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ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/checksum.txtftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2PAR_rep1.raw.mzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2UV_rep1.raw.mzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2PAR_rep2.raw.mzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2UV_rep2.raw.mzMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2UV_rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2UV_rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2PAR_rep2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2PAR_rep1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/210302_hsapiens_SwissProt_20381seq_MQ2030contaminants.fastaftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProRNAXL_PD2PAR_rep1_perc_0.0100_XLs.idXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2PAR_rep2_perc_0.0100_XLs.idXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2UV_rep2_perc_0.0100_XLs.idXMLftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD053619/LWelp_MR_N_Kanwal_270123_170223_ProtRNAXL_PD2UV_rep1_perc_0.0100_XLs.idXMLprimaryOK200katherine.bohnsack@med.uni-goettingen.deLuisa WelpData-dependent acquisitionMass SpectrometryNot availableMethyltransferaseCrosslinking mass spectrometryMethylationSnrnahttps://www.ebi.ac.uk/pride/archive/projects/PXD053619Cell CultureRNA-protein crosslinking and mass spectrometry for mapping RNA-protein contacts Sample preparation HEK293 cells expressing THUMPD2-His6-2xFLAG were washed in 1x PBS and crosslinked using UV (ultraviolet) or PAR (photoactivatable-ribonucleoside-enhanced) crosslinking methods in a Stratalinker (Stratagene). For UV-crosslinking, cells were exposed to UV light at a wavelength of 254 nm for a total energy of 2400 mJ/cm2. For PAR-crosslinking, cells were grown in media supplemented with 100 μM 4-thiouridine (Sigma-Aldrich) for 6 h prior to crosslinking at 365 nm for 360 mJ/cm2. Crosslinked cells were collected by scraping and pellets were lysed by sonicating in IP buffer (50 mM Tris–HCl pH 7.4, 150 mM NaCl, 0.5 mM EDTA, 0.1% (v/v) Triton X-100 and 10% (v/v) glycerol) supplemented with 1x cOmplete protease inhibitor cocktail (Roche). Lysates were centrifuged at 20,000 xg for 15 min and soluble proteins were added to Anti-FLAG® M2 magnetic beads (Sigma-Aldrich) pre-equilibrated in IP buffer. After incubating for 3 h at 4°C, the beads were washed five times with IP buffer. Proteins and RNA-protein complexes bound to beads were eluted using 250 μg/ml of 3x FLAG peptide (Sigma-Aldrich) in 1x TBS for 1 h at 4°C. Eluates were precipitated using 3 volumes of ethanol and further sample processing was performed as described in (1) with minor modifications. Briefly, the protein-RNA pellet was dissolved in 4 M urea, 50 mM Tris-HCl pH 7.5 by sonication, following dilution to 1 M urea with 50 mM Tris-HCl pH 7.5. For RNA digestion, 500 U PierceTM Universal Nuclease (Thermo Fisher Scientific) and 200 U nuclease p1 (NEB) were added following incubation at 37 °C for 2 h. 10 μg RNase A (EN0531, Thermo Fisher Scientific) and 1U RNase T1 (Thermo Fisher Scientific) were added subsequently followed by 2 h incubation at 37°C. Proteins were digested overnight at 37°C using 4 μg trypsin (Promega). Sample cleanup was performed twice using C18 micro spin columns (Harvard Apparatus) according to the manufacturer’s instructions. Briefly, samples were acidified to pH 3 using formic acid (FA) and adjusted to 2% (v/v) acetonitrile (ACN). After column equilibration, samples were loaded twice and washed three times with 5% (v/v) ACN, 0.1% (v/v) FA. Elution was performed in two steps using 80% (v/v) ACN, 0.1% (v/v) FA and 50% (v/v) ACN, 0.1% (v/v) FA. Eluates