{"gene":"RSL1D1","run_date":"2026-06-10T07:46:28","timeline":{"discoveries":[{"year":2008,"finding":"CSIG/RSL1D1 binds directly to the 5' UTR of PTEN mRNA and suppresses its translation, thereby reducing PTEN protein levels and downstream p27(Kip1) expression to promote cell proliferation and delay replicative senescence.","method":"RNA immunoprecipitation (RIP), luciferase reporter assay (PTEN 5' UTR), knockdown/overexpression with proliferation and senescence readouts (SA-β-gal), genetic epistasis using PTEN-silenced/deficient cells","journal":"Molecular and cellular biology","confidence":"High","confidence_rationale":"Tier 2 / Strong — multiple orthogonal methods (RIP, luciferase reporter, KD/OE, epistasis with PTEN-null cells) in a single rigorous study","pmids":["18678645"],"is_preprint":false},{"year":2012,"finding":"CSIG/RSL1D1 is a nucleolar protein that interacts with p33ING1; after UV irradiation, p33ING1 translocates to the nucleolus and binds CSIG, stabilizing CSIG protein. This p33ING1–CSIG complex promotes apoptosis via activation of BAX (Bcl-2-associated X protein).","method":"Co-immunoprecipitation, immunofluorescence localization, UV irradiation assay, apoptosis readouts, domain-mapping (p33ING1 nucleolar targeting sequence required for CSIG interaction)","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — reciprocal Co-IP and localization with functional apoptosis readout, single lab","pmids":["22419112"],"is_preprint":false},{"year":2015,"finding":"CSIG/RSL1D1 directly interacts with c-MYC protein and protects it from ubiquitination and proteasomal degradation, thereby increasing c-MYC protein levels and promoting hepatocellular carcinoma cell proliferation.","method":"Co-immunoprecipitation, ubiquitination assay, knockdown/overexpression with colony formation and xenograft assays","journal":"Oncotarget","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus ubiquitination assay plus in vivo xenograft, single lab","pmids":["25749381"],"is_preprint":false},{"year":2015,"finding":"Both the N-terminal ribosomal L1 domain and the C-terminal lysine-rich region of CSIG/RSL1D1 are individually necessary but not sufficient for its function; full-length CSIG reduces PTEN expression and promotes proliferation, while truncated fragments (NT or CT alone) fail to alter PTEN levels and instead inhibit proliferation and accelerate senescence. The two truncated fragments also display altered subcellular localization compared to wild-type CSIG.","method":"Domain-deletion/truncation expression, western blotting (PTEN levels), SA-β-gal senescence assay, cell proliferation assay, immunofluorescence for subcellular localization","journal":"Biochemical and biophysical research communications","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — structure-function dissection with multiple functional readouts, single lab","pmids":["26686419"],"is_preprint":false},{"year":2016,"finding":"CSIG/RSL1D1 translocates from the nucleolus to the nucleoplasm under nucleolar stress, directly binds the MDM2 RING finger domain, and inhibits MDM2 E3 ubiquitin ligase activity, thereby reducing p53 ubiquitination and degradation and enabling p53-dependent G1 arrest.","method":"Co-immunoprecipitation (CSIG–MDM2 interaction, mapping to RING finger domain), ubiquitination assay (MDM2-mediated p53 ubiquitination), knockdown with p53 protein level and cell-cycle readouts, immunofluorescence for nucleolar-to-nucleoplasm translocation","journal":"Scientific reports","confidence":"High","confidence_rationale":"Tier 1–2 / Strong — direct binding mapped to MDM2 RING domain, E3 ligase activity assay, localization, and functional cell-cycle readout, multiple orthogonal methods in one study","pmids":["27811966"],"is_preprint":false},{"year":2017,"finding":"Crystal structure of yeast Utp30 (ortholog of RSL1D1/Cic1 in small subunit preribosomes) at 2.65 Å resolution reveals a two-domain fold that fits into 90S cryo-EM density; Utp30 binds rearranged helix 41 of 18S rRNA and helix 4 of 5' ETS via its concaved domain I surface. Deletion of Utp30 does not affect 90S composition, consistent with its peripheral location.","method":"X-ray crystallography (2.65 Å), cryo-EM fitting, RNA-binding analysis, yeast deletion strain analysis of 90S composition","journal":"RNA (New York, N.Y.)","confidence":"High","confidence_rationale":"Tier 1 / Strong — crystal structure with cryo-EM validation and functional deletion analysis in yeast ortholog","pmids":["28951391"],"is_preprint":false},{"year":2022,"finding":"RSL1D1 directly interacts with the DNA-binding domain (aa 93-292, more precisely aa 93-224) of wild-type p53 and recruits p53 to HDM2, forming an RSL1D1/HDM2/p53 complex that enhances p53 ubiquitination and decreases p53 protein levels in CRC cells. Mutations in p53 (R175H) abolish this interaction, while R273H weakens it, preventing HDM2 recruitment and allowing mutant p53 accumulation.","method":"Co-immunoprecipitation, domain-mapping (p53 deletion mutants), ubiquitination assay, western blotting for p53 protein levels","journal":"Experimental cell research","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP with domain mapping and ubiquitination assay, single lab","pmids":["35597299"],"is_preprint":false},{"year":2022,"finding":"RSL1D1 interacts with RAN GTPase and competitively inhibits RAN deacetylation by Sirt7, thereby maintaining RAN in