{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063805/checksum.txt"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063805/XB03974B1DA.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063805/Results.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["gwj20190228@163.com"],"submitter":["Weijun Gao"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"disease":["Disease Free"],"software":[""],"submitter_keywords":["Lc-ms","Ssc","Mouse"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063805"],"tissue":["Testis","Stem Cell"],"sample_protocol":["RAP probes pull down the RNA binding protein.Through the organic combination of a series of cutting-edge technologies such as protein extraction, enzyme digestion, liquid chromatography-mass spectrometry tandem analysis, and bioinformatics analysis, the protein in the samples was quantified Research on the group."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Database retrieval is a complex computational process that requires the use of professional mass spectrometry data analysis software for data parsing. The raw data from the mass spectrometry machine is imported into the database search software, and the corresponding analysis parameters are set according to the experimental plan. In this experiment, the DIA data was retrieved using the Pulsar search engine embedded in Spectronaut (v 18) and the default parameters of the software. The database is Mus_musculus_10090_SP_20231220.fasta (17191 sequences), and an inverse database has been added to calculate the false positive rate (FDR) caused by random matching. The number of missed cut positions is set to 2; The cysteine alkylated Carbamidomethyl (C) was set as a fixed modification, and the variable modification was set as the oxidation of methionine, the acetylation of the N-terminal of the protein, and the FDR for protein, peptide and PSM identification was set to 1%."],"omics_type":["Proteomics"],"labhead":["Ji Wu"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Ningxia Medical University"],"species":["Mus Musculus (mouse)"],"publication":["42231399 Gao W, Xu B, Ma W, He X, Wu J. lncRNA-operated stem cell fate control: RPS3 mediates the in situ Gm16751-Zhx3 interactome to program spermatogonial stem cell differentiation. Cell Biosci. 2026 16(1):61 10.1186/s13578-026-01599-8"],"submitter_mail":["gwj20190228@163.com"],"submitter_affiliation":["Ningxia Medical University"],"submitter_country":["China"],"pubmed_abstract":["<h4>Background</h4>Long non-coding RNAs (lncRNAs) play pivotal regulatory roles in mammalian male gametogenesis. Advances in high-throughput technologies have demonstrated that lncRNAs orchestrate robust, flexible, and context-specific gene regulatory networks through dynamic interactions with proteins, DNA, and RNA, modulating transcriptional and post-transcriptional processes. However, the mechanistic role of in situ lncRNA-mRNA interactions in spermatogonial stem cell (SSC) differentiation remains poorly understood.<h4>Methods</h4>The differentially expressed transcripts, including lncRNA, mRNA and circRNA, were systematically identified through long RNA sequencing (LongRNA-seq). RNA-RNA in situ interactions were subsequently mapped using RNA in situ conformation sequencing (RIC-seq) technology. The Gm16751-Zhx3 interaction was validated using single-molecule fluorescence in situ hybridization (smFISH), coupled with RNA antisense purification followed by quantitative PCR (RAP-qPCR), and dual-luciferase reporter assay. Its functional impact on SSC differentiation was assessed via EdU staining, apoptosis assay, mRNA stability assay, RAP-qPCR, respectively. Liquid chromatography-tandem mass spectrometry (LC-MS) and RNA immunoprecipitation-qPCR (RIP-qPCR) were employed to screen and identify the RNA-binding protein (RBP) interacting with Gm16751 and Zhx3. Crosslinking immunoprecipitation followed by qPCR (CLIP-qPCR) further identified specific binding sequences. The regulation of RBP on the differentiation of SSC was verified using RAP-qPCR, RIP-qPCR, puromycin incorporation assay, and RNA stability assay.<h4>Results</h4>We employed RIC-seq and LongRNA-seq to systematically identify a functional interaction between lncRNA Gm16751 and Zhx3 mRNA during SSC differentiation, which was further visualized via a Circos plot. Mechanistically, we demonstrated that Gm16751 enhances the mRNA stability of Zhx3, thereby promoting SSC differentiation. Furthermore, mass spectrometry analysis revealed that RPS3 (Ribosomal Protein S3) serves as a critical RBP that bridges the interaction between Gm16751 and Zhx3, ultimately stabilizing Zhx3 mRNA and modulating SSC differentiation.