Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5' UTR of tumor-associated mRNAs.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:29129743", "kind": "science-record", "revision": 3, "content_hash": "sha256:b1afedda1859ed456ee26e8071a166c01e686be7e294e26dccbf1945e3e5f4c1", "created_at": "2026-11-01T17:32:03Z", "updated_at": "2026-11-01T21:21:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5' UTR of tumor-associated mRNAs.", "doi": "10.1016/j.biochi.2017.11.003", "pmid": "29129743", "authors": ["Tatsuo Serikawa", "Christos Spanos", "Annekathrin von Hacht", "Nediljko Budisa", "Juri Rappsilber", "Jens Kurreck"], "journal": "Biochimie", "year": 2018, "abstract": "G-quadruplex structures in the 5' UTR of mRNAs are widely considered to suppress translation without affecting transcription. The current study describes the comprehensive analysis of proteins binding to four different G-quadruplex motifs located in mRNAs of the cancer-related genes Bcl-2, NRAS, MMP16, and ARPC2. Following metabolic labeling (Stable Isotope Labeling with Amino acids in Cell culture, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched by pull-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions for the G-quadruplex motifs under investigation. While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively. The use of a control composed of samples from all G-quadruplex-forming sequences and their mutated controls ensured that the identified proteins are specific for RNA G-quadruplex structures and are not general RNA-binding proteins. Independent validation experiments based on pull-down assays and Western blotting confirmed the MS data. Among the interaction partners were many proteins known to bind to RNA, including multiple heterogenous nuclear ribonucleoproteins (hnRNPs). Several of the candidate proteins are likely to reflect stalling of the ribosome by RNA G-quadruplex structures. Interestingly, additional proteins were identified that have not previously been described to interact with RNA. Gene ontology analysis of the candidate proteins revealed that many interaction partners are known to be tumor related. The majority of the identified RNA G-quadruplex interacting proteins are thought to be involved in post-transcriptional processes, particularly in splicing. These findings indicate that protein-G-quadruplex interactions are not only important for the fine-tuning of translation but are also relevant to the regulation of mRNA maturation and may play an important role in tumor biology. Proteomic data are available via ProteomeXchange with identifier PXD005761.", "claims": [{"id": "claim-method", "statement": "The used static test was significance B calculating intensity-dependent significant outliers relative to a certain population from p-values [47].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29129743", "locator": "sections[10] \"Evaluation of RNA G-quadruplex-binding proteins\" paragraph 2", "quote": "The used static test was significance B calculating intensity-dependent significant outliers relative to a certain population from p-values [47]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Proteomic data are available via ProteomeXchange with identifier PXD005761.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:29129743", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Proteomic data are available via ProteomeXchange with identifier PXD005761."}], "state": "complete"}, {"id": "claim-target-result", "statement": "While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:29129743", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "While the G-quadruplexes in the mRNAs of NRAS and MMP16 specifically interacted with a small number of proteins, the Bcl-2 and ARPC2 G-quadruplexes exhibited a broad range of proteinaceous interaction partners with 99 and 82 candidate proteins identified in at least two replicates, respectively.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:29129743"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD005761"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:PXD005761"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:29129743", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.biochi.2017.11.003", "sha256": "sha256:e3b32513c61effe1a6dc32285763558a4995a9129ffce376440b2f5008906af4", "bytes": 60388, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.biochi.2017.11.003", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7618928", "source": "ncbi_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:PXD005761", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=PXD005761", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "PXD005761", "version": null, "note": "Proteomic data are available via ProteomeXchange with identifier PXD005761.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Proteomic data are available via ProteomeXchange with identifier PXD005761.", "access_statement_kind": "data_availability_statement", "sample_accessions": [], "sample_count": null, "group_sizes": null, "group_sizes_basis": null, "platform": null, "taxon": null, "title": "Comprehensive identification of proteins binding to RNA G-quadruplex motifs in the 5’ UTR of tumor-associated mRNAs", "resolution_checked_at": "2026-11-01T17:30:50Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:PXD005761 not downloaded", "asset:data:geo:PXD005761 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "significance B test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The used static test was significance B calculating intensity-dependent significant outliers relative to a certain population from p-values [47]."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "method", "blocked_on": "method:not_determinable", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (significance B test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["PXD005761"], "resolved_accessions": ["PXD005761"], "statements": ["Proteomic data are available via ProteomeXchange with identifier PXD005761."], "basis": "The paper names PXD005761 in ProteomeXchange Consortium via the PRIDE [49] partner repository and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:29129743", "data:geo:PXD005761"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:PXD005761"]}, "gaps": ["method:not_determinable"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T16:57:46Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 15999, "completion_tokens": 1353, "cached_tokens": 128}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:29129743", "type": "paper", "label": "pmid:29129743"}, {"id": "source:pmid:29129743", "type": "manuscript", "label": "PMID 29129743 full text"}, {"id": "data:geo:PXD005761", "type": "dataset", "label": "GEO PXD005761"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:29129743", "type": "paper", "label": "pmid:29129743"}, {"id": "source:pmid:29129743", "type": "manuscript", "label": "PMID 29129743 full text"}, {"id": "data:geo:PXD005761", "type": "dataset", "label": "GEO PXD005761"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-29129743", "type": "extraction", "used": ["source:pmid:29129743"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-PXD005761", "type": "accession_resolution", "used": ["data:geo:PXD005761"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:29129743", "parent_hash": "sha256:67cf3fbee72f78865f9f141c72e047cbbc58e6c4e9883b6fd8a335be8ea1879f", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:PXD005761 licence not read", "asset:data:geo:PXD005761 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "cell_culture", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.77, "evidence": ["e, SILAC) of proteins in the human cell line HEK293, G-quadruplex binding proteins were enriched"], "order_basis": "paper_text_order:517", "id": "assay:1"}, {"role": "data_generation", "definition_id": "mass_spectrometry", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ll-down assays and identified by LC-orbitrap mass spectrometry. We found different patterns of interactions", "lemented with 4.5 mg/ml glucose. LC-orbitrap mass spectrometry and data processing Coomassie stained gel ba", "ype and mutants) were analyzed together. The mass spectrometry proteomics data have been deposited to the P", "y). The peptide sample was then prepared for LC-MS/MS analysis by diluting it to 5 μl by 0.1% TFA."], "order_basis": "paper_text_order:619", "id": "assay:2"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["on experiments based on pull-down assays and Western blotting confirmed the MS data. Among the interaction"], "order_basis": "paper_text_order:1325", "id": "assay:3"}]}