an acetylated state, which inhibits nuclear STAT3 accumulation and STAT3-regulated autophagy, promoting CRC cell proliferation and metastasis.","method":"Co-immunoprecipitation (RSL1D1–RAN, RSL1D1–Sirt7 competitive binding), acetylation assay, nuclear fractionation for STAT3, autophagy flux assay, knockdown/overexpression with proliferation and invasion readouts","journal":"Cell death & disease","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — Co-IP plus competitive binding assay plus acetylation and functional readouts, single lab","pmids":["35013134"],"is_preprint":false},{"year":2022,"finding":"RSL1D1 directly binds the 3' UTR of PPARγ mRNA and stabilizes it in a HuR-dependent manner, increasing PPARγ mRNA and protein levels and thereby regulating downstream targets (PTEN/p27, NF-κB, GLUT4, ACL) to modulate cellular senescence and proliferation.","method":"RNA immunoprecipitation (RIP), biotin-labeled RNA pulldown, dual luciferase reporter assay, western blotting, real-time PCR, SA-β-gal staining, cell proliferation and colony formation assays","journal":"Life sciences","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP and RNA pulldown plus reporter assay, multiple functional readouts, single lab","pmids":["35940221"],"is_preprint":false},{"year":2023,"finding":"RSL1D1 directly binds the 3' UTR of FTH1 (ferritin heavy chain 1) mRNA and promotes its stability; RSL1D1 knockdown reduces FTH1 expression, increases transferrin receptor 1, causes intracellular ferrous iron accumulation, and induces ferroptosis (increased MDA, decreased GPX4). RSL1D1 protein is itself downregulated by ubiquitin-mediated proteolysis in senescent CRC cells.","method":"RNA immunoprecipitation (RIP), 3'-UTR binding assay, knockdown with iron metabolism readouts (ferrous iron assay, MDA, GPX4 western blot), cell proliferation and apoptosis assays, ubiquitination assay for RSL1D1 degradation","journal":"Carcinogenesis","confidence":"Medium","confidence_rationale":"Tier 2 / Moderate — RIP plus multiple functional iron metabolism readouts plus ubiquitination, single lab","pmids":["36913375"],"is_preprint":false},{"year":2025,"finding":"RSL1D1 interacts with NRF2 and inhibits its ubiquitination, thereby preventing NRF2 degradation and promoting lung adenocarcinoma cell proliferation.","method":"Co-immunoprecipitation (RSL1D1–NRF2 interaction), ubiquitination assay, knockdown/overexpression with proliferation readouts","journal":"Gene","confidence":"Low","confidence_rationale":"Tier 3 / Weak — single Co-IP plus ubiquitination assay, single lab, single study with limited methods detail in abstract","pmids":["40543689"],"is_preprint":false}],"current_model":"RSL1D1 (CSIG) is a nucleolar ribosomal L1 domain-containing RNA-binding protein that operates via multiple non-ribosomal mechanisms: it suppresses translation of PTEN mRNA by binding its 5' UTR, stabilizes PPARγ and FTH1 mRNAs by binding their 3' UTRs, and acts as a protein-level regulator by binding the MDM2 RING domain to inhibit p53 ubiquitination, stabilizing c-MYC from proteasomal degradation, recruiting wild-type p53 to HDM2 for degradation in cancer cells, blocking RAN deacetylation by Sirt7 to suppress STAT3-driven autophagy, and inhibiting NRF2 ubiquitination; both its N-terminal ribosomal L1 domain and C-terminal lysine-rich region are required for full function, and its crystal structure (solved in the yeast ortholog Utp30) reveals a two-domain fold that recognizes RNA duplexes via its concaved domain I surface."},"narrative":{"mechanistic_narrative":"RSL1D1 (CSIG) is a nucleolar ribosomal L1 domain-containing protein that functions as a multi-modal regulator of proliferation and senescence, acting both as a sequence-specific mRNA-binding protein and as a protein-level modulator of degradation pathways [PMID:18678645, PMID:27811966]. As an RNA-binding regulator it suppresses translation of PTEN mRNA by binding its 5' UTR, lowering PTEN and downstream p27(Kip1) to drive proliferation and delay replicative senescence [PMID:18678645], and conversely stabilizes target mRNAs by binding their 3' UTRs: it stabilizes PPARγ mRNA in a HuR-dependent manner [PMID:35940221] and FTH1 (ferritin heavy chain) mRNA, where its loss derepresses iron accumulation and triggers ferroptosis [PMID:36913375]. Both its N-terminal ribosomal L1 domain and C-terminal lysine-rich region are individually required for full activity and correct subcellular localization [PMID:26686419]. RSL1D1 also acts on the ubiquitin–proteasome system in a context-dependent manner, binding the MDM2 RING domain to inhibit p53 ubiquitination and enable p53-dependent G1 arrest under nucleolar stress [PMID:27811966], yet in colorectal cancer cells recruiting wild-type p53 to HDM2 to enhance its degradation [PMID:35597299], and stabilizing oncogenic c-MYC against proteasomal turnover [PMID:25749381]. Additional reported activities include competitive inhibition of Sirt7-mediated RAN deacetylation to restrain STAT3-driven autophagy [PMID:35013134] and a p33ING1-dependent pro-apoptotic role following UV stress [PMID:22419112]. Structural work on the yeast ortholog Utp30 defines a two-domain fold that recognizes rRNA duplexes (18S rRNA helix 41 and 5' ETS helix 4) through a concave domain I surface, placing the protein peripherally on small-subunit preribosomes [PMID:28951391].","teleology":[{"year":2008,"claim":"Established