were dried in a speed vac concentrator. Crosslinked peptides were enriched using TiO2 columns (in-house; Titansphere 5 μm; GL Sciences), as described previously (1). Briefly, samples were dissolved in buffer A (5% (v/v) glycerol, 80% (v/v) ACN, 5% (v/v) trifluoroacetic acid (TFA)) and loaded onto each three equilibrated TiO2 columns. Washing was performed three times with buffer A, three times with buffer B (60% (v/v) ACN, 5% (v/v) TFA) and once with 60% (v/v) ACN, 0.1% (v/v) TFA. Samples were eluted using ammonia solution and dried in a speed vac concentrator before LC-ESI-MS/MS analysis.” Mass Spectrometry Enriched peptide-(oligo)nucleotides were dissolved in 2% (v / v) ACN, 0.05% (v / v) TFA. LC–MS / MS analyses were performed on an Orbitrap Exploris 480 (Thermo Fisher Scientific) instrument coupled to a nanoflow liquid chromatography system (UltiMate™3000 RSLCnano, Thermo Fisher Scientific). Sample separation was performed over 58 min 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) and a linear gradient from 10% to 45% buffer B in 44 min. Eluting peptide-(oligo)nucleotides were analysed in positive mode using a data-dependent top 20 acquisition method. Resolution was set to 120 000 (MS1) and 30 000 FWHM (MS2); scan range ( m / z ), 350–1600; AGC targets, 10 6 (MS1) and 10 5 (MS2); normalized collision energy, 28%; dynamic exclusion, 9 s; maximum injection time, 60 (MS1) and 120 ms (MS2). Measurements were performed in two replicate injections.PrideNot availableMS data were analysed and manually validated using the OpenMS pipeline NuXL (unpublished) and OpenMS TOPPASViewer (1). Crosslink sites are reported at 1% spectrum level FDR.ProteomicsKatherine BohnsackUniversity Medical Center Göttingen Department of Molecular Biology,37073 Göttingen, GermanyPARTIALHomo Sapiens (human)lwelp@gwdg.de42031737 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 N2-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly. Nat Commun. 2026 17(1):3793 10.1038/s41467-026-72355-2Max-Planck-Institute for Biophysical ChemistryGermanyThe 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.2'-O-methylation-dependent installation of N2-methylguanosine in the U6 internal stem loop facilitates efficient spliceosome assembly.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 KEfalseMolecular insights into THUMPD2-mediated m2G methylation of the U6 snRNAMMARY 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 introduced.2026-05-252024-07-04PXD053619NEWT:3555NEWT:71647NEWT:330879NEWT:260201NEWT:35554NCBITaxon:12939NEWT:377960NEWT:32046NEWT:544496NEWT:59529NEWT:2042546NEWT:32049NEWT:1392696NEWT:259447NEWT:295546NCBITaxon:2719036NEWT:45351NEWT:445974NEWT:43179NEWT:180454NEWT:5722NCBITaxon:1280NEWT:112503NEWT:1129NEWT:309807NEWT:10245NEWT:55153NEWT:89184NEWT:309800NEWT:281395NEWT:1211601NEWT:876138NEWT:44271NEWT:193516NEWT:351581NEWT:43186NEWT:428146NEWT:1117NEWT:498257NEWT:10036NEWT:1590NEWT:498019NEWT:1351NEWT:1438992NEWT:1352NEWT:2649997NEWT:1147161NEWT:661410NEWT:638632NEWT:43150NEWT:263737NEWT:224326NEWT:1333499NEWT:376619NCBITaxon:79857NEWT:1096976NEWT:5702NEWT:95648NEWT:1589NEWT:135622NEWT:1349NEWT:35786NEWT:1580NEWT:399784NEWT:96731NEWT:383379NEWT:1401257NEWT:418106NEWT:10029NEWT:913645NEWT:44491NEWT:641809NEWT:27933NEWT:556484NEWT:317447NEWT:4688NEWT:7955NEWT:7719NEWT:7959NEWT:2261NEWT:868565NEWT:135674NEWT:94323NEWT:31156NEWT:3112NEWT:79329NEWT:4442NEWT:192875NEWT:1214915NEWT:30069NEWT:12637NEWT:59729NEWT:2164133NEWT:284218NEWT:295105NEWT:108061NEWT:60711NEWT:1316931NEWT:224308NEWT:3347NEWT:511145NEWT:160621NEWT:212790NEWT:931281NEWT:4432NEWT:5762NEWT:5763NEWT:658457NEWT:1310161NEWT:77133NEWT:295358NEWT:145481NEWT:1310165NEWT:29058NCBITaxon:79824NEWT:2246NEWT:2652724NEWT:5757NEWT:68