{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/N_Kleiber_181223_020224_Expl2_THUMPD2-FLAG-UV_Report_Spectronaut_ProteinGroups.tsv"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_CTRL-FLAG-UV_BR2_r1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_CTRL-FLAG-UV_BR4_r1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_CTRL-FLAG-UV_BR3_r1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_THUMPD2-FLAG-UV_BR3_r1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_THUMPD2-FLAG-UV_BR2_r2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_THUMPD2-FLAG-UV_BR1_r2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_THUMPD2-FLAG-UV_BR3_r2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_CTRL-FLAG-UV_BR2_r2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_CTRL-FLAG-UV_BR3_r2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_THUMPD2-FLAG-UV_BR4_r1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_CTRL-FLAG-UV_BR1_r2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_CTRL-FLAG-UV_BR4_r2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_THUMPD2-FLAG-UV_BR4_r2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_THUMPD2-FLAG-UV_BR2_r1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_CTRL-FLAG-UV_BR1_r1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/OD_MK_N_Kleiber_181223_020224_Expl2_DIA_THUMPD2-FLAG-UV_BR1_r1.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/N_Kleiber_THUMPD2-FLAG_20231218.fasta"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053510/N_Kleiber_181223_020224_Expl2_THUMPD2-FLAG-UV.sne"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["henning.urlaub@mpinat.mpg.de"],"submitter":["Olexandr Dybkov"],"technology_type":["Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry","Data-independent acquisition","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Rna methylation","Trmt112","Thumpd2","Uhplc-esi-msms","Dia","U6 snrna maturation"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD053510"],"sample_protocol":["LC–ESI-MS/MS analyses of peptides were performed on an Orbitrap Exploris 480 (Thermo Fisher Scientific) instrument coupled to a nanoflow liquid chromatography system (UltiMate™3000 RSLCnano, Thermo Fisher Scientific). Samples were separated using a 60-minute method at a flow rate of 300 nl / min using 0.1% (v / v) FA (buffer A) and 80% (v / v) ACN, 0.08% (v / v) FA (buffer B). Two-step linear gradient was applied: first, 10-36%B in 40 min, followed by 5-min of 36-52%B. Eluting peptides were measured in positive mode using a data-independent method with 40 variable m/z windows covering a range of 350-1650. Resolution was set to 120 000 (MS1) and 30 000 FWHM (MS2); AGC targets, 300% (MS1) and 1000% (MS2); normalized collision energy, 30%; dynamic exclusion, 20s; maximum injection time, 20 (MS1) and 54 ms (MS2). Four biological replicates were measured with two replicate injections."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["The raw MS files were processed using the Spectronaut software (version 18.3, Biognosys) and the MS/MS spectra were searched against a database containing a UniProt human reference proteome (release 2024-01-24) as well as sequences of the tagged THUMPD2 and of common contaminants found in MS experiments. Protein identifications were filtered to a false discovery rate of 1% at the protein level by selecting only samples with a q-value < 0.01, and further data processing and analysis was performed using R (Version 4.4.0). After removal of decoy hits and potential contaminant entries, only hits with observations across all four replicates of the THUMPD2-His6-2xFLAG samples were considered for differential abundance analysis. MS2-intensity based abundances of peptides (PG.Quantity) were normalised by quantile normalisation, log2 transformed and used as quantitative values for calculation of log2 fold change (THUMPD2-His6-2xFLAG over His6-2xFLAG). p-values were calculated using a Welch two-sided t-test and sorted for significance by considering p-values < 0.05. No imputation of missing values was performed."],"omics_type":["Proteomics"],"labhead":["Henning Urlaub"],"instrument_platform":[""],"labhead_affiliation":["Bioanalytical Mass Spectrometry Group, Max Planck Institute for Multidisciplinary Sciences, Germany Bioanalytics, Institute for Clinical Chemistry, University Medical Center Goettingen, Germany"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["odybkov@gwdg.de"],"publication":["42031737 Kleiber N, Petrosyan J, Greve M, Thomé CC, Dybkov O, Tay LLE, Welp LM, Hackert P, Touboul D, Stark H, Bohnsack MT, Urlaub H, Herzel L, Graille M, Höbartner C, Bohnsack KE. 2'-O-methylation-dependent installation of N<sup>2</sup>-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly. Nat Commun. 2026 17(1):3793 10.1038/s41467-026-72355-2"],"submitter_affiliation":["Max Planck Institute for Multidisciplinary Sciences"],"submitter_country":["Germany"],"pubmed_abstract":["The internal stem loop (ISL) of the human U6 snRNA, which catalyzes pre-mRNA splicing, contains LARP7-dependent, snoRNA-guided 2'-O-methylations and an N2-methylguanosine (m2G) that is required for splicing of weak splice sites. Here, we show that installation of m2G72 by the THUMPD2-TRMT112 methyltransferase complex is one of the last maturation events during U6 snRNP biogenesis. We dissect features of THUMPD2 required for association with U6 and present an experimentally validated model of the THUMPD2-TRMT112-U6 complex. Using in vitro methylation assays as well as a newly developed m2G-sensitive deoxyribozyme to monitor U6-m2G72 levels in cellular RNAs, we reveal that 2'-O-methylations within the U6 ISL enhance methylation of G72. We show that m2G72 and the 2'-O-methylations in U6 independently and interdependently influence alternative splicing. Furthermore, our data demonstrate that 2'-O-methylations in the ISL are required for incorporation of U6 into snRNPs whereas m2G72 influences the progression of the U6 snRNP into larger assemblies, highlighting distinct roles of these modifications during spliceosome assembly."],"pubmed_title":["2'-O-methylation-dependent installation of N<sup>2</sup>-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly."],"pubmed_authors":["Kleiber Nicole N, Petrosyan Jonny J, Greve Maria M, Thomé Chairini C CC, Dybkov Olexandr O, Tay Laurianne L E LLE, Welp Luisa M LM, Hackert Philipp P, Touboul David D, Stark Holger H, Bohnsack Markus T MT, Urlaub Henning H, Herzel Lydia L, Graille Marc M, Höbartner Claudia C, Bohnsack Katherine E KE"],"additional_accession":[]},"is_claimable":false,"name":"Molecular insights into THUMPD2-mediated m2G methylation of the U6 snRNA","description":"THUMPD2 installs N2-methylguanosine (m2G) at position 72 of the U6 snRNA, and this modification, which lies at the catalytic core of the spliceosome, is required for efficient splicing of weak splice sites. However, when during the U6 lifecycle this modification is installed and what features of the U6 snRNA and THUMPD2 are required for methylation of G72 remain elusive. Here, we show that U6 associated with THUMPD2 is not oligouridylated and that late-acting U6 snRNP biogenesis factors are enriched with THUMPD2. We map RNA crosslinking sites within the N-terminal region and C-terminal Rossman-fold methyltransferase domain of THUMPD2, and show the requirement of these domains for THUMPD2 interaction with U6 in cells. Using a newly developed m2G-sensitive deoxyribozyme to monitor U6-m2G72 levels in cellular RNAs, we demonstrate the requirement of SAM binding and interaction with the THUMPD2 cofactor TRMT112 for efficient methylation. Our data further reveal that 2’-O-methylation of C62, C63 and A70 do not increase the affinity of THUMPD2 for the U6 internal stem-loop (ISL), but enhance m2G methylation of G72. Nucleotide substitutions within the loop region of the ISL that extend the stem similarly increase m2G72 installation, demonstrating that the stability of the ISL is key for methylation by THUMPD2. Together these results provide a new layer of understanding of how an RNA modification that fine-tunes pre-mRNA splicing is 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