RSL1D1/CSIG's first non-ribosomal function: translational repression of a tumor suppressor to control the senescence/proliferation balance.","evidence":"RIP, PTEN 5' UTR luciferase reporter, knockdown/overexpression with senescence (SA-β-gal) and epistasis in PTEN-null cells","pmids":["18678645"],"confidence":"High","gaps":["Did not define the RNA-binding determinants on RSL1D1 itself","Did not address whether the same domain mediates other targets"]},{"year":2012,"claim":"Linked RSL1D1 to a stress-responsive apoptotic axis, showing its protein stability and pro-apoptotic output depend on a nucleolar partner.","evidence":"Reciprocal Co-IP, immunofluorescence, UV irradiation and BAX-dependent apoptosis readouts with p33ING1 domain mapping","pmids":["22419112"],"confidence":"Medium","gaps":["Mechanism of CSIG stabilization by p33ING1 unresolved","Single lab; no in vivo validation"]},{"year":2015,"claim":"Extended RSL1D1 beyond RNA regulation to direct protein stabilization, showing it protects oncogenic c-MYC from proteasomal degradation, and dissected its domain requirements.","evidence":"Co-IP, ubiquitination assay, colony formation and xenograft; separate truncation analysis with PTEN/senescence readouts","pmids":["25749381","26686419"],"confidence":"Medium","gaps":["Mechanism by which RSL1D1 blocks c-MYC ubiquitination not defined","Why isolated NT/CT fragments invert function and mislocalize unexplained"]},{"year":2016,"claim":"Resolved how nucleolar stress couples RSL1D1 to p53: relocalization to the nucleoplasm and direct inhibition of MDM2 E3 ligase activity stabilizes p53 and drives G1 arrest.","evidence":"Co-IP mapped to MDM2 RING domain, MDM2-mediated p53 ubiquitination assay, immunofluorescence translocation, cell-cycle readouts","pmids":["27811966"],"confidence":"High","gaps":["Signal triggering nucleolar-to-nucleoplasm translocation not identified","Stoichiometry/structure of the RSL1D1–MDM2–p53 complex unknown"]},{"year":2017,"claim":"Provided the structural basis for RSL1D1 as an RNA-binding protein, defining a two-domain fold that recognizes rRNA duplexes on small-subunit preribosomes via the yeast ortholog Utp30.","evidence":"X-ray crystallography (2.65 Å), cryo-EM fitting into 90S, RNA-binding analysis, yeast deletion strain composition analysis","pmids":["28951391"],"confidence":"High","gaps":["Whether the concave domain I surface mediates mammalian mRNA-target recognition not tested","Functional consequence of peripheral 90S binding in mammals unclear"]},{"year":2022,"claim":"Revealed context-dependent, opposing roles in p53 control and added mRNA-stabilizing and acetylation-modulating activities, broadening RSL1D1 into a multi-substrate cancer regulator.","evidence":"Co-IP/domain mapping and ubiquitination for p53–HDM2 recruitment; RIP/RNA pulldown/reporter for PPARγ 3' UTR; competitive Co-IP and acetylation/autophagy assays for RAN–Sirt7","pmids":["35597299","35940221","35013134"],"confidence":"Medium","gaps":["How RSL1D1 switches between stabilizing and degrading p53 across cell contexts unresolved","Each mechanism rests on single-lab Co-IP evidence without reciprocal cross-validation"]},{"year":2023,"claim":"Connected RSL1D1's 3' UTR-binding activity to iron homeostasis and ferroptosis, and showed RSL1D1 itself is subject to ubiquitin-mediated turnover in senescent cells.","evidence":"RIP, FTH1 3' UTR binding, knockdown with ferrous iron/MDA/GPX4 readouts, ubiquitination assay for RSL1D1 degradation","pmids":["36913375"],"confidence":"Medium","gaps":["E3 ligase degrading RSL1D1 not identified","How a single protein selects among many 3' UTR targets unknown"]},{"year":2025,"claim":"Added NRF2 to RSL1D1's roster of stabilized proteins, implicating it in oxidative-stress/proliferation control in lung adenocarcinoma.","evidence":"Co-IP and ubiquitination assay with proliferation readouts","pmids":["40543689"],"confidence":"Low","gaps":["Single Co-IP plus ubiquitination assay, single lab, limited methods detail","Direct binding interface and reciprocal validation absent"]},{"year":null,"claim":"It remains unresolved how one nucleolar L1-domain protein selects among such diverse RNA (5'/3' UTR) and protein targets, and what governs its switch between tumor-suppressive (p53 stabilization, ferroptosis promotion) and oncogenic (p53 degradation, c-MYC/NRF2 stabilization) outputs.","evidence":"","pmids":[],"confidence":"Low","gaps":["No unified model linking the conserved RNA-binding fold to target selection","Determinants of cell-context-dependent functional polarity unknown"]}],"mechanism_profile":{"molecular_activity":[{"term_id":"GO:0003723","term_label":"RNA binding","supporting_discovery_ids":[0,8,9,5]},{"term_id":"GO:0098772","term_label":"molecular function regulator activity","supporting_discovery_ids":[4,2,6,7]},{"term_id":"GO:0045182","term_label":"translation regulator activity","supporting_discovery_ids":[0]}],"localization":[{"term_id":"GO:0005730","term_label":"nucleolus","supporting_discovery_ids":[1,4]},{"term_id":"GO:0005654","term_label":"nucleoplasm","supporting_discovery_ids":[4]}],"pathway":[{"term_id":"R-HSA-8953854","term_label":"Metabolism of RNA","supporting_discovery_ids":[0,8,9,5]},{"term_id":"R-HSA-392499","term_label":"Metabolism of proteins","supporting_discovery_ids":[4,2,6,10]},{"term_id":"R-HSA-1640170","term_label":"Cell Cycle","supporting_discovery_ids":[4]},{"term_id":"R-HSA-5357801","term_label":"Programmed