{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/230511_SC1_1FDR_Final.xlsx"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/evidence.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/proteinGroups.txt","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/summary.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/ce2_2023Apr10_11_uc23406_sc1_2b.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/ce2_2023Apr10_06_uc23406_sc1_1a.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/ce2_2023Apr10_14_uc23406_sc1_3a.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/ce2_2023Apr10_10_uc23406_sc1_2a.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/ce2_2023Apr10_07_uc23406_sc1_1b.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/ce2_2023Apr10_15_uc23406_sc1_3b.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/230412_Human_Iso.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/230330_SC1_Gels.pptx","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/combined.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD051716/230413_SC1_1FDR.sps"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["wykim@sookmyung.ac.kr"],"submitter":["Donald Wolfgeher"],"technology_type":["Data-dependent acquisition","Mass Spectrometry"],"software":[""],"submitter_keywords":["Human","Variants","E3 ligase","Neurodegeneration","Lfq","Qe480","Rnf220","Muscle differentiation"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD051716"],"sample_protocol":["293T RNF220 Iso-1, Iso-2, and eGFP IP Proteomics.     Sample preparation for LC–MS/MS Samples were brought to 1x and 20ug was loaded onto 12% MOPS buffered 1D SDS-PAGE gel (Invitrogen NP0341BOX) and run at ~ 200 V for ~ 6 min, resulting in a ~2cM gel plug. The gel was stained with Imperial Stain (Thermo #24615) for 1 h at RT. Trypsin digestion Gel sections were washed in dH2O and destained using 100 mM NH4HCO3 (Sigma #285099) pH 7.5 in 50% acetonitrile (Fisher A998SK-4). A reduction step was performed by addition of 100 μL 50 mM NH4HCO3 pH 7.5 and 10 μL of 200 mM tris(2-carboxyethyl) phosphine HCl (Sigma #C4706-2G) at 37 °C for 30 min. The proteins were alkylated by addition of 100 μL of 50 mM iodoacetamide (Sigma #RPN6320V) prepared fresh in 50 mM NH4HCO3 pH 7.5 buffer and allowed to react in the dark at 20 °C for 30 min. Gel sections were washed in Millipore water, then acetonitrile, and vacuum dried. Trypsin digestion was carried out overnight at 37 °C with 1:50–1:100 enzyme–protein ratio of sequencing grade-modified trypsin (Promega #V5111) in 50 mM NH4HCO3 pH 7.5, and 20 mM CaCl2 (Sigma #C-1016). Peptides were extracted with 5% formic acid (Sigma #F0507-1L) in aqueous and 75% organic (ACN) combined and vacuum dried. Peptides were cleaned up using C18 spin columns (Thermo #89870) and sent to the Mayo Clinic Medical Genome Facility Proteomics Core for HPLC and LC–MS/MS data acquisition via Q-Exactive Orbitrap (Thermo). LC–MS/MS via MaxQuant Peptide samples were re-suspended in Burdick & Jackson HPLC-grade water containing 0.2% formic acid (Fluka #60-006-17), 0.1% TFA (Pierce #28903), and 0.002% Zwittergent 3–16 (Millipore Sigma #693023), a sulfobetaine detergent that contributes the following distinct peaks at the end of chromatograms: MH+ at 392, and in-source dimer [2 M+ H+] at 783, and some minor impurities of Zwittergent 3–12 seen as MH+ at 336. The peptide samples were loaded onto a 100 μm × 40 cm PicoFrit column self-packed with 2.7 μm Agilent Poroshell 120, EC-C18, washed, then switched in-line with a 0.33 uL Optimize EXP2 Stem Traps, packed spray tip nano column packed with Halo 2.7 μm Pep ES-C18, for a 2-step gradient. Mobile phase A was water/acetonitrile/formic acid (98/2/0.2) and mobile phase B was acetonitrile/isopropanol/water/formic acid (80/10/10/0.2). Using a flow rate of 350 nL/min, a 90 min, 2-step LC gradient was run from 5% B to 50% B in 60 min, followed by 50–95% B over the next 10 min, hold 10 min at 95% B, back to starting conditions and re-equilibrated. Electrospray tandem mass spectrometry (LC–MS/MS) was performed at the Mayo Clinic Proteomics Core on a Thermo Orbitrap Exploris 480 mass spectrometer, using a 70,000 RP (70 K Resolving Power at 400 Da) survey scan in profile mode, m/z 340–1800 Da, with lockmasses, followed by 20 MSMS HCD fragmentation scans at 17,500 resolution on doubly and triply charged precursors. Single charged ions were excluded, and ions selected for MS/MS were placed on an exclusion list for 60 s."