{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T03:37:09Z","timestamp":1793158629486,"version":"4.5.0"},"reference-count":83,"publisher":"Oxford University Press (OUP)","issue":"14","license":[{"start":{"date-parts":[[2022,7,15]],"date-time":"2022-07-15T00:00:00Z","timestamp":1657843200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100003329","name":"Ministry of Economy and Competitiveness","doi-asserted-by":"publisher","award":["BFU2015-68741-P"],"award-info":[{"award-number":["BFU2015-68741-P"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100003329","name":"MINECO","doi-asserted-by":"publisher","award":["PGC2018-099697-B-I00"],"award-info":[{"award-number":["PGC2018-099697-B-I00"]}],"id":[{"id":"10.13039\/501100003329","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004837","name":"MICINN","doi-asserted-by":"publisher","award":["100010434"],"award-info":[{"award-number":["100010434"]}],"id":[{"id":"10.13039\/501100004837","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Marat\u00f3-TV3 Foundation","award":["20131430"],"award-info":[{"award-number":["20131430"]}]},{"name":"Catalan Agency for Research and Universities","award":["2017SGR534"],"award-info":[{"award-number":["2017SGR534"]}]},{"name":"Catalan Agency for Research and Universities","award":["PT17\/0019"],"award-info":[{"award-number":["PT17\/0019"]}]},{"DOI":"10.13039\/501100004587","name":"Instituto de Salud Carlos III","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008530","name":"ERDF","doi-asserted-by":"publisher","award":["2017SGR595"],"award-info":[{"award-number":["2017SGR595"]}],"id":[{"id":"10.13039\/501100008530","id-type":"DOI","asserted-by":"publisher"}]},{"name":"MRC Career Development","award":["MR\/L019434\/1"],"award-info":[{"award-number":["MR\/L019434\/1"]}]},{"name":"Centro de Excelencia Severo Ochoa","award":["CEX2020-001049-S"],"award-info":[{"award-number":["CEX2020-001049-S"]}]},{"name":"Centro de Excelencia Severo Ochoa","award":["MCIN\/AEI \/10.13039\/501100011033"],"award-info":[{"award-number":["MCIN\/AEI \/10.13039\/501100011033"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,8,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>RNA-binding proteins (RBPs) have been relatively overlooked in cancer research despite their contribution to virtually every cancer hallmark. Here, we use RNA interactome capture (RIC) to characterize the melanoma RBPome and uncover novel RBPs involved in melanoma progression. Comparison of RIC profiles of a non-tumoral versus a metastatic cell line revealed prevalent changes in RNA-binding capacities that were not associated with changes in RBP levels. Extensive functional validation of a selected group of 24 RBPs using five different in vitro assays unveiled unanticipated roles of RBPs in melanoma malignancy. As proof-of-principle we focused on PDIA6, an ER-lumen chaperone that displayed a novel RNA-binding activity. We show that PDIA6 is involved in metastatic progression, map its RNA-binding domain, and find that RNA binding is required for PDIA6 tumorigenic properties. These results exemplify how RIC technologies can be harnessed to uncover novel vulnerabilities of cancer cells.<\/jats:p>","DOI":"10.1093\/nar\/gkac605","type":"journal-article","created":{"date-parts":[[2022,7,18]],"date-time":"2022-07-18T13:35:37Z","timestamp":1658151337000},"page":"8207-8225","source":"Crossref","is-referenced-by-count":22,"title":["Melanoma RBPome identification reveals PDIA6 as an unconventional RNA-binding protein involved in metastasis"],"prefix":"10.1093","volume":"50","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-9410-4075","authenticated-orcid":false,"given":"Neus","family":"Mestre-Farr\u00e0s","sequence":"first","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3473-7214","authenticated-orcid":false,"given":"Santiago","family":"Guerrero","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4531-7998","authenticated-orcid":false,"given":"Nadine","family":"Bley","sequence":"additional","affiliation":[{"name":"Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg , 06120 Halle , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ezequiel","family":"Rivero","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Olga","family":"Coll","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5100-7809","authenticated-orcid":false,"given":"Eva","family":"Borr\u00e0s","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"},{"name":"Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF) ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6506-7714","authenticated-orcid":false,"given":"Eduard","family":"Sabid\u00f3","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"},{"name":"Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF) ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alberto","family":"Indacochea","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos","family":"Casillas-Serra","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aino\u00a0I","family":"J\u00e4rvelin","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Oxford , South Parks Road , Oxford OX1 3QU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0702-0250","authenticated-orcid":false,"given":"Baldomero","family":"Oliva","sequence":"additional","affiliation":[{"name":"Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF) ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alfredo","family":"Castello","sequence":"additional","affiliation":[{"name":"Department of Biochemistry, University of Oxford , South Parks Road , Oxford OX1 3QU, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9335-4227","authenticated-orcid":false,"given":"Stefan","family":"H\u00fcttelmaier","sequence":"additional","affiliation":[{"name":"Institute of Molecular Medicine, Section for Molecular Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg , 06120 Halle , Germany"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7563-0013","authenticated-orcid":false,"given":"F\u00e1tima","family":"Gebauer","sequence":"additional","affiliation":[{"name":"Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology ,\u00a008003\u00a0 Barcelona , Spain"},{"name":"Department of Health and Experimental Sciences, Universitat Pompeu Fabra (UPF) ,\u00a008003\u00a0 Barcelona , Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2022,7,15]]},"reference":[{"key":"2022081200011043000_B1","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1038\/s41568-020-00302-4","article-title":"Non-genetic mechanisms of therapeutic resistance in cancer","volume":"20","author":"Marine","year":"2020","journal-title":"Nat. Rev. Cancer"},{"key":"2022081200011043000_B2","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1016\/j.trecan.2018.01.001","article-title":"The genetic\/non-genetic duality of drug \u2018resistance\u2019 in cancer","volume":"4","author":"Salgia","year":"2018","journal-title":"Trends Cancer"},{"key":"2022081200011043000_B3","doi-asserted-by":"crossref","first-page":"eaal2380","DOI":"10.1126\/science.aal2380","article-title":"Epigenetic plasticity and the hallmarks of cancer","volume":"357","author":"Flavahan","year":"2017","journal-title":"Science"},{"key":"2022081200011043000_B4","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1016\/j.trecan.2017.05.003","article-title":"RNA-Binding proteins in cancer: old players and new actors","volume":"3","author":"Pereira","year":"2017","journal-title":"Trends Cancer"},{"key":"2022081200011043000_B5","doi-asserted-by":"crossref","first-page":"248","DOI":"10.2183\/pjab.94.017","article-title":"Post-transcriptional regulation of immune responses by RNA binding proteins","volume":"94","author":"Mino","year":"2018","journal-title":"Proc. Jpn. Acad. Ser. B Phys. Biol. Sci."