Cell Death","supporting_discovery_ids":[1,9]}],"complexes":[],"partners":["MDM2","TP53","MYC","ING1","RAN","SIRT7","NFE2L2","HUR"],"other_free_text":[]}},"prefetch_data":{"uniprot":{"accession":"O76021","full_name":"Ribosomal L1 domain-containing protein 1","aliases":["CATX-11","Cellular senescence-inhibited gene protein","Protein PBK1"],"length_aa":490,"mass_kda":55.0,"function":"Regulates cellular senescence through inhibition of PTEN translation. Acts as a pro-apoptotic regulator in response to DNA damage","subcellular_location":"Nucleus, nucleolus","url":"https://www.uniprot.org/uniprotkb/O76021/entry"},"depmap":{"release":"DepMap","has_data":true,"is_common_essential":true,"resolved_as":"","url":"https://depmap.org/portal/gene/RSL1D1","classification":"Common Essential","n_dependent_lines":1205,"n_total_lines":1208,"dependency_fraction":0.9975165562913907},"opencell":{"profiled":true,"resolved_as":"","ensg_id":"ENSG00000171490","cell_line_id":"CID001044","localizations":[{"compartment":"nucleolus_gc","grade":3}],"interactors":[{"gene":"KPNA3","stoichiometry":10.0},{"gene":"U2SURP","stoichiometry":10.0},{"gene":"SUB1","stoichiometry":10.0},{"gene":"CHERP","stoichiometry":10.0},{"gene":"SRSF6","stoichiometry":10.0},{"gene":"CCDC97","stoichiometry":10.0},{"gene":"RSRC1","stoichiometry":10.0},{"gene":"RBM17","stoichiometry":10.0},{"gene":"SUPT16H","stoichiometry":10.0},{"gene":"ARGLU1","stoichiometry":10.0}],"url":"https://opencell.sf.czbiohub.org/target/CID001044","total_profiled":1310},"omim":[{"mim_id":"620319","title":"OOCYTE/ZYGOTE/EMBRYO MATURATION ARREST 17; OZEMA17","url":"https://www.omim.org/entry/620319"},{"mim_id":"615874","title":"RIBOSOMAL L1 DOMAIN-CONTAINING PROTEIN 1; RSL1D1","url":"https://www.omim.org/entry/615874"},{"mim_id":"614107","title":"KARYOPHERIN ALPHA-7; KPNA7","url":"https://www.omim.org/entry/614107"},{"mim_id":"601728","title":"PHOSPHATASE AND TENSIN HOMOLOG; PTEN","url":"https://www.omim.org/entry/601728"},{"mim_id":"191840","title":"PLASMINOGEN ACTIVATOR, URINARY; PLAU","url":"https://www.omim.org/entry/191840"}],"hpa":{"profiled":true,"resolved_as":"","reliability":"Approved","locations":[{"location":"Nucleoli rim","reliability":"Approved"},{"location":"Mitotic chromosome","reliability":"Approved"},{"location":"Vesicles","reliability":"Additional"},{"location":"Primary cilium","reliability":"Additional"}],"tissue_specificity":"Low tissue specificity","tissue_distribution":"Detected in all","driving_tissues":[],"url":"https://www.proteinatlas.org/search/RSL1D1"},"hgnc":{"alias_symbol":["Cic1","PBK1","L12","DKFZP564M182","CSIG","UTP30"],"prev_symbol":[]},"alphafold":{"accession":"O76021","domains":[{"cath_id":"3.30.190.20","chopping":"34-53_60-271","consensus_level":"medium","plddt":89.0671,"start":34,"end":271}],"viewer_url":"https://alphafold.ebi.ac.uk/entry/O76021","model_url":"https://alphafold.ebi.ac.uk/files/AF-O76021-F1-model_v6.cif","pae_url":"https://alphafold.ebi.ac.uk/files/AF-O76021-F1-predicted_aligned_error_v6.png","plddt_mean":66.75},"mouse_models":{"mgi_url":"https://www.informatics.jax.org/marker/summary?nomen=RSL1D1","jax_strain_url":"https://www.jax.org/strain/search?query=RSL1D1"},"sequence":{"accession":"O76021","fasta_url":"https://rest.uniprot.org/uniprotkb/O76021.fasta","uniprot_url":"https://www.uniprot.org/uniprotkb/O76021/entry","alphafold_viewer_url":"https://alphafold.ebi.ac.uk/entry/O76021"}},"corpus_meta":[{"pmid":"8845168","id":"PMC_8845168","title":"Mutations in dominant human myotonia congenita drastically alter the voltage dependence of the CIC-1 chloride channel.","date":"1995","source":"Neuron","url":"https://pubmed.ncbi.nlm.nih.gov/8845168","citation_count":155,"is_preprint":false},{"pmid":"7951242","id":"PMC_7951242","title":"Genomic organization of the human muscle chloride channel CIC-1 and analysis of novel mutations leading to Becker-type myotonia.","date":"1994","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/7951242","citation_count":113,"is_preprint":false},{"pmid":"9158157","id":"PMC_9158157","title":"Identification of functionally important regions of the muscular chloride channel CIC-1 by analysis of recessive and dominant myotonic mutations.","date":"1997","source":"Human molecular genetics","url":"https://pubmed.ncbi.nlm.nih.gov/9158157","citation_count":65,"is_preprint":false},{"pmid":"11500370","id":"PMC_11500370","title":"Cic1, an adaptor protein specifically linking the 26S proteasome to its substrate, the SCF component Cdc4.","date":"2001","source":"The EMBO journal","url":"https://pubmed.ncbi.nlm.nih.gov/11500370","citation_count":42,"is_preprint":false},{"pmid":"18678645","id":"PMC_18678645","title":"CSIG inhibits PTEN translation in replicative senescence.","date":"2008","source":"Molecular and cellular biology","url":"https://pubmed.ncbi.nlm.nih.gov/18678645","citation_count":41,"is_preprint":false},{"pmid":"10217531","id":"PMC_10217531","title":"Modulation of the gating of CIC-1 by S-(-) 2-(4-chlorophenoxy) propionic acid.","date":"1999","source":"British journal of pharmacology","url":"https://pubmed.ncbi.nlm.nih.gov/10217531","citation_count":32,"is_preprint":false},{"pmid":"35013134","id":"PMC_35013134","title":"RSL1D1 promotes the progression of colorectal cancer through RAN-mediated autophagy