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Database searching and Data Analysis Tandem mass spectra MS/MS samples were analyzed using MaxQuant (version 2.5.0). MaxQuant was set up to search the 211102_Uniprot_Human_5640.fasta database assuming the digestion enzyme strict trypsin. MaxQuant was searched with a fragment ion mass tolerance, and a parent ion tolerance of 20 PPM. MQ 1FDR results file (proteingroups.txt) was processed in Perseus (version 2.0.6.0) Proteins were filtered out which included “Identified by site”, “reversed”, and “potential contaminants”, Log 2 transformed, imputed via default settings, and annotated against the Human db.  P-values were determined by student’s T-test within Perseus and a significance cutoff was applied to ratios above NegLog10 P-value >= 1.3 and fold-change above 20% or log2 >= 0.26.  Proteins only detected in Iso1 or Iso2 IP were also determined significant.  Log2 Ratios determined for Iso1/Ctrl, Iso2/Ctrl, and Iso1/Iso2.   Significant “hits” were subjected to Reactome pathway analysis and a top level “super pathway” NegLog10FDR enrichment score and protein count were plotted for upregulated pathways."],"omics_type":["Proteomics"],"labhead":["Dr. Woo-Young Kim"],"instrument_platform":[""],"labhead_affiliation":["College of Pharmacy, Sookmyung Women’s University, Seoul 04310, Republic of Korea."],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"publication":["40609864 Choi S, Ha S, Wolfgeher DJ, Kim JW, Go YH, Cha HJ, Bae GU, Kron SJ, Kim WY. N-Terminal deleted isoforms of E3 ligase RNF220 are ubiquitously expressed and required for mouse muscle differentiation. Mol Cells. 2025 48(9):100250 10.1016/j.mocell.2025.100250"],"submitter_mail":["donw@uchicago.edu"],"submitter_affiliation":["University of Chicago"],"submitter_country":["United States"],"pubmed_abstract":["Four isoform peptides of the novel E3 ligase ring finger protein 220 (RNF220) have been identified in humans. However, all of the previous studies have predominantly focused on isoform 1 (the full-length form), which consists of 566 amino acids. Here, we show that a shorter isoform, which is 308 amino acids lacking most of the N-terminus (human isoform 4; mouse isoform 3; ΔN-RNF220), is the predominant and ubiquitously expressed variant that warrants functional investigation. Both isoform 1 and ΔN-RNF220 are expressed in the brain; however, ΔN-RNF220 is the major isoform expressed in all other tissues in mice. Consistently, H3K4me3 ChIP-seq data from ENCODE reveal that the transcription start site for ΔN-RNF220 demonstrates broader and stronger activity across human tissues than that of isoform 1. ΔN-RNF220 produces 2 peptides (4a and 4b) through alternative translation initiation, with isoform 4b displaying distinct subcellular localization, subnuclear structures and interaction with a nuclear protein WDR5. Notably, during embryonic stem cell differentiation into neural stem cells, isoform 1 expression increases, whereas ΔN-RNF220 expression decreases. In murine myoblasts, ΔN-RNF220 is the sole expressed isoform and is required for MyoD and myogenin expression, as well as for muscle differentiation. Our findings highlight ΔN-RNF220 as the ubiquitously and highly expressed variant, likely playing a fundamental role across tissues while exhibiting functional differences from isoform 1. These results emphasize the critical importance of ΔN-RNF220 in future studies investigating the biological functions of RNF220."],"pubmed_title":["N-Terminal deleted isoforms of E3 ligase RNF220 are ubiquitously expressed and required for mouse muscle differentiation."],"pubmed_authors":["Choi SeokGyeong S, Ha Sojung S, Wolfgeher Donald J DJ, Kim Jee Won JW, Go Young-Hyun YH, Cha Hyuk-Jin HJ, Bae Gyu-Un GU, Kron Stephen J SJ, Kim Woo-Young WY"],"additional_accession":[]},"is_claimable":false,"name":"Short isoforms of E3 ligase RNF220 are broadly expressed and impact differentiation.","description":"The human RNF220 coding gene is located at Chr1: p34.1 (NCBI Gene ID: 55182). To date, four isoforms of the RNF220 protein have been described. Prior functional studies have investigated 70 kDa proteins, primarily isoform 1 but potentially isoform 3. Here, we show that the shorter isoforms of RNF220 that lack much of the N-terminus, the 353 AA isoform 2 and 308 AA isoform 4, are broadly expressed at high levels. While targets of RNF220 ubiquitination have been identified and their physiological roles elucidated [3,11], these studies have been limited to substrates of isoform 1. We hypothesized that the ubiquitous, highly expressed short isoforms may play a more fundamental role in most tissues. The shorter isoforms were found to perform distinct functions including in myoblast differentiation. These findings strongly argue for the investigation of these short isoforms in future studies on RNF220 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