},{"key":"2022081200011043000_B6","doi-asserted-by":"crossref","first-page":"65","DOI":"10.3389\/fmolb.2019.00065","article-title":"Post-transcriptional regulation of colorectal cancer: a focus on RNA-binding proteins","volume":"6","author":"Garc\u00eda-C\u00e1rdenas","year":"2019","journal-title":"Front. Mol. Biosci."},{"key":"2022081200011043000_B7","doi-asserted-by":"crossref","first-page":"e1520","DOI":"10.1002\/wrna.1520","article-title":"Diverse roles of RNA-binding proteins in cancer traits and their implications in gastrointestinal cancers","volume":"10","author":"Masuda","year":"2019","journal-title":"Wiley Interdiscip. Rev. RNA"},{"key":"2022081200011043000_B8","doi-asserted-by":"crossref","first-page":"881","DOI":"10.1016\/j.bbagrm.2014.10.001","article-title":"RNA-binding proteins, multifaceted translational regulators in cancer","volume":"1849","author":"Wurth","year":"2015","journal-title":"Biochim. Biophys. Acta"},{"key":"2022081200011043000_B9","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1038\/nrm.2017.130","article-title":"A brave new world of RNA-binding proteins","volume":"19","author":"Hentze","year":"2018","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"2022081200011043000_B10","doi-asserted-by":"crossref","first-page":"185","DOI":"10.1038\/s41576-020-00302-y","article-title":"RNA-binding proteins in human genetic disease","volume":"22","author":"Gebauer","year":"2021","journal-title":"Nat. Rev. Genet."},{"key":"2022081200011043000_B11","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1016\/j.tem.2015.09.012","article-title":"Metabolic enzymes enjoying new partnerships as RNA-Binding proteins","volume":"26","author":"Castello","year":"2015","journal-title":"Trends Endocrinol. Metab."},{"key":"2022081200011043000_B12","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1016\/j.gde.2017.11.006","article-title":"Expanding horizons: new roles for non-canonical RNA-binding proteins in cancer","volume":"48","author":"Moore","year":"2018","journal-title":"Curr. Opin. Genet. Dev."},{"key":"2022081200011043000_B13","doi-asserted-by":"crossref","first-page":"2917","DOI":"10.1002\/1873-3468.13161","article-title":"Unconventional RNA-binding proteins: an uncharted zone in RNA biology","volume":"592","author":"Albihlal","year":"2018","journal-title":"FEBS Lett."},{"key":"2022081200011043000_B14","doi-asserted-by":"crossref","first-page":"971","DOI":"10.1016\/S0140-6736(18)31559-9","article-title":"Melanoma","volume":"392","author":"Schadendorf","year":"2018","journal-title":"Lancet"},{"key":"2022081200011043000_B15","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1111\/pcmr.12475","article-title":"The state of melanoma: challenges and opportunities","volume":"29","author":"Merlino","year":"2016","journal-title":"Pigment Cell Melanoma Res."},{"key":"2022081200011043000_B16","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nrc.2016.37","article-title":"From melanocytes to melanomas","volume":"16","author":"Shain","year":"2016","journal-title":"Nat. Rev. Cancer"},{"key":"2022081200011043000_B17","doi-asserted-by":"crossref","first-page":"5771","DOI":"10.1038\/onc.2017.189","article-title":"Melanocytic nevi and melanoma: unraveling a complex relationship","volume":"36","author":"Damsky","year":"2017","journal-title":"Oncogene"},{"key":"2022081200011043000_B18","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1101\/gad.290940.116","article-title":"Translation reprogramming is an evolutionarily conserved driver of phenotypic plasticity and therapeutic resistance in melanoma","volume":"31","author":"Falletta","year":"2017","journal-title":"Genes Dev."},{"key":"2022081200011043000_B19","doi-asserted-by":"crossref","first-page":"1865","DOI":"10.1038\/s41591-020-1073-3","article-title":"Midkine rewires the melanoma microenvironment toward a tolerogenic and immune-resistant state","volume":"26","author":"Cerezo-Wallis","year":"2020","journal-title":"Nat. Med."