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Nielsen"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Novo Nordisk Foundation Center for Protein Research"],"publication":["28648085 Mullari M, Lyon D, Jensen LJ, Nielsen ML. Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification. J Proteome Res. 2017 16(8):2762-2772 10.1021/acs.jproteome.7b00042"],"submitter_affiliation":["Novo Nordisk Foundation Center for Protein Research"],"labhead_mail":["michael.lund.nielsen@cpr.ku.dk"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"disease":["Disease Free"],"submitter_keywords":["Human cell lines"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD005739"],"quantification_method":[""],"modification":[""],"data_protocol":["Standard proteomic data processing using maxquant software suite"],"omics_type":["Proteomics"],"species":["Homo Sapiens (human)"],"submitter_mail":["michael.lund.nielsen@cpr.ku.dk"],"curator_keywords":["Biological"],"submitter_country":["Denmark"],"pubmed_abstract":["RNA-binding proteins (RBPs) allow cells to carry out pre-RNA processing and post-transcriptional regulation of gene expression, and aberrations in RBP functions have been linked to many diseases, including neurological disorders and cancer. Human cells encode thousands of RNA-binding proteins with unique RNA-binding properties. These properties are regulated through modularity of a large variety of RNA-binding domains, rendering RNA-protein interactions difficult to study. Recently, the introduction of proteomics methods has provided novel insights into RNA-binding proteins at a systems level. However, determining the exact protein sequence regions that interact with RNA remains challenging and laborious, especially considering that many RBPs lack canonical RNA-binding domains. Here we describe a streamlined proteomic workflow called peptide cross-linking and affinity purification (pCLAP) that allows rapid characterization of RNA-binding regions in proteins. pCLAP is based upon the combined use of UV cross-linking and enzymatic digestion of RNA-bound proteins followed by single-shot mass spectrometric analysis. To benchmark our method, we identified the binding regions for polyadenylated RNA-binding proteins in HEK293 cells, allowing us to map the mRNA interaction regions of more than 1000 RBPs with very high reproducibility from replicate single-shot analyses. Our results show specific enrichment of many known RNA-binding regions on many known RNA-binding proteins, confirming the specificity of our approach."],"pubmed_title":["Specifying RNA-Binding Regions in Proteins by Peptide Cross-Linking and Affinity Purification."],"pubmed_authors":["Mullari Meeli M, Lyon David D, Jensen Lars Juhl LJ, Nielsen Michael L ML"],"description_synonyms":["ribonucleic acid, Acid, RNA, Ribonucleic, human being, Man (Taxonomy), ribose nucleic acid, Non Polyadenylated RNA, ligand, Modern, Proteins, ribonucleic acids, Non-Polyadenylated, Gene, RNS, Ribonucleic Acid, procedures, human, Non-Polyadenylated RNA, Human, Protein Gene Products, Gene Proteins, Homo sapiens, yeast nucleic acid, Ribonukleinsaeure, Modern Man, Protein, Gene Products, pentosenucleic acids, Ribonucleic acids, techniques, methodology., Non Polyadenylated, Man, RNA Gene Products"],"data_synonyms":["Applications Software, Open Source Softwares, Open Source, Software Applications, Computer Software, Source Software, Software Application, Open, Engineering, Open Source Software, Computer Programs and Programming, Computer, Source Softwares, Software Tools, Computer Software Application, Tool, Programs, Computer Programs, data analysis, Program, Computer Applications, Applications, Software Tool, data processing, Applications Softwares, Tools, Computer Software Applications., Computer Applications Software, Computer Applications Softwares, Software Engineering, Softwares, Software, Computer Program, Application"],"pubmed_title_synonyms":["ribonucleic