Scientific papers
Thapa P, Chikale RV, Szulc NA, Pandrea MT, Sztyler A, Jaggi K, Niklewicz M, Serwa RA, Hoppe T, Pokrzywa W. HSP70 inhibits CHIP E3 ligase activity to maintain germline function in Caenorhabditis elegans. J Biol Chem. 2024 Nov; 300(11):107864. doi: 10.1016/j.jbc.2024.107864
https://www.jbc.org/article/S0021-9258(24)02366-4/fulltext
Czarnocka-Cieciura A, Poznański J, Turtola M, Tomecki R, Krawczyk PS, Mroczek S, Orzeł W, Saha U, Jensen TH, Dziembowski A, Tudek A. Modeling of mRNA deadenylation rates reveal a complex relationship between mRNA deadenylation and decay. EMBO J. 2024 Dec;43(24):6525-6554. doi: 10.1038/s44318-024-00258-3
https://www.embopress.org/doi/full/10.1038/s44318-024-00258-3
Badepally NG, de Moura TR, Purta E, Baulin EF, Bujnicki JM. Cryo-EM Structure of raiA ncRNA From Clostridium Reveals a New RNA 3D Fold. J Mol Biol. 2024 Dec 1;436(23):168833. doi: 10.1016/j.jmb.2024.168833
https://www.sciencedirect.com/science/article/pii/S0022283624004625?via%3Dihub
Rydzanicz M, Kuzniewska B, Magnowska M, Wójtowicz T, Stawikowska A, Hojka A, Borsuk E, Meyza K, Gewartowska O, Gruchota J, Miłek J, Wardaszka P, Chojnicka I, Kondrakiewicz L, Dymkowska D, Puścian A, Knapska E, Dziembowski A, Płoski R, Dziembowska M. Mutation in the mitochondrial chaperone TRAP1 leads to autism with more severe symptoms in males. EMBO Mol Med. 2024 Nov;16(11):2976-3004. doi: 10.1038/s44321-024-00147-6
https://www.embopress.org/doi/full/10.1038/s44321-024-00147-6
Wolczyk M, Szymanski J, Trus I, Naz Z, Tame T, Bolembach A, Choudhury NR, Kasztelan K, Rappsilber J, Dziembowski A, Michlewski G. 5′ terminal nucleotide determines the immunogenicity of IVT RNAs. Nucleic Acids Res. 2025 Jan 24;53(3):gkae1252. doi: 10.1093/nar/gkae1252
https://academic.oup.com/nar/article/53/3/gkae1252/7929375?login=false
Czarnocka-Cieciura A, Brouze M, Gumińska N, Mroczek S, Gewartowska O, Krawczyk PS, Dziembowski A. Comprehensive analysis of poly(A) tails in mouse testes and ovaries using Nanopore Direct RNA Sequencing. Sci Data. 2025 Jan 10;12(1):43. doi: 10.1038/s41597-024-04226-8
https://www.nature.com/articles/s41597-024-04226-8
Idlin N, Krishnamoorthy S, Wolczyk M, Fakhri M, Lechowski M, Stec N, Milek J, Mandal PK, Cendrowski J, Spanos C, Dziembowska M, Mleczko-Sanecka K, Rappsilber J, Michlewski G. Effects of genetic ablation and pharmacological inhibition of HuR on gene expression, iron metabolism, and hormone levels. BMC Biol. 2025 Jan 23;23(1):24. doi: 10.1186/s12915-025-02131-z
https://bmcbiol.biomedcentral.com/articles/10.1186/s12915-025-02131-z
Szulc NA, Pokrzywa W. DEGRONOPEDIA: A practical guide to identifying and targeting protein degrons. Methods Enzymol. 2025;719:67-94. doi: 10.1016/bs.mie.2025.06.014
https://doi.org/10.1016/bs.mie.2025.06.014
Piechota M, Pokrzywa W. Quantitative insights into protein turnover and ubiquitination with HiBiT and NanoBRET. Methods Enzymol. 2025;719:95-120. doi: 10.1016/bs.mie.2025.06.026