suppression.","date":"2022","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/35013134","citation_count":27,"is_preprint":false},{"pmid":"22419112","id":"PMC_22419112","title":"Nucleolar protein CSIG is required for p33ING1 function in UV-induced apoptosis.","date":"2012","source":"Cell death & disease","url":"https://pubmed.ncbi.nlm.nih.gov/22419112","citation_count":25,"is_preprint":false},{"pmid":"25749381","id":"PMC_25749381","title":"CSIG promotes hepatocellular carcinoma proliferation by activating c-MYC expression.","date":"2015","source":"Oncotarget","url":"https://pubmed.ncbi.nlm.nih.gov/25749381","citation_count":21,"is_preprint":false},{"pmid":"27811966","id":"PMC_27811966","title":"Regulation of the MDM2-p53 pathway by the nucleolar protein CSIG in response to nucleolar stress.","date":"2016","source":"Scientific reports","url":"https://pubmed.ncbi.nlm.nih.gov/27811966","citation_count":19,"is_preprint":false},{"pmid":"15139012","id":"PMC_15139012","title":"Expression of novel isoforms of the CIC-1 chloride channel in astrocytic glial cells in vitro.","date":"2004","source":"Glia","url":"https://pubmed.ncbi.nlm.nih.gov/15139012","citation_count":14,"is_preprint":false},{"pmid":"36913375","id":"PMC_36913375","title":"RSL1D1 knockdown induces ferroptosis and mediates ferrous iron accumulation in senescent cells by inhibiting FTH1 mRNA stability.","date":"2023","source":"Carcinogenesis","url":"https://pubmed.ncbi.nlm.nih.gov/36913375","citation_count":13,"is_preprint":false},{"pmid":"26686419","id":"PMC_26686419","title":"Ribosomal L1 domain and lysine-rich region are essential for CSIG/ RSL1D1 to regulate proliferation and senescence.","date":"2015","source":"Biochemical and biophysical research communications","url":"https://pubmed.ncbi.nlm.nih.gov/26686419","citation_count":13,"is_preprint":false},{"pmid":"16629771","id":"PMC_16629771","title":"Novel mutations at carboxyl terminus of CIC-1 channel in myotonia congenita.","date":"2006","source":"Acta neurologica Scandinavica","url":"https://pubmed.ncbi.nlm.nih.gov/16629771","citation_count":8,"is_preprint":false},{"pmid":"35940221","id":"PMC_35940221","title":"RSL1D1 modulates cell senescence and proliferation via regulation of PPARγ mRNA stability.","date":"2022","source":"Life sciences","url":"https://pubmed.ncbi.nlm.nih.gov/35940221","citation_count":7,"is_preprint":false},{"pmid":"35597299","id":"PMC_35597299","title":"Mutations in DNA binding domain of p53 impede RSL1D1-p53 interaction to escape from degradation in human colorectal cancer cells.","date":"2022","source":"Experimental cell research","url":"https://pubmed.ncbi.nlm.nih.gov/35597299","citation_count":6,"is_preprint":false},{"pmid":"28951391","id":"PMC_28951391","title":"Structure and RNA recognition of ribosome assembly factor Utp30.","date":"2017","source":"RNA (New York, N.Y.)","url":"https://pubmed.ncbi.nlm.nih.gov/28951391","citation_count":2,"is_preprint":false},{"pmid":"40543689","id":"PMC_40543689","title":"RSL1D1 regulates lung adenocarcinoma progression by inhibiting NRF2 ubiquitination.","date":"2025","source":"Gene","url":"https://pubmed.ncbi.nlm.nih.gov/40543689","citation_count":1,"is_preprint":false},{"pmid":null,"id":"bio_10.1101_2025.05.25.25328297","title":"Maternal DNA Methylation Signatures of Gestational Diabetes across all Stages of Pregnancy","date":"2025-05-25","source":"bioRxiv","url":"https://doi.org/10.1101/2025.05.25.25328297","citation_count":0,"is_preprint":true}],"cost":{"stage1":{"model":"claude-sonnet-4-6","input_tokens":10728,"output_tokens":3017,"usd":0.038719,"stage1_stop_reason":"end_turn"},"stage2":{"model":"claude-opus-4-8","input_tokens":10419,"output_tokens":3333,"usd":0.06771,"stage2_stop_reason":"end_turn"},"total_usd":0.106429,"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\": 2008,\n      \"finding\": \"CSIG/RSL1D1 binds directly to the 5' UTR of PTEN mRNA and suppresses its translation, thereby reducing PTEN protein levels and downstream p27(Kip1) expression to promote cell proliferation and delay replicative senescence.\",\n      \"method\": \"RNA immunoprecipitation (RIP), luciferase reporter assay (PTEN 5' UTR), knockdown/overexpression with proliferation and senescence readouts (SA-β-gal), genetic epistasis using PTEN-silenced/deficient cells\",\n      \"journal\": \"Molecular and cellular biology\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 2 / Strong — multiple orthogonal methods (RIP, luciferase reporter, KD/OE, epistasis with PTEN-null cells) in a single rigorous study\",\n      \"pmids\": [\"18678645\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2012,\n      \"finding\": \"CSIG/RSL1D1 is a nucleolar protein that interacts with p33ING1; after UV irradiation, p33ING1 translocates to the nucleolus and binds CSIG, stabilizing CSIG protein. This p33ING1–CSIG complex promotes apoptosis via activation of BAX (Bcl-2-associated X protein).