},{"key":"2022081200011043000_B20","doi-asserted-by":"crossref","first-page":"605","DOI":"10.1038\/s41586-018-0243-7","article-title":"Codon-specific translation reprogramming promotes resistance to targeted therapy","volume":"558","author":"Rapino","year":"2018","journal-title":"Nature"},{"key":"2022081200011043000_B21","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.ccell.2018.11.008","article-title":"p62\/SQSTM1 fuels melanoma progression by opposing mRNA decay of a selective set of Pro-metastatic factors","volume":"35","author":"Karras","year":"2019","journal-title":"Cancer Cell"},{"key":"2022081200011043000_B22","doi-asserted-by":"crossref","first-page":"3573","DOI":"10.1016\/j.celrep.2019.05.069","article-title":"The X-linked DDX3X RNA helicase dictates translation reprogramming and metastasis in melanoma","volume":"27","author":"Phung","year":"2019","journal-title":"Cell Rep."},{"key":"2022081200011043000_B23","doi-asserted-by":"crossref","first-page":"2249","DOI":"10.1038\/s41467-017-02353-y","article-title":"Systems analysis identifies melanoma-enriched pro-oncogenic networks controlled by the RNA binding protein CELF1","volume":"8","author":"Cifdaloz","year":"2017","journal-title":"Nat. Commun."},{"key":"2022081200011043000_B24","doi-asserted-by":"crossref","first-page":"694","DOI":"10.1016\/j.ccell.2016.10.004","article-title":"UNR\/CSDE1 drives a Post-transcriptional program to promote melanoma invasion and metastasis","volume":"30","author":"Wurth","year":"2016","journal-title":"Cancer Cell"},{"key":"2022081200011043000_B25","doi-asserted-by":"crossref","first-page":"13418","DOI":"10.1038\/ncomms13418","article-title":"Lineage-specific roles of the cytoplasmic polyadenylation factor CPEB4 in the regulation of melanoma drivers","volume":"7","author":"P\u00e9rez-Guijarro","year":"2016","journal-title":"Nat. Commun."},{"key":"2022081200011043000_B26","doi-asserted-by":"crossref","first-page":"8049","DOI":"10.1093\/nar\/gku480","article-title":"siPools: highly complex but accurately defined siRNA pools eliminate off-target effects","volume":"42","author":"Hannus","year":"2014","journal-title":"Nucleic Acids Res."},{"key":"2022081200011043000_B27","doi-asserted-by":"crossref","first-page":"671","DOI":"10.1038\/nmeth.2089","article-title":"NIH image to imagej: 25 years of image analysis","volume":"9","author":"Schneider","year":"2012","journal-title":"Nat. Methods"},{"key":"2022081200011043000_B28","doi-asserted-by":"crossref","first-page":"529","DOI":"10.1261\/rna.065417.117","article-title":"Dicer-2 promotes mRNA activation through cytoplasmic polyadenylation","volume":"24","author":"Coll","year":"2018","journal-title":"RNA"},{"key":"2022081200011043000_B29","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/nprot.2013.020","article-title":"System-wide identification of RNA-binding proteins by interactome capture","volume":"8","author":"Castello","year":"2013","journal-title":"Nat. Protoc."},{"key":"2022081200011043000_B30","doi-asserted-by":"crossref","first-page":"3551","DOI":"10.1002\/(SICI)1522-2683(19991201)20:18<3551::AID-ELPS3551>3.0.CO;2-2","article-title":"Probability-based protein identification by searching sequence databases using mass spectrometry data","volume":"20","author":"Perkins","year":"1999","journal-title":"Electrophoresis"},{"key":"2022081200011043000_B31","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1038\/s41587-018-0001-2","article-title":"Comprehensive identification of RNA\u2013protein interactions in any organism using orthogonal organic phase separation (OOPS)","volume":"37","author":"Queiroz","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"2022081200011043000_B32","doi-asserted-by":"crossref","first-page":"e0189209","DOI":"10.1371\/journal.pone.0189209","article-title":"QCloud: a cloud-based quality control system for mass spectrometry-based proteomics laboratories","volume":"13","author":"Chiva","year":"2018","journal-title":"PLoS One"},{"key":"2022081200011043000_B33","doi-asserted-by":"crossref","first-page":"2010","DOI":"10.1021\/acs.jproteome.0c00853","article-title":"QCloud2: an improved Cloud-based quality-control system for Mass-Spectrometry-based proteomics laboratories","volume":"20","author":"Olivella","year":"2021","journal-title":"J. Proteome Res."