acid, Acid, RNA, Ribonucleic, ribose nucleic acid, Non Polyadenylated RNA, ligand, Proteins, ribonucleic acids, Non-Polyadenylated, Gene, RNS, purification, Ribonucleic Acid, isolation., Non-Polyadenylated RNA, Protein Gene Products, isolation and purification, Gene Proteins, yeast nucleic acid, Ribonukleinsaeure, Protein, Gene Products, pentosenucleic acids, Ribonucleic acids, Non Polyadenylated, RNA Gene Products"],"sample_synonyms":["l(2)k04204, l(2)k05434, OG12X, l(2)k10821, Grv, determination, kop, l(2)k03010, Su(Mir)1, CG18076, chemical analysis., kak, 6330543G17Rik, CG18637, SHOT, sample population, OG12, shortstop/kakapo, l(2)k05821, l(2)k15606, grv, sample, DmelCG18076, l(2)CA4, assay, Og12x, Prx3, 42/4, Shot"],"pubmed_abstract_synonyms":["l(1)d norm-12, l(2)k04204, Ribonucleic, Disorders, EG:17A9.1, PhrB photolyase activity, BR_C, acetylglucosaminyltransferase-like protein, 2Bc, Tumor, Healthcare Benchmarking, RBP, l(1)2Bad, l(1)2Bab, Neurologic Disorders, Method, br-Z1, br-Z3, Post Transcriptional, 2, 3, NUP96, HEK 293, RNA Modification, Analysis, Work Flow, myd, epithelium, l(1)dn1, Posttranscriptional RNA Processing, Non Polyadenylated, WMS, RNA Binding Proteins, F23858, RBP9, SF4, adenomas, rbp, DmelCG9874, RRM10, L-methionine aminopeptidase activity, like-acetylglucosaminyltransferase, BR, Su(Mir)1, Mbp-1, procedures, Br-C-Z3, SUPPRESSOR OF AUXIN RESISTANCE 3, isolation and purification, Post-Transcriptional RNA Modifications, Benchmarking, Smurf, ds RNA-Binding Proteins, Br, BRC-Z2, BRC-Z3, BRC-Z1, Homo sapiens disease, Best Practice, BRC-Z4, RNA Binding Protein, Prx3, CG4943, SGS, 293 Cell, rdp, Tumors, rds, Polyadenylated, ds, Modifications, dTBP, dTbp, l(1)d.norm.1, MYH-associated polyposis, Metrics, l(1)npr-1, Procedure, Lack, HEK 293 Cell, l(1)npr1, ACMICD, Workflows, Benign, RNA-Binding Domain, mKIAA0609, Domains, dipyrimidine photolyase (photosensitive), numerical data, Specificity and Sensitivity., Ribonucleic acids, Double-Stranded RNA-Binding, RNA-Binding Protein, Polyadenylated Messenger RNA, fg, Acid, RUTBC3, Non Polyadenylated mRNA, protein_coding_transcript, RBP9-2, Grv, Processing, Benign Neoplasms, Methodological, PRO2222, human, Non-Polyadenylated mRNA, RNA Binding Domains, Malignant Neoplasms, MDC1D, enr, HEK 293 Cells, grv, Cells, multiple colorectal, dtbp, l(1)pp-2, RNA Binding Motifs, l(1)pp-1, 42/4, Poly(A) RNA, Work Flows, OG12X, Peptidomics, RNA Processing, Neoplasms, HEK293 Cell, protein-containing complex, DmelCG3151, LARGE1, Human, l(2)k05821, CG11511, CG11514, l(2)k15606, isolation, RNA Modifications, Gene Products, disease or disorder, TBP38, Man, Technique, MAP, Modification, ds RNA-Binding Protein, MDDGB6, ligand, familial adenomatous polyposis 2, F23A5.3, messenger RNA, Neoplasias, Study, Neurologic, template RNA, 293T Cells, l(1)PP1, l(1)pp1, l(1)pp2, Cancer, EG:123F11.1, RNA, Neurologic Disorder, use, Malignant Neoplasm, CG3151, Proteins, disorders, CG18076, Messenger RNA, RNS, l(1)G0284a, Nervous System Disorder, Dsmurf, Cell, dSmurf, Posttranscriptional RNA, MT, native protein, Poly(A)+ mRNA, Smurf ubiquitin ligase, chemical analysis, Neoplasm, INSDC_feature:mRNA, condition, Post-Transcriptional RNA, MFS1, RNA-Binding Domains, primary cancer, RPE, Post Transcriptional RNA Processing, mRNA, Posttranscriptional, Specificity, kak, Cancers, Ribonucleic Acid, malignant tumor, primary structure of sequence macromolecule, OG12, p. pigmentosa retinae, plan specification, Gene Proteins, Post-Transcriptional, like-glycosyltransferase, l(1)G0401, Best Practice Analysis, BRC, Nervous System Disorders, MAP syndrome, deoxyribonucleate pyrimidine dimer lyase (photosensitive), Og12x, Polyadenylated mRNA, rbp9a, Neoplasia, Neurological, 293T Cell, ds RNA-Binding, 293 Cells, determination, methionine aminopeptidase activity, Human Embryonic Kidney Cell Line 293, Mbp1, protein, 6330543G17Rik, BR-C, pigmented epithelium, Techniques, DSmurf, Double