{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Msf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD072229/wc_QE_061521_XueDong_DN_control.msf"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD072229/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD072229/wc_QE_061521_XueDong_DN_control.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD072229/wc_QE_061521_XueDong_GR-1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD072229/20210605_GN.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD072229/wc_QE_061521_XueDong_DR.raw"],"Mztab":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD072229/wc_QE_061521_XueDong_DN_control.mzTab"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["mtouma@mednet.ucla.edu"],"submitter":["Calvin Pan"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":[""],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD072229"],"tissue":["Myoblast","Cell Culture"],"sample_protocol":["Biotin-labeled RNAs were synthesized using the T7 and SP6 RNA polymerase kits (Promega) together with the Biotin RNA Labeling Mix (Roche). After incubation of the biotinylated RNA with cell extracts at 4°C, washed Dynabeads™ M-280 Streptavidin (Thermo Fisher Scientific) were added to the pull-down mixture. Following a 1-hour incubation at 4°C, the beads were collected using a magnetic stand and washed thoroughly with binding buffer. Immunoprecipitated proteins were heated at 95 o C in elution buffer (12 mM sodium lauroyl sarcosine, 0.5% sodium deoxycholate, 50 mM triethylammonium bicarbonate (TEAB), Halt™ Protease and Phosphatase Inhibitor Cocktail (Thermo Fisher Scientific)) containing tris(2-carboxyethyl)phosphine (10 mM) and chloroacetamide (40 mM) for 10 minutes. The samples were then diluted 5-fold with 50 mM TEAB and digested with trypsin (1 ug) for 16 hours at 37 °C. The samples were desalted using a modified version of Rappsilber's protocol [Ref. 1]. Aliquots of each sample were injected onto a reverse phase nanobore HPLC column (AcuTech Scientific, C18, 1.8um particle size, 360 um x 20 cm, 150 um ID), equilibrated in solvent A (water/acetonitrile/FA, 98/2/0.1, v/v/v) and eluted (300 nL/min) with an increasing concentration of solvent B (acetonitrile/water/FA, 98/2/0.1, v/v/v: min/% F; 0/0, 5/3, 18/7, 74/12, 144/24, 153/27, 162/40, 164/80, 174/80, 176/0, 180/0) using an EASY-nLC II (Thermo Fisher Scientific). The effluent from the column was directed to a nanospray ionization source connected to a hybrid quadrupole-Orbitrap mass spectrometer (Q Exactive Plus, Thermo Fisher Scientific) acquiring mass spectra in a data-dependent mode alternating between a full scan (m/z 350-1700, automated gain control (AGC) target 3 x 106, 50 ms maximum injection time, FWHM resolution 70,000 at m/z 200) and up to 15 MS/MS scans (quadrupole isolation of charge states 2-7, isolation window 0.7 m/z) with previously optimized fragmentation conditions (normalized collision energy of 32, dynamic exclusion of 30 s, AGC target 1 x 105, 100 ms maximum injection time, FWHM resolution 35,000 at m/z 200)."],"repository":["Pride"],"modification":[""],"quantification_method":["Not available"],"data_protocol":["Raw proteomic data were searched against a Uniprot database containing the complete mouse proteome using SEQUEST-HT (including dynamic modifications: oxidation (+15.995) on M, deamidation (+0.984) on N/Q, and carbamidomethyl (+57.021), phosphorylation (+79.966) on S/T/Y, methylation (+14.016) on K/R, acetylation (+42.011) on K and protein N-terminus) in Proteome Discoverer (Version 3.1, Thermo Scientific), which provided measurements of relative abundance of the identified peptides. Decoy database searching was used to generate high confidence tryptic peptides (FDR < 1%). Tryptic peptides containing amino acid sequences unique to individual proteins were used to identify and provide relative quantification between different proteins in each sample."],"omics_type":["Proteomics"],"labhead":["Marlin Touma"],"instrument_platform":[""],"labhead_affiliation":["1. Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, CA.  2. Neonatal/Congenital Heart Laboratory, Cardiovascular Research Laboratory, David Geffen School of Medicine, University of California, Los Angeles, CA."],"species":["Mus Musculus (mouse)"],"submission_type":["COMPLETE"],"publication":["42152677 Kang X, Zhao Y, Nelson SF, Pyle A, Lusis AJ, Touma M. Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) maintains muscle progenitor identity by stabilizing the Ppp1r1b-lncRNA-PRC2 complex. Nucleic Acids Res. 2026 54(9):gkag497 10.1093/nar/gkag497"],"submitter_mail":["calvinpan@mednet.ucla.edu"],"submitter_affiliation":["UCLA"],"submitter_country":["United States"],"doi":["10.6019/PXD072229"],"pubmed_abstract":["Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) is a multifunctional RNA-binding protein of the hnRNP family, yet its role in long non-coding RNA (lncRNA)-mediated epigenetic regulation during myogenesis remains unclear. The lncRNA Ppp1r1b-lncRNA is an established regulator of myogenesis that functions through interaction with Polycomb repressive complex 2 (PRC2) at myogenic gene promoters. Here, we investigated the role of hnRNPA1 in Ppp1r1b-lncRNA-mediated regulation of myogenesis. Fluorescence in situ hybridization (FISH) revealed the subcellular localization of Ppp1r1b-lncRNA, and RNA pulldown coupled with mass spectrometry identified associated proteins. Both hnRNPA1 and EZH2 were found to bind Ppp1r1b-lncRNA, but at distinct regions. Knockdown of hnRNPA1 in mouse C2C12 myoblasts reduced the interaction between Ppp1r1b-lncRNA and EZH2, as determined by RNA immunoprecipitation (RIP), decreased promoter occupancy of Ppp1r1b-lncRNA, as assessed by chromatin isolation by RNA purification (CHIRP), and reduced H3K27me3 levels at the MyoD1 and Myogenin promoters, as shown by chromatin immunoprecipitation (ChIP). These changes led to increased expression of muscle-specific transcription factors and sarcomeric genes, thereby disrupting the undifferentiated state. Furthermore, hnRNPA1 knockdown disrupted the interaction between the human ortholog PPP1R1B-lncRNA and PRC2 in human skeletal muscle precursor cells (hSMPCs). Together, these findings demonstrate that hnRNPA1 maintains the integrity of the Ppp1r1b-lncRNA-PRC2 complex and ensures proper epigenetic regulation of myogenic gene expression. This conserved hnRNPA1-Ppp1r1b-lncRNA-PRC2 regulatory axis represents a potential therapeutic target for muscle regeneration."],"pubmed_title":["Heterogeneous nuclear ribonucleoprotein A1 (hnRNPA1) maintains muscle progenitor identity by stabilizing the Ppp1r1b-lncRNA-PRC2 complex."],"pubmed_authors":["Kang Xuedong X, Zhao Yan Y, Nelson Stanley F SF, Pyle April A, Lusis Aldons J AJ, Touma Marlin M"],"additional_accession":[]},"is_claimable":false,"name":"Heterogeneous Nuclear Ribonucleoprotein A1 (hnRNPA1) Maintains Muscle Progenitor Identity by Stabilizing the Ppp1r1b-lncRNA-PRC2 Complex","description":"The Pierce™ Magnetic RNA–Protein Pull-Down Kit (Thermo Fisher Scientific) was used to examine proteins associated with Ppp1r1b-lncRNA. The assay was performed using C2C12 cell lysates prepared from both undifferentiated and differentiated states. Full-length in vitro–transcribed Ppp1r1b-lncRNA was used as the positive probe, and in vitro–transcribed antisense Ppp1r1b-lncRNA was used as the negative 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