},{"key":"2022081200011043000_B34","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"Ggplot2: elegant graphics for data analysis","author":"Wickham","year":"2016"},{"key":"2022081200011043000_B35","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1016\/j.jprot.2013.10.023","article-title":"SAINTexpress: improvements and additional features in significance analysis of interactome software","volume":"100","author":"Teo","year":"2014","journal-title":"J. Proteomics"},{"key":"2022081200011043000_B36","doi-asserted-by":"crossref","first-page":"391","DOI":"10.1016\/j.cell.2018.11.004","article-title":"The human RNA-Binding proteome and its dynamics during translational arrest","volume":"176","author":"Trendel","year":"2019","journal-title":"Cell"},{"key":"2022081200011043000_B37","doi-asserted-by":"crossref","first-page":"990","DOI":"10.1038\/s41467-019-08942-3","article-title":"Purification of cross-linked RNA-protein complexes by phenol-toluol extraction","volume":"10","author":"Urdaneta","year":"2019","journal-title":"Nat. Commun."},{"key":"2022081200011043000_B38","doi-asserted-by":"crossref","first-page":"D476","DOI":"10.1093\/nar\/gki107","article-title":"Inparanoid: a comprehensive database of eukaryotic orthologs","volume":"33","author":"O\u2019Brien","year":"2005","journal-title":"Nucleic Acids Res."},{"key":"2022081200011043000_B39","doi-asserted-by":"crossref","first-page":"1393","DOI":"10.1016\/j.cell.2012.04.031","article-title":"Insights into RNA biology from an atlas of mammalian mRNA-binding proteins","volume":"149","author":"Castello","year":"2012","journal-title":"Cell"},{"key":"2022081200011043000_B40","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1007\/978-1-4939-3067-8_8","article-title":"Comprehensive identification of RNA-Binding proteins by RNA interactome capture","volume":"1358","author":"Castello","year":"2016","journal-title":"Methods Mol. Biol."},{"key":"2022081200011043000_B41","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1093\/bioinformatics\/btp677","article-title":"On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics","volume":"26","author":"Pham","year":"2010","journal-title":"Bioinformatics"},{"key":"2022081200011043000_B42","doi-asserted-by":"crossref","first-page":"614","DOI":"10.1093\/bioinformatics\/btt016","article-title":"Grape RNA-Seq analysis pipeline environment","volume":"29","author":"Knowles","year":"2013","journal-title":"Bioinformatics"},{"key":"2022081200011043000_B43","doi-asserted-by":"crossref","first-page":"11.14.1","DOI":"10.1002\/0471250953.bi1114s51","article-title":"Mapping RNA-seq reads with STAR","volume":"51","author":"Dobin","year":"2015","journal-title":"Curr. Protoc. Bioinformatics"},{"key":"2022081200011043000_B44","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"Li","year":"2011","journal-title":"BMC Bioinf."},{"key":"2022081200011043000_B45","doi-asserted-by":"crossref","first-page":"3439","DOI":"10.1093\/bioinformatics\/bti525","article-title":"BioMart and bioconductor: a powerful link between biological databases and microarray data analysis","volume":"21","author":"Durinck","year":"2005","journal-title":"Bioinformatics"},{"key":"2022081200011043000_B46","doi-asserted-by":"crossref","first-page":"674","DOI":"10.1016\/j.molcel.2012.05.021","article-title":"The mRNA-Bound proteome and its global occupancy profile on protein-coding transcripts","volume":"46","author":"Baltz","year":"2012","journal-title":"Mol. Cell"},{"key":"2022081200011043000_B47","doi-asserted-by":"crossref","first-page":"1047","DOI":"10.1038\/ng1634","article-title":"The melanocyte differentiation program predisposes to metastasis following neoplastic transformation","volume":"37","author":"Gupta","year":"2005","journal-title":"Nat. Genet."