Stranded RNA Binding Proteins, A18, br-C, diseases, Binding Domain, PP1, PP2, diseases and disorders, RNA Binding Domain, Post-Transcriptional RNA Processing, protein aggregate, BR-c, Br-C, RNA Gene Products, peptidase M activity, Br-Z4, rabGAPLP, human disease, Man (Taxonomy), l(1)G0318, de12, Polyadenylated Messenger, pigmented retina, l(1)n34, BrC-Z1, RabGAP-5, purification, Post Transcriptional RNA Modification, DNA cyclobutane dipyrimidine photolyase activity, Double-Stranded RNA-Binding Protein, fs(2)B, Methodological Studies, Benchmarks, malignant neoplasm, RUSC3, Malignancies, l(2)CA4, GPHYSD2, CG11491, D-smurf, PRE, ribose nucleic acid, gyltl1b-b, statistics and numerical data, Rbp10, deoxyribonucleic cyclobutane dipyrimidine photolyase activity, Modern, BR-C Z1, Post-Transcriptional RNA Modification, ribonucleic acids, autosomal recessive familial adenomatous polyposis, Maps, Double-Stranded, CG15402, uq, shortstop/kakapo, retinal pigment, MDDGA6, Double-Stranded RNA-Binding Proteins, Ribonukleinsaeure, DmelCG18076, Diseases, pentosenucleic acids, nrp1, KIAA0609, retinal pigment layer, acetylglucosaminyltransferase-like 1A, Domain, autosomal recessive, gyltl1b, DmelCG4943, RNA-Binding Proteins, mdc1d, Rpb9, npr-1, MASS, LARGE_HUMAN, Methodological Study, SHOT, RNA Binding Motif, RABGAP5, HEK 293 Cell Line, disease, phr A photolyase activity, DNA-photoreactivating enzyme, dTFIID, HEK, npr, CG9874, other disease, human being, Procedures, Health Care Benchmarking, l(1)G0018, DmelCG11491, dSmurf1, Double Stranded RNA Binding Protein, Benign Neoplasm, l(1)ts144, FBN, Gene, l(1)2Ba, l(1)2Bb, Z1, l(1)2Bc, posttranscriptional regulation of gene expression, Z2, photoreactivating enzyme activity, Z3, Z4, Malignant, froggy, Gyltl1a, 293T, method, RNA Binding, EG:25D2.1, Homo sapiens, utilization, ECTOL1, Messenger, nrp, method used in an experiment, Br-C Z2, l(1)ts132, Studies, l(1)ts376, stratum pigmentosa retinae, familial adenomatous polyposis, Shot, l(1)ESHS5, study, Nervous System, MOS3, deoxyribocyclobutadipyrimidine pyrimidine-lyase activity, l(2)k10821, PRECOCIOUS, Malignancy, nprl, Binding Domains, LARGE, Neurological Disorder, ds RNA Binding Protein, non-neoplastic, Non-Polyadenylated RNA, OCTD, autosomal recessive multiple colorectal adenomas, BPFD#36, l(1)G0042, l(1)G0284, d-smurf, l(1)2Bd, RNA-Binding Motif, Disorder, Neurological Disorders, npr1, disorder, Sensitivity, rrm10, TFIIDtau, Healthcare, F23A5_3, Disease, MUTYH-Associated Polyposis, protein complex, kop, Human Kidney Cell Line 293, ecs, fes, BrZ3, medical condition, Benchmark, rrm9, CG18637, TfIID, TBP, MODIFIER OF SNC1, o.c.c., yeast nucleic acid, Protein, deoxyribonucleic photolyase activity, Nervous System Disease, sequence, TFIID, Health Care, techniques, Polyadenylated RNA, WMS2, ribonucleic acid, l(2)k05434, Poly(A)+ RNA, Poly(A) Tail, photolyase activity, rbp9, l(1)ts358, Non Polyadenylated RNA, l(2)k03010, Non-Polyadenylated, HEK293, MYH-Associated Polyposis, Protein Gene Products, 2B5, RRM9, Modern Man, SSKS, assay, FAP2, glycosyltransferase-like protein LARGE1, methodology, colorectal adenomatous polyposis"],"name_synonyms":["ribonucleic acid, Acid, RNA, Ribonucleic, human being, Man (Taxonomy), ribose nucleic acid, protein complex, Non Polyadenylated RNA, ligand, Modern, Proteins, ribonucleic acids, Non-Polyadenylated, Gene, RNS, Ribonucleic Acid, protein, protein-containing complex, human, Non-Polyadenylated RNA, Protein Gene Products, Human, Gene Proteins, native protein, Homo sapiens, yeast nucleic acid, Ribonukleinsaeure, Modern Man, Protein, Gene Products, pentosenucleic acids, Cell., Ribonucleic acids, protein aggregate, Non Polyadenylated, Man, RNA Gene Products"],"additional_accession":[]},"is_claimable":false,"name":"RNA-binding protein regions in human cells","description":"Idenfication of RNA-binding regions in human proteins using pCLAP 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