc-1","Proliferation-associated cytokine-inducible protein CIP29"],"length_aa":210,"mass_kda":23.7,"function":"Binds both single-stranded and double-stranded DNA with higher affinity for the single-stranded form. Specifically binds to scaffold/matrix attachment region DNA. Also binds single-stranded RNA. Enhances RNA unwinding activity of DDX39A. May participate in important transcriptional or translational control of cell growth, metabolism and carcinogenesis. Component of the TREX complex which is thought to couple mRNA transcription, processing and nuclear export, and specifically associates with spliced mRNA and not with unspliced pre-mRNA (PubMed:15338056, PubMed:17196963, PubMed:20844015). The TREX complex is recruited to spliced mRNAs by a transcription-independent mechanism, binds to mRNA upstream of the exon-junction complex (EJC) and is recruited in a splicing- and cap-dependent manner to a region near the 5' end of the mRNA where it functions in mRNA export to the cytoplasm via the TAP/NXF1 pathway (PubMed:15338056, PubMed:17196963, PubMed:20844015). Associates with DDX39B, which facilitates RNA binding of DDX39B and likely plays a role in mRNA export (PubMed:37578863)","subcellular_location":"Nucleus; Nucleus speckle","url":"https://www.uniprot.org/uniprotkb/P82979/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/SARNP","classification":"Common Essential","n_dependent_lines":603,"n_total_lines":1208,"dependency_fraction":0.4991721854304636},"opencell":{"profiled":false,"resolved_as":"","ensg_id":"","cell_line_id":"","localizations":[],"interactors":[{"gene":"CNBP","stoichiometry":0.2},{"gene":"CPSF6","stoichiometry":0.2},{"gene":"DDX39B","stoichiometry":0.2},{"gene":"RTCB","stoichiometry":0.2}],"url":"https://opencell.sf.czbiohub.org/search/SARNP","total_profiled":1310},"omim":[{"mim_id":"619906","title":"DExD-BOX HELICASE 39A; DDX39A","url":"https://www.omim.org/entry/619906"},{"mim_id":"611585","title":"TESCALCIN; TESC","url":"https://www.omim.org/entry/611585"},{"mim_id":"610049","title":"SAP DOMAIN-CONTAINING RIBONUCLEOPROTEIN; SARNP","url":"https://www.omim.org/entry/610049"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Supported","locations":[{"location":"Nuclear speckles","reliability":"Supported"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/SARNP"},"hgnc":{"alias_symbol":["THO1","Hcc-1","CIP29"],"prev_symbol":[]},"alphafold":{"accession":"P82979","domains":[{"cath_id":"-","chopping":"146-206","consensus_level":"medium","plddt":80.0228,"start":146,"end":206},{"cath_id":"1.10.720","chopping":"1-50","consensus_level":"medium","plddt":87.8762,"start":1,"end":50}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/P82979","model_url":"https://alphafold.ebi.ac.uk/files/AF-P82979-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-P82979-F1-predicted_aligned_error_v6.png","plddt_mean":74.38},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=SARNP","jax_strain_url":"https://www.jax.org/strain/search?query=SARNP"},"sequence":{"accession":"P82979","fasta_url":"https://rest.uniprot.org/uniprotkb/P82979.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/P82979/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/P82979"}},"corpus_meta":[{"pmid":"20844015","id":"PMC_20844015","title":"ATP is required for interactions between UAP56 and two conserved mRNA export proteins, Aly and CIP29, to assemble the TREX complex.","date":"2010","source":"Genes & development","url":"https://pubmed.ncbi.nlm.nih.gov/20844015","citation_count":148,"is_preprint":false},{"pmid":"16738307","id":"PMC_16738307","title":"Tho1, a novel hnRNP, and Sub2 provide alternative pathways for mRNP biogenesis in yeast THO mutants.","date":"2006","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/16738307","citation_count":48,"is_preprint":false},{"pmid":"11922608","id":"PMC_11922608","title":"Cloning and characterization of a proliferation-associated cytokine-inducible protein, CIP29.","date":"2002","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/11922608","citation_count":31,"is_preprint":false},{"pmid":"37578863","id":"PMC_37578863","title":"Structural basis for high-order complex of SARNP and DDX39B to facilitate mRNP assembly.","date":"2023","source":"Cell reports","url":"https://pubmed.ncbi.nlm.nih.gov/37578863","citation_count":17,"is_preprint":false},{"pmid":"31313837","id":"PMC_31313837","title":"SARNP, a participant in mRNA splicing and export, negatively regulates E-cadherin expression via interaction with pinin.","date":"2019","source":"Journal of cellular physiology","url":"https://pubmed.ncbi.nlm.nih.gov/31313837","citation_count":15,"is_preprint":false},{"pmid":"27189710","id":"PMC_27189710","title":"Interactions