},{"key":"2022081200011043000_B48","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/nmeth.2557","article-title":"The CRAPome: a contaminant repository for affinity purification\u2013mass spectrometry data","volume":"10","author":"Mellacheruvu","year":"2013","journal-title":"Nat. Methods"},{"key":"2022081200011043000_B49","doi-asserted-by":"crossref","first-page":"11212","DOI":"10.1038\/ncomms11212","article-title":"Serial interactome capture of the human cell nucleus","volume":"7","author":"Conrad","year":"2016","journal-title":"Nat. Commun."},{"key":"2022081200011043000_B50","doi-asserted-by":"crossref","first-page":"4408","DOI":"10.1038\/s41467-018-06557-8","article-title":"Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture","volume":"9","author":"Perez-Perri","year":"2018","journal-title":"Nat. Commun."},{"key":"2022081200011043000_B51","doi-asserted-by":"crossref","first-page":"D941","DOI":"10.1093\/nar\/gky1015","article-title":"COSMIC: the catalogue of somatic mutations in cancer","volume":"47","author":"Tate","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"2022081200011043000_B52","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1002\/(SICI)1098-1004(200001)15:1<57::AID-HUMU12>3.0.CO;2-G","article-title":"Online mendelian inheritance in man (OMIM)","volume":"15","author":"Hamosh","year":"2000","journal-title":"Hum. Mutat."},{"key":"2022081200011043000_B53","doi-asserted-by":"crossref","first-page":"D258","DOI":"10.1093\/nar\/gkh036","article-title":"The gene ontology (GO) database and informatics resource","volume":"32","author":"Harris","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2022081200011043000_B54","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/s41568-020-0290-x","article-title":"A compendium of mutational cancer driver genes","volume":"20","author":"Mart\u00ednez-Jim\u00e9nez","year":"2020","journal-title":"Nat. Rev. Cancer"},{"key":"2022081200011043000_B55","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1111\/j.1087-0024.2005.200407.x","article-title":"Normal human melanocyte homeostasis as a paradigm for understanding melanoma","volume":"10","author":"Haass","year":"2005","journal-title":"J. Investig. Dermatol. Symp. Proc."},{"key":"2022081200011043000_B56","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1016\/j.cell.2017.06.010","article-title":"Defining a cancer dependency map","volume":"170","author":"Tsherniak","year":"2017","journal-title":"Cell"},{"key":"2022081200011043000_B57","doi-asserted-by":"crossref","first-page":"401","DOI":"10.1158\/2159-8290.CD-12-0095","article-title":"The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data","volume":"2","author":"Cerami1","year":"2012","journal-title":"Cancer Discov."},{"key":"2022081200011043000_B58","doi-asserted-by":"crossref","first-page":"pl1","DOI":"10.1126\/scisignal.2004088","article-title":"Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal","volume":"6","author":"Gao","year":"2013","journal-title":"Sci. Signal"},{"key":"2022081200011043000_B59","doi-asserted-by":"crossref","first-page":"653","DOI":"10.1096\/fj.15-275883","article-title":"PDIA6 regulates insulin secretion by selectively inhibiting the RIDD activity of IRE1","volume":"30","author":"Eletto","year":"2016","journal-title":"FASEB J."