https://doi.org/10.1016/bs.mie.2025.06.026
Gumińska N, Matylla-Kulińska K, Krawczyk PS, Maj M, Orzeł W, Mackiewicz Z, Brouze A, Mroczek S, Dziembowski A. Direct profiling of non-adenosines in poly(A) tails of endogenous and therapeutic mRNAs with Ninetails. Nat Commun. 2025 Mar 18;16(1):2664. doi: 10.1038/s41467-025-57787-6
https://doi.org/10.1038/s41467-025-57787-6
Abu Nahia K, Winata CL. Protocol for the preparation of zebrafish whole heart cell suspension for single-cell analyses. STAR Protoc. 2025 Mar 21;6(1):103586. doi: 10.1016/j.xpro.2024.103586
https://doi.org/10.1016/j.xpro.2024.103586
Brouze M, Szpila M, Czerwińska AM, Antczak W, Mroczek S, Kuliński TM, Hojka-Osińska AM, Cysewski D, Gewartowska O, Adamska D, Gruchota J, Borsuk E, Dziembowski A. DIS3L, cytoplasmic exosome catalytic subunit, is essential for development but not cell viability in mice. RNA. 2025 Apr;31(5):646-662. doi: 10.1261/rna.080350.124
https://doi.org/10.1261/rna.080350.124
Krawczyk PS, Mazur M, Orzeł W, Gewartowska O, Jeleń S, Antczak W, Kasztelan K, Brouze A, Matylla-Kulińska K, Gumińska N, Tarkowski B, Owczarek EP, Affek K, Turowski P, Tudek A, Sroka M, Śpiewla T, Kusio-Kobiałka M, Wesołowska A, Nowis D, Golab J, Kowalska J, Jemielity J, Dziembowski A, Mroczek S. Re-adenylation by TENT5A enhances efficacy of SARS-CoV-2 mRNA vaccines. Nature. 2025 May;641(8064):984-992. doi: 10.1038/s41586-025-08842-1
https://doi.org/10.1038/s41586-025-08842-1
Kaus-Drobek M, Nowacka M, Gewartowska M, Korzeniowska nee Wiweger M, Jensen MR, Møretrø T, Heir E, Nowak E, Sabała I. From discovery to potential application: engineering a novel M23 peptidase to combat Listeria monocytogenes. Sci Rep. 2025 May 5;15(1):15628. doi: 10.1038/s41598-025-99141-2
https://doi.org/10.1038/s41598-025-99141-2
Slyvka A, Rathore I, Yang R, Gewartowska O, Kanai T, Lountos GT, Skowronek K, Czarnocki-Cieciura M, Wlodawer A, Bochtler M. Activity and structure of human (d)CTP deaminase CDADC1. Proc Natl Acad Sci U S A. 2025 May 13;122(19):e2424245122. doi: 10.1073/pnas.2424245122
https://doi.org/10.1073/pnas.2424245122
Wardaszka-Pianka P, Kuźniewska B, Gumińska N, Hojka-Osińska A, Puchalska M, Miłek J, Stawikowska A, Krawczyk P, Pauzin FP, Wojtowicz T, Radwanska K, Bramham CR, Dziembowski A, Dziembowska M. Terminal nucleotidyltransferase Tent2 microRNA A-tailing enzyme regulates excitatory/inhibitory balance in the hippocampus. RNA. 2025 Jun;31(6):756-771. doi: 10.1261/rna.080240.124
https://doi.org/10.1261/rna.080240.124
Sołtys K, Skowronek K, Bystranowska D, Wycisk K, Ożyhar A. The intrinsically disordered AB region: a key modulator of the molecular properties of human RXRγ. Cell Commun Signal. 2025 May 26;23(1):243. doi: 10.1186/s12964-025-02247-3
https://doi.org/10.1186/s12964-025-02247-3
Hurley JH, Coyne AN, Miączyńska M, Stenmark H. The expanding repertoire of ESCRT functions in cell biology and disease. Nature. 2025 Jun 25;642(8069):877-888. doi: 10.1038/s41586-025-08950-y