between KSHV ORF57 and the novel human TREX proteins, CHTOP and CIP29.","date":"2016","source":"The Journal of general virology","url":"https://pubmed.ncbi.nlm.nih.gov/27189710","citation_count":8,"is_preprint":false},{"pmid":"32874448","id":"PMC_32874448","title":"The use of touch DNA analysis in forensic identification focusing on Short Tandem Repeat- Combined DNA Index System loci THO1, CSF1PO and TPOX.","date":"2020","source":"Infectious disease reports","url":"https://pubmed.ncbi.nlm.nih.gov/32874448","citation_count":4,"is_preprint":false},{"pmid":"9813453","id":"PMC_9813453","title":"The short tandem repeat loci hTPO, THO1 and FGA.","date":"1998","source":"Human heredity","url":"https://pubmed.ncbi.nlm.nih.gov/9813453","citation_count":4,"is_preprint":false},{"pmid":"35047725","id":"PMC_35047725","title":"THE APPLICATION OF CELL-FREE FETAL DNA (cff-DNA) AND SIBLINGS DNA METHODS IN THE PROCESS OF PATERNITY TEST THROUGH CODIS STR LOCI (CSF1PO, THO1, TPOX, AND vWA).","date":"2021","source":"African journal of infectious diseases","url":"https://pubmed.ncbi.nlm.nih.gov/35047725","citation_count":2,"is_preprint":false},{"pmid":"27303905","id":"PMC_27303905","title":"High-resolution NMR structures of the domains of Saccharomyces cerevisiae Tho1.","date":"2016","source":"Acta crystallographica. Section F, Structural biology communications","url":"https://pubmed.ncbi.nlm.nih.gov/27303905","citation_count":2,"is_preprint":false},{"pmid":"28715428","id":"PMC_28715428","title":"Cip29 is phosphorylated following activation of the DNA damage response in Xenopus egg extracts.","date":"2017","source":"PloS one","url":"https://pubmed.ncbi.nlm.nih.gov/28715428","citation_count":1,"is_preprint":false},{"pmid":"40308289","id":"PMC_40308289","title":"Comparative antiviral resistance induction by CIP-29, a ribosome-inactivating protein from Clerodendrum inerme, and salicylic acid, a chemical.","date":"2025","source":"3 Biotech","url":"https://pubmed.ncbi.nlm.nih.gov/40308289","citation_count":1,"is_preprint":false},{"pmid":"41543169","id":"PMC_41543169","title":"Tho1 and MOS11 promote nucleic acid double-strand unwinding by facilitating DEAD-box helicase oligomerization.","date":"2026","source":"Nucleic acids research","url":"https://pubmed.ncbi.nlm.nih.gov/41543169","citation_count":0,"is_preprint":false},{"pmid":"15626663","id":"PMC_15626663","title":"[Genetic polymorphisms of STR loci THO1, TPOX, CSF1PO in Guizhou Han population].","date":"2004","source":"Yi chuan = Hereditas","url":"https://pubmed.ncbi.nlm.nih.gov/15626663","citation_count":0,"is_preprint":false},{"pmid":"8752987","id":"PMC_8752987","title":"Frequency of the three STR loci (TPOX, CSF1PO, THo1), in a Japanese population determined using a Gene Print STR multiplex kit.","date":"1996","source":"Nihon hoigaku zasshi = The Japanese journal of legal medicine","url":"https://pubmed.ncbi.nlm.nih.gov/8752987","citation_count":0,"is_preprint":false}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":8603,"output_tokens":2409,"usd":0.030972,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":9537,"output_tokens":3071,"usd":0.06223,"stage2_stop_reason":"end_turn"},"total_usd":0.093202,"stage1_batch_id":"msgbatch_013LWZZT6MWaqB9qyTSeQBmU","stage2_batch_id":"msgbatch_0194ZzQaTGNpruoNJBbEMbt3","note":"batch pricing = 50% of standard"},"stage1_raw":"```json\n{\n  \"discoveries\": [\n    {\n      \"year\": 2010,\n      \"finding\": \"CIP29 (SARNP) is a component of the human TREX mRNA export complex. UAP56 (DDX39B) mediates an ATP-dependent interaction between the THO complex and both CIP29 and Aly. Using recombinant proteins, UAP56, Aly, and CIP29 form an ATP-dependent trimeric complex in which UAP56 bridges the interaction between CIP29 and Aly. TREX assembly is therefore ATP-dependent.\",\n      \"method\": \"Proteomic analysis of immunopurified TREX complex; recombinant protein reconstitution in vitro; ATP-dependence assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with recombinant proteins plus proteomic identification, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"20844015\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2010,\n      \"finding\": \"A portion of CIP29 (SARNP) localizes to nuclear speckle domains, and its efficient recruitment to mRNA is both splicing- and cap-dependent, consistent with cotranscriptional mRNP assembly.