\",\n      \"method\": \"Co-immunoprecipitation, immunofluorescence localization, UV irradiation assay, apoptosis readouts, domain-mapping (p33ING1 nucleolar targeting sequence required for CSIG interaction)\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — reciprocal Co-IP and localization with functional apoptosis readout, single lab\",\n      \"pmids\": [\"22419112\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"CSIG/RSL1D1 directly interacts with c-MYC protein and protects it from ubiquitination and proteasomal degradation, thereby increasing c-MYC protein levels and promoting hepatocellular carcinoma cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation, ubiquitination assay, knockdown/overexpression with colony formation and xenograft assays\",\n      \"journal\": \"Oncotarget\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus ubiquitination assay plus in vivo xenograft, single lab\",\n      \"pmids\": [\"25749381\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2015,\n      \"finding\": \"Both the N-terminal ribosomal L1 domain and the C-terminal lysine-rich region of CSIG/RSL1D1 are individually necessary but not sufficient for its function; full-length CSIG reduces PTEN expression and promotes proliferation, while truncated fragments (NT or CT alone) fail to alter PTEN levels and instead inhibit proliferation and accelerate senescence. The two truncated fragments also display altered subcellular localization compared to wild-type CSIG.\",\n      \"method\": \"Domain-deletion/truncation expression, western blotting (PTEN levels), SA-β-gal senescence assay, cell proliferation assay, immunofluorescence for subcellular localization\",\n      \"journal\": \"Biochemical and biophysical research communications\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — structure-function dissection with multiple functional readouts, single lab\",\n      \"pmids\": [\"26686419\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2016,\n      \"finding\": \"CSIG/RSL1D1 translocates from the nucleolus to the nucleoplasm under nucleolar stress, directly binds the MDM2 RING finger domain, and inhibits MDM2 E3 ubiquitin ligase activity, thereby reducing p53 ubiquitination and degradation and enabling p53-dependent G1 arrest.\",\n      \"method\": \"Co-immunoprecipitation (CSIG–MDM2 interaction, mapping to RING finger domain), ubiquitination assay (MDM2-mediated p53 ubiquitination), knockdown with p53 protein level and cell-cycle readouts, immunofluorescence for nucleolar-to-nucleoplasm translocation\",\n      \"journal\": \"Scientific reports\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1–2 / Strong — direct binding mapped to MDM2 RING domain, E3 ligase activity assay, localization, and functional cell-cycle readout, multiple orthogonal methods in one study\",\n      \"pmids\": [\"27811966\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2017,\n      \"finding\": \"Crystal structure of yeast Utp30 (ortholog of RSL1D1/Cic1 in small subunit preribosomes) at 2.65 Å resolution reveals a two-domain fold that fits into 90S cryo-EM density; Utp30 binds rearranged helix 41 of 18S rRNA and helix 4 of 5' ETS via its concaved domain I surface. Deletion of Utp30 does not affect 90S composition, consistent with its peripheral location.\",\n      \"method\": \"X-ray crystallography (2.65 Å), cryo-EM fitting, RNA-binding analysis, yeast deletion strain analysis of 90S composition\",\n      \"journal\": \"RNA (New York, N.Y.)\",\n      \"confidence\": \"High\",\n      \"confidence_rationale\": \"Tier 1 / Strong — crystal structure with cryo-EM validation and functional deletion analysis in yeast ortholog\",\n      \"pmids\": [\"28951391\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RSL1D1 directly interacts with the DNA-binding domain (aa 93-292, more precisely aa 93-224) of wild-type p53 and recruits p53 to HDM2, forming an RSL1D1/HDM2/p53 complex that enhances p53 ubiquitination and decreases p53 protein levels in CRC cells. Mutations in p53 (R175H) abolish this interaction, while R273H weakens it, preventing HDM2 recruitment and allowing mutant p53 accumulation.\",\n      \"method\": \"Co-immunoprecipitation, domain-mapping (p53 deletion mutants), ubiquitination assay, western blotting for p53 protein levels\",\n      \"journal\": \"Experimental cell research\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP with domain mapping and ubiquitination assay, single lab\",\n      \"pmids\": [\"35597299\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RSL1D1 interacts with RAN GTPase and competitively inhibits RAN deacetylation by Sirt7, thereby maintaining RAN in an acetylated state, which inhibits nuclear STAT3 accumulation and STAT3-regulated autophagy, promoting CRC cell proliferation and metastasis.\",\n      \"method\": \"Co-immunoprecipitation (RSL1D1–RAN, RSL1D1–Sirt7 competitive binding), acetylation assay, nuclear fractionation for STAT3, autophagy flux assay, knockdown/overexpression with proliferation and invasion readouts\",\n      \"journal\": \"Cell death & disease\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — Co-IP plus competitive binding assay plus acetylation and functional readouts, single lab\",\n      \"pmids\": [\"35013134\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2022,\n      \"finding\": \"RSL1D1 directly binds the 3' UTR of PPARγ mRNA and stabilizes it in a HuR-dependent manner, increasing PPARγ mRNA and protein levels and thereby regulating downstream targets (PTEN/p27, NF-κB, GLUT4, ACL) to modulate cellular senescence and proliferation.