https://doi.org/10.1038/s41586-025-08950-y
Domagala J, Grzywa TM, Baranowska I, Justyniarska M, Tannir R, Graczyk-Jarzynka A, Kusowska A, Lecka M, Poreba M, Fidyt K, Marhelava K, Pilch Z, Picard LK, Wegierski T, Jastrzebski K, Krawczyk M, Klopotowska M, Granica M, Urlaub D, Hajduk S, Neeser A, Moros S, Kozlowski P, Bobrowicz M, Miączyńska M, Ma L, Watzl C, Winiarska M. Ammonia suppresses the antitumor activity of natural killer cells and T cells by decreasing mature perforin. Cancer Res. 2025 Jul 2;85(13):2448-2467. doi: 10.1158/0008-5472.CAN-24-0749
https://doi.org/10.1158/0008-5472.CAN-24-0749
Taylor GCA, Macdonald L, Szulc NA, Gudauskaite E, Hernandez Moran B, Brisbane JM, Donald M, Taylor E, Zheng D, Gu B, Mill P, Yeyati PL, Pokrzywa W, Ribeiro de Almeida C, Wood AJ. Tissue-specific consequences of tag fusions on protein expression in transgenic mice. PLoS Genet. 2025 Aug 25;21(8):e1011830. doi: 10.1371/journal.pgen.1011830
https://doi.org/10.1371/journal.pgen.1011830
Mackiewicz Z, Liudkovska V, Dziembowski A. Excretory gland cell and NSPC genes in C. elegans: investigating their physiological roles. Genetics. 2025 Sep 3;231(1):iyaf125. doi: 10.1093/genetics/iyaf125
https://doi.org/10.1093/genetics/iyaf125
Urbanska M, Sadowski K, Stawikowska A, Liszewska E, Mlostek M, Grajkowska W, Kotulska K. Trifluoperazine, an Antipsychotic Drug, Inhibits Viability of Cells Derived From SEGA and Cortical Tubers Cultured In Vitro. J Neurochem. 2025 Oct;169(10):e70247. doi: 10.1111/jnc.70247
https://doi.org/10.1111/jnc.70247
Gumińska N, Pauzin FP, Kuźniewska B, Miłek J, Wardaszka-Pianka P, Krawczyk PS, Mroczek S, Jeleń S, Pagenhart PU, Bramham CR, Dziembowski A, Dziembowska M. Polyadenylation landscape of in vivo long-term potentiation in the rat brain. RNA. 2025 Dec;31(12):1712-1734. doi: 10.1261/rna.080485.125
https://doi.org/10.1261/rna.080485.125
Nirwal S, Czarnocki-Cieciura M, Zajko W, Skowronek K, Szczepanowski RH, Nowotny M. Structural snapshots of the mechanism of ATP-dependent DNA damage recognition by UvrA. Nat Commun. 2026 Jan;17(1):387. doi: 10.1038/s41467-025-67075-y
https://doi.org/10.1038/s41467-025-67075-y
Neary MT, Mulder LM, Leime CO, MacLoughlin R, Grassiri B, Baranowski Ł, Kowalski PS, Crean AM, Ryan KB. Pulmonary delivery of siRNA lipoplexes and lipid nanoparticles using a vibrating mesh nebuliser. Eur J Pharm Sci. 2026 Jan 1;216:107386. doi: 10.1016/j.ejps.2025.107386
https://doi.org/10.1016/j.ejps.2025.107386
Sordyl D, Boileau E, Bernat A, Maiti S, Mukherjee S, Moafinejad SN, Amiri Farsani M, Shavina A, Cappannini A, Agostini G, Conticello SG, Stefaniak F, Dieterich C, Purta E, Bujnicki JM. MODOMICS: a database of RNA modifications and related information. 2025 update and 20th anniversary. Nucleic Acids Res. 2026 Jan 6;54(D1):D219-D225. doi: 10.1093/nar/gkaf1284
https://doi.org/10.1093/nar/gkaf1284