\",\n      \"method\": \"Subcellular localization imaging; RNA immunoprecipitation with splicing/cap dependency assays\",\n      \"journal\": \"Genes & development\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct localization experiment with functional context, single lab but two orthogonal methods\",\n      \"pmids\": [\"20844015\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2006,\n      \"finding\": \"Yeast Tho1 (ortholog of SARNP) is a conserved RNA-binding nuclear protein that binds to transcribed chromatin in a THO-complex- and RNA-dependent manner, and its multicopy expression suppresses mRNA accumulation, export defects, and hyperrecombination of THO mutants (hpr1Δ). The RNA-binding activity resides in the C-terminal half (after the SAP domain).\",\n      \"method\": \"Genetic epistasis (multicopy suppressor analysis in yeast); chromatin immunoprecipitation; in vitro RNA binding assays\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — genetic epistasis combined with ChIP and in vitro RNA binding, replicated across multiple mutant backgrounds\",\n      \"pmids\": [\"16738307\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2002,\n      \"finding\": \"CIP29 (SARNP) contains an N-terminal SAP DNA-binding motif and overexpression of CIP29-GFP in HEK293 cells enhances cell cycle progression. Its upregulation by Epo in UT7/Epo cells was associated with cell cycle progression rather than anti-apoptosis.\",\n      \"method\": \"cDNA cloning; GFP overexpression; cell cycle analysis by flow cytometry\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — overexpression with cell cycle readout, single lab, two complementary approaches\",\n      \"pmids\": [\"11922608\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"High-resolution NMR structures of both the N-terminal SAP domain and the C-terminal RNA-binding domain of yeast Tho1 (SARNP ortholog) were determined, confirming domain architecture: the SAP domain at the N-terminus and a distinct C-terminal RNA-binding domain.\",\n      \"method\": \"High-resolution NMR structure determination\",\n      \"journal\": \"Acta crystallographica. Section F, Structural biology communications\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Moderate — atomic-resolution NMR structures of both domains, single lab but rigorous structural method\",\n      \"pmids\": [\"27303905\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"KSHV ORF57 interacts with CIP29 (SARNP) and CHTOP. Depletion of CIP29 affects ORF57-mediated viral mRNA processing, indicating CIP29 is recruited to the ORF57-mediated viral ribonucleoprotein particle (vRNP).\",\n      \"method\": \"Co-immunoprecipitation; siRNA knockdown with viral mRNA processing readout\",\n      \"journal\": \"The Journal of general virology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 3 / Moderate — Co-IP plus functional knockdown, single lab, two orthogonal methods\",\n      \"pmids\": [\"27189710\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Xenopus Cip29 (SARNP ortholog) is rapidly phosphorylated in response to DNA double-strand breaks in egg extracts, dependent on the ATM kinase activity. A conserved serine residue was identified as the damage-dependent phosphorylation site. However, Cip29 was found NOT required for efficient DNA end-joining in egg extracts.\",\n      \"method\": \"Xenopus egg extract system; immunoblot for phosphorylation; ATM kinase inhibition; phosphorylation-site identification; DNA end-joining assay\",\n      \"journal\": \"PloS one\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — direct biochemical phosphorylation mapping with kinase inhibition and site identification, single lab\",\n      \"pmids\": [\"28715428\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2019,\n      \"finding\": \"SARNP binds UAP56 and Aly within the TREX complex, and its overexpression enhances mRNA splicing while its knockdown suppresses mRNA export. SARNP downregulates E-cadherin expression through interaction with pinin, thereby promoting epithelial-to-mesenchymal transition.\",\n      \"method\": \"Co-immunoprecipitation; SARNP overexpression and shRNA knockdown; mRNA splicing/export assays; in vivo tumor xenograft model\",\n      \"journal\": \"Journal of cellular physiology\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP plus functional KD/OE with defined molecular readouts, single lab\",\n      \"pmids\": [\"31313837\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"Crystal structure of a Tho1/DDX39B/RNA complex reveals that SARNP (Tho1) engages DDX39B through tandem DDX39B-interacting motifs, forming a high-order complex in which human SARNP can simultaneously engage up to five DDX39B molecules. RNA-seq from SARNP knockdown cells showed GC-rich mRNAs are most affected in nuclear export.