},{"key":"2022081200011043000_B60","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1016\/j.molcel.2014.01.004","article-title":"Protein disulfide isomerase A6 controls the decay of IRE1\u03b1 signaling via disulfide-dependent association","volume":"53","author":"Eletto","year":"2014","journal-title":"Mol. Cell"},{"key":"2022081200011043000_B61","doi-asserted-by":"crossref","first-page":"ra54","DOI":"10.1126\/scisignal.2004983","article-title":"Interplay between the oxidoreductase PDIA6 and microRNA-322 controls the response to disrupted endoplasmic reticulum calcium homeostasis","volume":"7","author":"Groenendyk","year":"2014","journal-title":"Sci. Signal"},{"key":"2022081200011043000_B62","doi-asserted-by":"crossref","first-page":"482","DOI":"10.1038\/nature05768","article-title":"Disulphide-isomerase-enabled shedding of tumour-associated NKG2D ligands","volume":"447","author":"Kaiser","year":"2007","journal-title":"Nature"},{"key":"2022081200011043000_B63","doi-asserted-by":"crossref","first-page":"e27089","DOI":"10.4161\/onci.27089","article-title":"How to exploit stress-related immunity against hodgkin's lymphoma: targeting ERp5 and ADAM sheddases","volume":"2","author":"Poggi","year":"2013","journal-title":"Oncoimmunology"},{"key":"2022081200011043000_B64","doi-asserted-by":"crossref","first-page":"6696","DOI":"10.1073\/pnas.0701145104","article-title":"In vivo selection for metastasis promoting genes in the mouse","volume":"104","author":"Gumireddy","year":"2007","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"2022081200011043000_B65","doi-asserted-by":"crossref","first-page":"685","DOI":"10.1038\/cdd.2013.193","article-title":"The protein disulfide isomerases PDIA4 and PDIA6 mediate resistance to cisplatin-induced cell death in lung adenocarcinoma","volume":"21","author":"Tufo","year":"2014","journal-title":"Cell Death Differ."},{"key":"2022081200011043000_B66","doi-asserted-by":"crossref","first-page":"696","DOI":"10.1016\/j.molcel.2016.06.029","article-title":"Comprehensive identification of RNA-Binding domains in human cells","volume":"63","author":"Castello","year":"2016","journal-title":"Mol. Cell"},{"key":"2022081200011043000_B67","doi-asserted-by":"crossref","first-page":"2762","DOI":"10.1021\/acs.jproteome.7b00042","article-title":"Specifying RNA-binding regions in proteins by peptide cross-linking and affinity purification","volume":"16","author":"Mullari","year":"2017","journal-title":"J. Proteome Res."},{"key":"2022081200011043000_B68","doi-asserted-by":"crossref","first-page":"312","DOI":"10.1089\/ars.2006.8.312","article-title":"Extracellular disulfide exchange and the regulation of cellular function","volume":"8","author":"Jordan","year":"2006","journal-title":"Antioxid. Redox. Signal."},{"key":"2022081200011043000_B69","doi-asserted-by":"crossref","first-page":"W174","DOI":"10.1093\/nar\/gkv342","article-title":"I-TASSER server: new development for protein structure and function predictions","volume":"43","author":"Yang","year":"2015","journal-title":"Nucleic Acids Res."},{"key":"2022081200011043000_B70","doi-asserted-by":"crossref","first-page":"1027","DOI":"10.1038\/nsmb.3128","article-title":"Conserved mRNA-binding proteomes in eukaryotic organisms","volume":"22","author":"Matia-Gonz\u00e1lez","year":"2015","journal-title":"Nat. Struct. Mol. Biol."},{"key":"2022081200011043000_B71","doi-asserted-by":"crossref","first-page":"12128","DOI":"10.1038\/ncomms12128","article-title":"Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in drosophila","volume":"7","author":"Sysoev","year":"2016","journal-title":"Nat. Commun."},{"key":"2022081200011043000_B72","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1007\/978-1-4939-7213-5_27","article-title":"Systematic detection of poly(a) + RNA-Interacting proteins and their differential binding","volume":"1649","author":"Milek","year":"2018","journal-title":"Methods Mol. Biol."},{"key":"2022081200011043000_B73","doi-asserted-by":"crossref","first-page":"2699","DOI":"10.1074\/mcp.M115.056564","article-title":"Identification of RNA-binding proteins in macrophages by interactome capture","volume":"15","author":"Liepelt","year":"2016","journal-title":"Mol. Cell. Proteomics"},{"key":"2022081200011043000_B74","doi-asserted-by":"crossref","first-page":"1184","DOI":"10.1101\/gr.215954.116","article-title":"Dynamic RNA\u2013protein interactions underlie the zebrafish maternal-to-zygotic transition","volume":"27","author":"Despic","year":"2017","journal-title":"Genome Res."