Wasilewska I, Majewski Ł, Adamek-Urbańska D, Baranykova S, Castañeda-Tamez P, Wittig I, Macias M, Szybińska A, Methner A. Tmbim5 and Slc8b1 cooperate in tissue-specific mitochondrial calcium regulation in zebrafish. Commun Biol. 2026 Jan 8;9(1):218. doi: 10.1038/s42003-025-09494-7
https://doi.org/10.1038/s42003-025-09494-7
Fedenko A, Czapinska H, Krämer A, Stölzel F, Bochtler T, Bochtler M. Etiology of TP53 mutated complex karyotype acute myeloid leukemia. Leukemia. 2026 Feb;40(2):444-448. doi: 10.1038/s41375-025-02835-9
https://doi.org/10.1038/s41375-025-02835-9
Zurawska G, Sas Z, Jończy A, Mahadeva R, Slusarczyk P, Chwałek M, Seehofer D, Damm G, Mazgaj R, Skórzyński M, Kulecka M, Rumieńczyk I, Moulin M, Jastrzębski K, Waldron K, Mikula M, Etzerodt A, Serwa R, Miączyńska M, Rygiel TP, Mleczko-Sanecka K. Liver sinusoidal endothelial cells constitute a major route for hemoglobin clearance. EMBO Rep. 2026 Feb;27(3):598-628. doi: 10.1038/s44319-025-00673-5
https://doi.org/10.1038/s44319-025-00673-5
Kuliński TM, Gewartowska O, Mahé M, Kasztelan K, Durys N, Stroynowska-Czerwińska A, Jedynak-Slyvka M, Owczarek EP, Chaudhury D, Nowotny M, Pękowska A, Séraphin B, Dziembowski A. DIS3 mutations enhance AID-driven translocations during B-cell activation, promoting transformation to multiple myeloma. Nat Commun. 2026 Mar 14;17(1):3976. doi: 10.1038/s41467-026-70386-3
https://doi.org/10.1038/s41467-026-70386-3
Antczak W, Szpila M, Sałas K, Daszczuk P, Linke V, Miączyńska M, Dziembowski A, Gewartowska O. Degron models: a toolbox for rapid in vivo depletion of essential proteins regulating mRNA metabolism. Commun Biol. 2026 Mar 18;9:615. doi: 10.1038/s42003-026-09828-z
https://doi.org/10.1038/s42003-026-09828-z
Silva RMB, Slyvka A, Lee YJ, Guan C, Lund SR, Raleigh EA, Skowronek K, Kuska MS, Bochtler M, Weigele PR. A single viral enzyme drives tRNA-dependent hypermodification of DNA at adenine. Nat Commun. 2026 Apr 3;17(1):4787. doi: 10.1038/s41467-026-70671-1
https://doi.org/10.1038/s41467-026-70671-1
Mackiewicz Z, Liudkovska V, Dziembowski A. TENT-5 polyadenylates and regulates male-specific transcripts in Caenorhabditis elegans. G3 (Bethesda). 2026 May 6;16(5):jkag058. doi: 10.1093/g3journal/jkag058
https://doi.org/10.1093/g3journal/jkag058
Wolczyk M, Szymanski J, Trus I, Naz Z, Idlin N, Lechowski M, Baranowska E, Bis A, Nowak JS, Tame T, Jackiewicz J, Nowak E, Wuebben C, Hartmann G, Rappsilber J, Michlewski G. 5′-Triphosphate guanosine RNAs recruit GTP-binding proteins to suppress RIG-I/IFN type I signaling. Mol Cell. 2026 Jun 4;86(11):2124-2140.e11. doi: 10.1016/j.molcel.2026.04.014
https://doi.org/10.1016/j.molcel.2026.04.014
Sordyl D, Cielesz J, Bohdan DR, Baulin EF, Bujnicki JM. ARTEM server: an online tool for nucleic acid 3D motif searches, 3D structure superposition and structure-based alignment. Nucleic Acids Res. 2026 Jul 11;54(W1):W177-W183. doi: 10.1093/nar/gkag428
https://doi.org/10.1093/nar/gkag428