\",\n      \"method\": \"X-ray crystallography; biochemical binding assays; RNA-seq from SARNP knockdown cells\",\n      \"journal\": \"Cell reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with functional validation by RNA-seq knockdown, multiple orthogonal methods in a single rigorous study\",\n      \"pmids\": [\"37578863\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2026,\n      \"finding\": \"The C-terminal domain (CTD) of Tho1 (SARNP ortholog) stimulates the helicase activity of Sub2 (yeast DDX39B/UAP56 homolog) by acting as a rigid scaffold that promotes Sub2 oligomerization on RNA. The Tho1-CTD has two conserved α-helical motifs, each binding one Sub2 molecule, and both motifs are essential for stimulation. This scaffolding/helicase-activation mechanism is conserved in human SARNP.\",\n      \"method\": \"In vitro helicase activity assays; mutagenesis of α-helical motifs; biochemical oligomerization assays; cross-species functional complementation\",\n      \"journal\": \"Nucleic acids research\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — in vitro reconstitution with mutagenesis and cross-species validation, multiple orthogonal methods\",\n      \"pmids\": [\"41543169\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"SARNP (CIP29/THO1) is a conserved component of the TREX mRNA export complex that uses tandem DDX39B-interacting motifs in its C-terminal RNA-binding domain to scaffold multiple DDX39B/UAP56 molecules, stimulating their helicase activity via oligomerization; its association with the THO complex and Aly is bridged by UAP56 in an ATP-dependent manner, enabling cotranscriptional mRNP assembly and nuclear export of GC-rich mRNAs, while its N-terminal SAP domain and ATM-dependent phosphorylation upon DNA damage further link it to nuclear RNA regulation and the DNA damage response.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"SARNP (CIP29/THO1) is a conserved RNA-binding component of the TREX mRNA export complex that couples cotranscriptional mRNP assembly to nuclear export [#0, #2]. Within TREX, an ATP-dependent interaction mediated by UAP56/DDX39B bridges SARNP and Aly, with UAP56 forming a trimeric complex that scaffolds SARNP onto the THO complex [#0, #7]. SARNP engages DDX39B through tandem DDX39B-interacting motifs in its C-terminal RNA-binding domain, enabling a single SARNP molecule to simultaneously bind up to five DDX39B molecules and stimulate DDX39B/Sub2 helicase activity by acting as a rigid scaffold that promotes its oligomerization on RNA [#8, #9]. This activity is required for efficient nuclear export of mRNAs, with GC-rich transcripts most dependent on SARNP, and its recruitment to mRNA is splicing- and cap-dependent, consistent with cotranscriptional loading [#1, #8]. The protein has a bipartite architecture: an N-terminal SAP DNA-binding domain and a distinct C-terminal RNA-binding domain that carries the helicase-stimulating motifs [#4, #2]. Beyond export, SARNP is phosphorylated on a conserved serine in an ATM-dependent manner upon DNA double-strand breaks, though it is dispensable for DNA end-joining [#6], and through interaction with pinin it downregulates E-cadherin to promote epithelial-to-mesenchymal transition [#7].\",\n  \"teleology\": [\n    {\n      \"year\": 2002,\n      \"claim\": \"Before its RNA-export role was known, the question was what cellular process CIP29 participates in; identifying an N-terminal SAP DNA-binding motif and a cell-cycle-promoting effect gave the first functional foothold.\",\n      \"evidence\": \"cDNA cloning and GFP overexpression with flow-cytometry cell cycle analysis in HEK293 and UT7/Epo cells\",\n      \"pmids\": [\"11922608\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Overexpression readout does not establish endogenous function\", \"SAP domain DNA-binding activity not biochemically demonstrated\", \"No mechanistic link to mRNA biology yet\"]\n    },\n    {\n      \"year\": 2006,\n      \"claim\": \"The yeast ortholog Tho1 was placed in the mRNA biogenesis pathway by showing it binds transcribed chromatin in a THO- and RNA-dependent manner and genetically suppresses THO-mutant export and recombination defects, establishing a conserved RNA-export-linked function.\",\n      \"evidence\": \"Multicopy suppressor genetics in hpr1Δ yeast, ChIP, and in vitro RNA binding localizing activity to the C-terminal half\",\n      \"pmids\": [\"16738307\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Direct partners within THO/TREX not biochemically defined\", \"Conservation to human protein assumed, not shown here\"]\n    },\n    {\n      \"year\": 2010,\n      \"claim\": \"The architecture of human TREX was resolved by showing UAP56 bridges CIP29 and Aly into an ATP-dependent trimeric complex, defining how SARNP is incorporated and that assembly requires ATP.