<h4>Conclusions</h4>Our study identified a novel lncRNA-mRNA interaction pair, Gm16751/Zhx3, which is mediated by RPS3 and facilitates the differentiation of SSC. This discovery provides important mechanistic insights into the regulation of male germ cell development and offers a new perspective for understanding molecular controls in spermatogenesis."],"pubmed_title":["lncRNA-operated stem cell fate control: RPS3 mediates the in situ Gm16751-Zhx3 interactome to program spermatogonial stem cell differentiation."],"pubmed_authors":["Gao Weijun W, Xu Bo B, Ma Wenzhi W, He Xiaojin X, Wu Ji J"],"additional_accession":[]},"is_claimable":false,"name":"mouse spermatogonial stem cells LC-MS","description":"Long non-coding RNAs (lncRNAs) play pivotal regulatory roles in mammalian male gametogenesis. Advances in high-throughput technologies have demonstrated that lncRNAs orchestrate robust, flexible, and context-specific gene regulatory networks through dynamic interactions with proteins, DNA, and RNA, modulating transcriptional and post-transcriptional processes. However, the mechanistic role of in situ lncRNA-mRNA interactions in spermatogonial stem cell (SSC) differentiation remains poorly understood. In this study, we employed RIC-seq (RNA in situ conformation sequencing) and LongRNA-seq to systematically identify a functional interaction between lncRNA Gm16751 and Zhx3 mRNA during SSC differentiation, which was further visualized via a Circos plot. Mechanistically, we demonstrated that Gm16751 enhances the mRNA stability of Zhx3, thereby promoting SSC differentiation. Furthermore, mass spectrometry analysis revealed that RPS3 (Ribosomal Protein S3) serves as a critical RNA-binding protein (RBP) that bridges the interaction between Gm16751 and Zhx3, ultimately stabilizing Zhx3 mRNA and modulating SSC differentiation. Our findings provide novel mechanistic insights into the lncRNA-mRNA regulatory axis in SSC differentiation and establish a foundation for understanding the molecular etiology of male germ cell developmental disorders and spermatogenic dysfunction.","dates":{"publication":"2026-06-08","submission":"2025-05-09"},"accession":"PXD063805","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:259447","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:180454","NEWT:5722","NEWT:1247","NEWT:1129","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:317548","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:28909","NEWT:515849","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:143361","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4442","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:44586","NEWT:626528","NEWT:3347","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:747078","NEWT:1282","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:294381","NEWT:197","NEWT:1390363","NEWT:77133","NEWT:288705","NEWT:29176","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:556182","NEWT:1270","NEWT:374990","NEWT:1392","NEWT:498217","NEWT:156471","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:156476","NEWT:286","NEWT:391619","NEWT:360104","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:1143","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:296543","NEWT:316435","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:105023","NEWT:866628","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:9378","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NEWT:8175","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:1077286","NEWT:243277","NEWT:990119","NEWT:2850","NEWT:408172","NEWT:227321","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:3827","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:46704","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:572307","NEWT:1432138","NEWT:269796","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:54571","NEWT:9598","NEWT:8030","NEWT:9483","NCBITaxon:40559","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:759272","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:109757","NEWT:943146","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:508771","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:180923","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:118499","NEWT:169963","NEWT:32644","NEWT:527796","NEWT:225117","NEWT:746128","NEWT:499175","NEWT:109779","NEWT:43665","NEWT:1266464","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:375451","NEWT:352472","NEWT:357","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:1328426","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:40483","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:1428","NEWT:327159","NEWT:178876","NEWT:1660","NEWT:327160","NEWT:573","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:1055524","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:7237","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:187878","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1821314","NEWT:1249668","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