},{"key":"2022081200011043000_B75","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1016\/j.molcel.2019.01.017","article-title":"System-wide profiling of RNA-Binding proteins uncovers key regulators of virus infection","volume":"74","author":"Garcia-Moreno","year":"2019","journal-title":"Mol. Cell"},{"key":"2022081200011043000_B76","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1016\/j.isci.2019.11.039","article-title":"Activation of hypoxia-inducible factor signaling modulates the RNA protein interactome in caenorhabditis elegans","volume":"22","author":"Esmaillie","year":"2019","journal-title":"iScience"},{"key":"2022081200011043000_B77","doi-asserted-by":"crossref","first-page":"1023","DOI":"10.1021\/acs.jproteome.5b01091","article-title":"A description of the clinical proteomic tumor analysis consortium (CPTAC) common data analysis pipeline","volume":"15","author":"Rudnick","year":"2016","journal-title":"J. Proteome Res."},{"key":"2022081200011043000_B78","doi-asserted-by":"crossref","first-page":"2851","DOI":"10.1016\/j.molcel.2021.05.023","article-title":"Global analysis of protein-RNA interactions in SARS-CoV-2-infected cells reveals key regulators of infection","volume":"81","author":"Kamel","year":"2021","journal-title":"Mol. Cell"},{"key":"2022081200011043000_B79","doi-asserted-by":"crossref","first-page":"1029","DOI":"10.1007\/s00424-016-1819-4","article-title":"The expanding universe of ribonucleoproteins: of novel RNA-binding proteins and unconventional interactions","volume":"468","author":"Beckmann","year":"2016","journal-title":"Pfl\u00fcgers Arch"},{"key":"2022081200011043000_B80","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1089\/ars.2015.6530","article-title":"Extracellular thiol isomerases and their role in thrombus formation","volume":"24","author":"Schulman","year":"2016","journal-title":"Antioxid. Redox. Signal."},{"key":"2022081200011043000_B81","doi-asserted-by":"crossref","first-page":"473","DOI":"10.1016\/j.cell.2019.05.027","article-title":"Atlas of subcellular RNA localization revealed by APEX-Seq","volume":"178","author":"Fazal","year":"2019","journal-title":"Cell"},{"key":"2022081200011043000_B82","doi-asserted-by":"crossref","first-page":"8628","DOI":"10.1093\/nar\/gkr452","article-title":"Classification of pseudo pairs between nucleotide bases and amino acids by analysis of nucleotide-protein complexes","volume":"39","author":"Kondo","year":"2011","journal-title":"Nucleic Acids Res."},{"key":"2022081200011043000_B83","doi-asserted-by":"crossref","first-page":"D447","DOI":"10.1093\/nar\/gkv1145","article-title":"2016 update of the PRIDE database and its related tools","volume":"44","author":"Vizca\u00edno","year":"2016","journal-title":"Nucleic Acids Res."}],"container-title":["Nucleic Acids Research"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/14\/8207\/45290087\/gkac605.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/nar\/article-pdf\/50\/14\/8207\/45290087\/gkac605.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,8,12]],"date-time":"2022-08-12T00:08:12Z","timestamp":1660262892000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/nar\/article\/50\/14\/8207\/6644950"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,7,15]]},"references-count":83,"journal-issue":{"issue":"14","published-online":{"date-parts":[[2022,7,15]]},"published-print":{"date-parts":[[2022,8,12]]}},"URL":"https:\/\/doi.org\/10.1093\/nar\/gkac605","relation":{},"ISSN":["0305-1048","1362-4962"],"issn-type":[{"value":"0305-1048","type":"print"},{"value":"1362-4962","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2022,8,12]]},"published":{"date-parts":[[2022,7,15]]}}}