\",\n      \"evidence\": \"Proteomics of immunopurified TREX plus recombinant protein reconstitution and ATP-dependence assays; localization to nuclear speckles with splicing/cap-dependent RNA recruitment\",\n      \"pmids\": [\"20844015\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Structural basis of the bridging interaction unknown\", \"Functional consequence of SARNP within TREX for export not directly tested\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Two structural and functional questions were addressed: the domain architecture of the protein was defined atomically, and a viral context for SARNP recruitment was identified.\",\n      \"evidence\": \"NMR structures of the yeast Tho1 SAP and C-terminal RNA-binding domains; Co-IP and siRNA knockdown showing CIP29 in the KSHV ORF57 vRNP\",\n      \"pmids\": [\"27303905\", \"27189710\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"NMR structures lack RNA or partner-bound complexes\", \"How ORF57 redirects SARNP to viral mRNAs not mechanistically defined\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Whether SARNP participates in the DNA damage response was tested, revealing ATM-dependent phosphorylation on a conserved serine but no requirement for end-joining, narrowing its DDR role to a regulated modification of uncertain output.\",\n      \"evidence\": \"Xenopus egg extract DSB system with ATM inhibition, phospho-site mapping, and DNA end-joining assays\",\n      \"pmids\": [\"28715428\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Functional consequence of the phosphorylation unknown\", \"Whether phosphorylation modulates mRNA export untested\"]\n    },\n    {\n      \"year\": 2019,\n      \"claim\": \"The functional output of human SARNP in mRNA metabolism and disease was tied together: it binds UAP56 and Aly, promotes splicing and export, and drives EMT by repressing E-cadherin via pinin.\",\n      \"evidence\": \"Reciprocal Co-IP, overexpression and shRNA knockdown with splicing/export assays, and a tumor xenograft model\",\n      \"pmids\": [\"31313837\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism linking export function to E-cadherin repression unclear\", \"Single-lab functional data without structural detail\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"The molecular logic of SARNP–DDX39B engagement was solved structurally, showing tandem DDX39B-interacting motifs let one SARNP bind up to five DDX39B molecules, with GC-rich mRNAs most export-dependent on SARNP.\",\n      \"evidence\": \"X-ray crystallography of a Tho1/DDX39B/RNA complex, biochemical binding assays, and RNA-seq from SARNP knockdown cells\",\n      \"pmids\": [\"37578863\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Why GC-rich mRNAs are preferentially affected not resolved\", \"In vivo stoichiometry of the high-order complex unknown\"]\n    },\n    {\n      \"year\": 2026,\n      \"claim\": \"The enzymatic purpose of the scaffolding was established: the Tho1/SARNP C-terminal domain stimulates DDX39B/Sub2 helicase activity by promoting its oligomerization on RNA through two essential conserved α-helical motifs.\",\n      \"evidence\": \"In vitro helicase and oligomerization assays, α-helical motif mutagenesis, and cross-species functional complementation\",\n      \"pmids\": [\"41543169\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"How helicase stimulation translates to directional mRNP packaging in cells untested\", \"Regulation of this activity (e.g. by phosphorylation) unknown\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unknown how SARNP's DNA-damage phosphorylation and its EMT/E-cadherin functions mechanistically connect to its core TREX helicase-scaffolding role.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"No unifying model linking DDR phosphorylation to export activity\", \"SAP domain function in vivo undefined\", \"Selectivity for GC-rich transcripts unexplained\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [2, 8]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [9]},\n      {\"term_id\": \"GO:0060090\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"GO:0003677\", \"supporting_discovery_ids\": [3, 4]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [1]},\n      {\"term_id\": \"GO:0005634\", \"supporting_discovery_ids\": [1, 2]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 8]},\n      {\"term_id\": \"R-HSA-74160\", \"supporting_discovery_ids\": [2, 7]}\n    ],\n    \"complexes\": [\"TREX complex\"],\n    \"partners\": [\"DDX39B\", \"ALYREF\", \"PNN\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"win","faith_supported":6,"faith_total":6,"faith_pct":100.0}}