\",\n      \"method\": \"RNA immunoprecipitation (RIP), biotin-labeled RNA pulldown, dual luciferase reporter assay, western blotting, real-time PCR, SA-β-gal staining, cell proliferation and colony formation assays\",\n      \"journal\": \"Life sciences\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP and RNA pulldown plus reporter assay, multiple functional readouts, single lab\",\n      \"pmids\": [\"35940221\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2023,\n      \"finding\": \"RSL1D1 directly binds the 3' UTR of FTH1 (ferritin heavy chain 1) mRNA and promotes its stability; RSL1D1 knockdown reduces FTH1 expression, increases transferrin receptor 1, causes intracellular ferrous iron accumulation, and induces ferroptosis (increased MDA, decreased GPX4). RSL1D1 protein is itself downregulated by ubiquitin-mediated proteolysis in senescent CRC cells.\",\n      \"method\": \"RNA immunoprecipitation (RIP), 3'-UTR binding assay, knockdown with iron metabolism readouts (ferrous iron assay, MDA, GPX4 western blot), cell proliferation and apoptosis assays, ubiquitination assay for RSL1D1 degradation\",\n      \"journal\": \"Carcinogenesis\",\n      \"confidence\": \"Medium\",\n      \"confidence_rationale\": \"Tier 2 / Moderate — RIP plus multiple functional iron metabolism readouts plus ubiquitination, single lab\",\n      \"pmids\": [\"36913375\"],\n      \"is_preprint\": false\n    },\n    {\n      \"year\": 2025,\n      \"finding\": \"RSL1D1 interacts with NRF2 and inhibits its ubiquitination, thereby preventing NRF2 degradation and promoting lung adenocarcinoma cell proliferation.\",\n      \"method\": \"Co-immunoprecipitation (RSL1D1–NRF2 interaction), ubiquitination assay, knockdown/overexpression with proliferation readouts\",\n      \"journal\": \"Gene\",\n      \"confidence\": \"Low\",\n      \"confidence_rationale\": \"Tier 3 / Weak — single Co-IP plus ubiquitination assay, single lab, single study with limited methods detail in abstract\",\n      \"pmids\": [\"40543689\"],\n      \"is_preprint\": false\n    }\n  ],\n  \"current_model\": \"RSL1D1 (CSIG) is a nucleolar ribosomal L1 domain-containing RNA-binding protein that operates via multiple non-ribosomal mechanisms: it suppresses translation of PTEN mRNA by binding its 5' UTR, stabilizes PPARγ and FTH1 mRNAs by binding their 3' UTRs, and acts as a protein-level regulator by binding the MDM2 RING domain to inhibit p53 ubiquitination, stabilizing c-MYC from proteasomal degradation, recruiting wild-type p53 to HDM2 for degradation in cancer cells, blocking RAN deacetylation by Sirt7 to suppress STAT3-driven autophagy, and inhibiting NRF2 ubiquitination; both its N-terminal ribosomal L1 domain and C-terminal lysine-rich region are required for full function, and its crystal structure (solved in the yeast ortholog Utp30) reveals a two-domain fold that recognizes RNA duplexes via its concaved domain I surface.\"\n}\n```","stage2_raw":"{\n  \"mechanistic_narrative\": \"RSL1D1 (CSIG) is a nucleolar ribosomal L1 domain-containing protein that functions as a multi-modal regulator of proliferation and senescence, acting both as a sequence-specific mRNA-binding protein and as a protein-level modulator of degradation pathways [#0, #4]. As an RNA-binding regulator it suppresses translation of PTEN mRNA by binding its 5' UTR, lowering PTEN and downstream p27(Kip1) to drive proliferation and delay replicative senescence [#0], and conversely stabilizes target mRNAs by binding their 3' UTRs: it stabilizes PPARγ mRNA in a HuR-dependent manner [#8] and FTH1 (ferritin heavy chain) mRNA, where its loss derepresses iron accumulation and triggers ferroptosis [#9]. Both its N-terminal ribosomal L1 domain and C-terminal lysine-rich region are individually required for full activity and correct subcellular localization [#3]. RSL1D1 also acts on the ubiquitin–proteasome system in a context-dependent manner, binding the MDM2 RING domain to inhibit p53 ubiquitination and enable p53-dependent G1 arrest under nucleolar stress [#4], yet in colorectal cancer cells recruiting wild-type p53 to HDM2 to enhance its degradation [#6], and stabilizing oncogenic c-MYC against proteasomal turnover [#2]. Additional reported activities include competitive inhibition of Sirt7-mediated RAN deacetylation to restrain STAT3-driven autophagy [#7] and a p33ING1-dependent pro-apoptotic role following UV stress [#1]. Structural work on the yeast ortholog Utp30 defines a two-domain fold that recognizes rRNA duplexes (18S rRNA helix 41 and 5' ETS helix 4) through a concave domain I surface, placing the protein peripherally on small-subunit preribosomes [#5].\",\n  \"teleology\": [\n    {\n      \"year\": 2008,\n      \"claim\": \"Established RSL1D1/CSIG's first non-ribosomal function: translational repression of a tumor suppressor to control the senescence/proliferation balance.\",\n      \"evidence\": \"RIP, PTEN 5' UTR luciferase reporter, knockdown/overexpression with senescence (SA-β-gal) and epistasis in PTEN-null cells\",\n      \"pmids\": [\"18678645\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Did not define the RNA-binding determinants on RSL1D1 itself\", \"Did not address whether the same domain mediates other targets\"]\n    },\n    {\n      \"year\": 2012,\n      \"claim\": \"Linked RSL1D1 to a stress-responsive apoptotic axis, showing its protein stability and pro-apoptotic output depend on a nucleolar partner.\",\n      \"evidence\": \"Reciprocal Co-IP, immunofluorescence, UV irradiation and BAX-dependent apoptosis readouts with p33ING1 domain mapping\",\n      \"pmids\": [\"22419112\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism of CSIG stabilization by p33ING1 unresolved\", \"Single lab; no in vivo validation\"]\n    },\n    {\n      \"year\": 2015,\n      \"claim\": \"Extended RSL1D1 beyond RNA regulation to direct protein stabilization, showing it protects oncogenic c-MYC from proteasomal degradation, and dissected its domain requirements.