415NCBITaxon:4563NEWT:5755NEWT:44688NEWT:44689NEWT:44447NEWT:752555NEWT:498211NEWT:5759NEWT:347256NEWT:1736231NEWT:5518NEWT:398007NEWT:1527468NEWT:1392NEWT:498217NEWT:498216NEWT:2242NEWT:11320NEWT:286NEWT:391619NEWT:246196NEWT:287NEWT:246197NEWT:145458NEWT:633149NEWT:1149786NEWT:10239NEWT:68895NEWT:44685NEWT:161934NEWT:4897NEWT:1148NEWT:5744NEWT:72901NEWT:213863NEWT:5508NEWT:3329NEWT:5507NEWT:410661NEWT:55571NEWT:35500NEWT:1235816NEWT:1140NCBITaxon:2157NEWT:1143NEWT:4896NEWT:1287689NEWT:1390NEWT:11557NEWT:1094343NEWT:1462472NEWT:1336795NEWT:644042NEWT:294NEWT:1773NEWT:1182590NEWT:3712NEWT:82380NEWT:3711NEWT:935293NEWT:375146NEWT:270643NEWT:2065263NEWT:177437NEWT:1772NEWT:10418NEWT:118698NEWT:1616117NEWT:263NEWT:118696NEWT:34865NEWT:52283NEWT:11988NEWT:284812NEWT:8175NEWT:400667NEWT:43330NEWT:1603293NEWT:408169NEWT:44664NEWT:47946NEWT:459758NEWT:3702NEWT:1245466NEWT:243277NEWT:1246791NEWT:7067NEWT:118694NEWT:586722NEWT:2850NEWT:118691NEWT:34871NEWT:33548NEWT:274NEWT:7070NCBITaxon:287NEWT:408172NEWT:408170NEWT:96794NEWT:3708NEWT:332648NEWT:44670NEWT:536231NEWT:376219NEWT:219813NEWT:1510NEWT:1436733NEWT:460519NEWT:1247411NEWT:1515NEWT:572307NEWT:1432138NEWT:9238NEWT:1424507NEWT:1194599NEWT:272844NEWT:1303443NEWT:9483NEWT:333760NEWT:485NEWT:34607NEWT:56636NEWT:1513458NEWT:1233681NCBITaxon:40559NEWT:506599NEWT:2853422NEWT:81077NEWT:84588NEWT:1679718NEWT:480NEWT:65349NEWT:67767NEWT:46835NEWT:109757NEWT:582580NEWT:300852NEWT:1502NEWT:128017NEWT:376686NEWT:95486NEWT:508771NEWT:1883446NEWT:253NCBITaxon:2759NEWT:1233435NEWT:93061NEWT:93062NEWT:34613NCBITaxon:4932NEWT:1748NEWT:109760NEWT:29031NEWT:108673NEWT:943274NEWT:644223NEWT:1263082NEWT:235443NEWT:108458NEWT:5936NEWT:272623NEWT:272624NEWT:320637NEWT:886559NEWT:3750NEWT:55521NEWT:983964NEWT:118499NEWT:11706NEWT:32644NEWT:527796NEWT:1130798NEWT:55529NEWT:499175NEWT:109779NEWT:3745NEWT:1715989NCBITaxon:4751NEWT:476272NEWT:3747NEWT:195051NEWT:3988NEWT:1116234NEWT:561007NEWT:1255228NEWT:649908NEWT:410289NEWT:373153NEWT:3983NEWT:203696NEWT:472NEWT:352472NEWT:97441NEWT:1154756NEWT:1071661NEWT:1202531NEWT:1202532NEWT:360094NEWT:1408223NEWT:470NEWT:1408224NEWT:41364NEWT:5911NEWT:1313NEWT:1218097NEWT:1080348NCBITaxon:50557NEWT:1314NEWT:39251NEWT:39491NEWT:212142NCBITaxon:5811NEWT:29491NEWT:101841NEWT:153481NEWT:2014887NEWT:1499105NEWT:33952NEWT:445NEWT:153009NEWT:261756NEWT:571256NEWT:40483NEWT:63366NEWT:63367NEWT:688333NEWT:215402NCBITaxon:548681NEWT:318586NCBITaxon:5820NEWT:1547NEWT:272634NEWT:198107NEWT:9031NEWT:27292NEWT:1872122NEWT:1308NEWT:7091NEWT:1034015NEWT:760568NEWT:141262NEWT:108931NEWT:1293497NEWT:1055524NEWT:4087NEWT:9778NEWT:306NEWT:150475NEWT:303NEWT:267872NEWT:97477NEWT:7111NEWT:347515NEWT:172269NEWT:9534NEWT:6269NEWT:5180NEWT:256737NEWT:4090NEWT:4092NEWT:9541NEWT:8694NEWT:4093NEWT:33936NEWT:4096NEWT:8692NEWT:2903NEWT:185579NEWT:941442NEWT:536088NEWT:13076NEWT:1226408NEWT:7108NEWT:40479NEWT:43989NEWT:4076NEWT:142615NEWT:317NEWT:1006581NEWT:33940NEWT:885318NEWT:39488NEWT:550NEWT:4081NEWT:273068NEWT:554NEWT:98334NEWT:451516NEWT:552NEWT:231663NEWT:4084NEWT:1325291NEWT:63577NEWT:36185NEWT:1054211NEWT:1225786NEWT:7574NEWT:1715256NEWT:30640NEWT:575412NEWT:929793NEWT:1507179NEWT:29204NEWT:28112NEWT:114155NEWT:6493NEWT:6494NEWT:6491NEWT:507601NEWT:520NEWT:186441NEWT:634955NEWT:643680NEWT:214092NCBITaxon:6157NEWT:6239NEWT:13095NEWT:162425NEWT:104105NEWT:216257NEWT:102169NEWT:208893NEWT:9986NEWT:4054NEWT:8654NEWT:8658NEWT:1268063NEWT:8657NEWT:8655NEWT:5147NEWT:98351NEWT:1263854NEWT:118503NEWT:2059687NEWT:160488NEWT:63558NEWT:28104NEWT:207559NEWT:407821NCBITaxon:2NEWT:85057NEWT:985076NEWT:568708NEWT:1215323NEWT:986NEWT:52641NEWT:7159NEWT:267671NEWT:28532NEWT:7160NEWT:353152NEWT:8496NEWT:7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