\",\n      \"evidence\": \"Co-IP, ubiquitination assay, colony formation and xenograft; separate truncation analysis with PTEN/senescence readouts\",\n      \"pmids\": [\"25749381\", \"26686419\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"Mechanism by which RSL1D1 blocks c-MYC ubiquitination not defined\", \"Why isolated NT/CT fragments invert function and mislocalize unexplained\"]\n    },\n    {\n      \"year\": 2016,\n      \"claim\": \"Resolved how nucleolar stress couples RSL1D1 to p53: relocalization to the nucleoplasm and direct inhibition of MDM2 E3 ligase activity stabilizes p53 and drives G1 arrest.\",\n      \"evidence\": \"Co-IP mapped to MDM2 RING domain, MDM2-mediated p53 ubiquitination assay, immunofluorescence translocation, cell-cycle readouts\",\n      \"pmids\": [\"27811966\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Signal triggering nucleolar-to-nucleoplasm translocation not identified\", \"Stoichiometry/structure of the RSL1D1–MDM2–p53 complex unknown\"]\n    },\n    {\n      \"year\": 2017,\n      \"claim\": \"Provided the structural basis for RSL1D1 as an RNA-binding protein, defining a two-domain fold that recognizes rRNA duplexes on small-subunit preribosomes via the yeast ortholog Utp30.\",\n      \"evidence\": \"X-ray crystallography (2.65 Å), cryo-EM fitting into 90S, RNA-binding analysis, yeast deletion strain composition analysis\",\n      \"pmids\": [\"28951391\"],\n      \"confidence\": \"High\",\n      \"gaps\": [\"Whether the concave domain I surface mediates mammalian mRNA-target recognition not tested\", \"Functional consequence of peripheral 90S binding in mammals unclear\"]\n    },\n    {\n      \"year\": 2022,\n      \"claim\": \"Revealed context-dependent, opposing roles in p53 control and added mRNA-stabilizing and acetylation-modulating activities, broadening RSL1D1 into a multi-substrate cancer regulator.\",\n      \"evidence\": \"Co-IP/domain mapping and ubiquitination for p53–HDM2 recruitment; RIP/RNA pulldown/reporter for PPARγ 3' UTR; competitive Co-IP and acetylation/autophagy assays for RAN–Sirt7\",\n      \"pmids\": [\"35597299\", \"35940221\", \"35013134\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"How RSL1D1 switches between stabilizing and degrading p53 across cell contexts unresolved\", \"Each mechanism rests on single-lab Co-IP evidence without reciprocal cross-validation\"]\n    },\n    {\n      \"year\": 2023,\n      \"claim\": \"Connected RSL1D1's 3' UTR-binding activity to iron homeostasis and ferroptosis, and showed RSL1D1 itself is subject to ubiquitin-mediated turnover in senescent cells.\",\n      \"evidence\": \"RIP, FTH1 3' UTR binding, knockdown with ferrous iron/MDA/GPX4 readouts, ubiquitination assay for RSL1D1 degradation\",\n      \"pmids\": [\"36913375\"],\n      \"confidence\": \"Medium\",\n      \"gaps\": [\"E3 ligase degrading RSL1D1 not identified\", \"How a single protein selects among many 3' UTR targets unknown\"]\n    },\n    {\n      \"year\": 2025,\n      \"claim\": \"Added NRF2 to RSL1D1's roster of stabilized proteins, implicating it in oxidative-stress/proliferation control in lung adenocarcinoma.\",\n      \"evidence\": \"Co-IP and ubiquitination assay with proliferation readouts\",\n      \"pmids\": [\"40543689\"],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"Single Co-IP plus ubiquitination assay, single lab, limited methods detail\", \"Direct binding interface and reciprocal validation absent\"]\n    },\n    {\n      \"year\": null,\n      \"claim\": \"It remains unresolved how one nucleolar L1-domain protein selects among such diverse RNA (5'/3' UTR) and protein targets, and what governs its switch between tumor-suppressive (p53 stabilization, ferroptosis promotion) and oncogenic (p53 degradation, c-MYC/NRF2 stabilization) outputs.\",\n      \"evidence\": \"\",\n      \"pmids\": [],\n      \"confidence\": \"Low\",\n      \"gaps\": [\"No unified model linking the conserved RNA-binding fold to target selection\", \"Determinants of cell-context-dependent functional polarity unknown\"]\n    }\n  ],\n  \"mechanism_profile\": {\n    \"molecular_activity\": [\n      {\"term_id\": \"GO:0003723\", \"supporting_discovery_ids\": [0, 8, 9, 5]},\n      {\"term_id\": \"GO:0098772\", \"supporting_discovery_ids\": [4, 2, 6, 7]},\n      {\"term_id\": \"GO:0045182\", \"supporting_discovery_ids\": [0]}\n    ],\n    \"localization\": [\n      {\"term_id\": \"GO:0005730\", \"supporting_discovery_ids\": [1, 4]},\n      {\"term_id\": \"GO:0005654\", \"supporting_discovery_ids\": [4]}\n    ],\n    \"pathway\": [\n      {\"term_id\": \"R-HSA-8953854\", \"supporting_discovery_ids\": [0, 8, 9, 5]},\n      {\"term_id\": \"R-HSA-392499\", \"supporting_discovery_ids\": [4, 2, 6, 10]},\n      {\"term_id\": \"R-HSA-1640170\", \"supporting_discovery_ids\": [4]},\n      {\"term_id\": \"R-HSA-5357801\", \"supporting_discovery_ids\": [1, 9]}\n    ],\n    \"complexes\": [],\n    \"partners\": [\"MDM2\", \"TP53\", \"MYC\", \"ING1\", \"RAN\", \"SIRT7\", \"NFE2L2\", \"HUR\"],\n    \"other_free_text\": []\n  }\n}","audit_flag":null,"evaluation":{"pairwise":"tie","faith_supported":6,"faith_total":6,"faith_pct":100.0}}