Publications

2025

Zakrzewska-Placzek M, Golisz-Mocydlarz A, Kwasnik A, Krzyszton M, Niedzwiecka K, Kufel J. Defective Processing of Cytoplasmic and Chloroplast Ribosomal RNA in the Absence of Arabidopsis DXO1.  Plant Cell Environ. 2025 Feb 10. doi: 10.1111/pce.15425.

Tierney JAS, Świrski MI, Tjeldnes H, Kiran AM, Carancini G, Kiniry SJ, Michel AM, Kufel J, Valen E, Baranov PV. RiboSeq.Org: an integrated suite of resources for ribosome profiling data analysis and visualization. Nucleic Acids Res. 2025 Jan 6;53(D1):D268-D274. doi: 10.1093/nar/gkae1020.

2024

Tierney JAS, Świrski M, Tjeldnes H, Mudge JM, Kufel J, Whiffin N, Valen E, Baranov PV.(2024) Ribosome Decision Graphs for the Representation of Eukaryotic RNA Translation Complexity.Genome Res. 2024 May 15;34(4):530-538. doi: 10.1101/gr.278810.123.

2023

Zakrzewska-Placzek M, Golisz-Mocydlarz A, Krzyszton M, Piotrowska J, Lichocka M, Kufel J. (2023) The nucleolar protein NOL12 is required for processing of large ribosomal subunit rRNA precursors in Arabidopsis BMC Plant Biol. 2023 Nov 3;23(1):538. doi: 10.1186/s12870-023-04561-9.

Mititelu MB, Hudeček O, Gozdek A, Benoni R, Nešuta O, Krasnodębski S, Kufel J, Cahová H. (2023) Arabidopsis thaliana NudiXes have RNA-decapping activity. RSC Chem Biol. 2023 Jan 9;4(3):223-228. doi: 10.1039/d2cb00213b. 

2022

Kufel J., Diachenko N., Golisz A. (2022) Alternative splicing as a key player in the fine-tuning of the immunity response in Arabidopsis. Molecular Plant Pathology 23:1226-1238 doi:10.1111/mpp.13228

Krzyszton M, Kufel J (2022) Analysis of mRNA-derived siRNAs in mutants of mRNA maturation and surveillance pathways in Arabidopsis thaliana Sci Rep. 2022 Jan 27;12(1):1474. doi: 10.1038/s41598-022-05574-4.

2021

Golisz A, Krzyszton M, Stepien M, Dolata J, Piotrowska J, Szweykowska-Kulinska Z, Jarmolowski A, Kufel JM (2021)  Arabidopsis spliceosome factor SmD3 modulates immunity to Pseudomonas syringae infection Front Plant Sci. 3;12:765003.

2020

Doamekpor S , Gozdek A , Kwasnik A, Kufel J , Tong L (2020) A novel 5′-hydroxyl dinucleotide hydrolase activity for the DXO/Rai1 family of enzymes Nucleic Acids Res. 10;48(1):349-358.

Clerget G, Bourguignon-Igel V, Marmier-Gourrier N, Rolland N, Wacheul L, Manival X, Charron C, Kufel J, Méreau A, Senty-Ségault V, Tollervey D, L J Lafontaine D, Branlant C, Rederstorff M (2020) Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA Nucleic Acids Res. Apr 17;48(7):3848-3868

2019

Sulkowska A, Auber A, Sikorski PJ, Silhavy D, Auth M, Sitkiewicz E, Jean V, Merret R, Bousquet-Antonelli C, Kufel J (2019) RNA Helicases From the DEA(D/H)-box Family Contribute to Plant NMD Efficiency. Plant Cell Physiol 61, 144-157.

Monteuuis G, Miścicka A, Świrski M, Zenad L, Niemitalo O, Wrobel L, Alam J, Chacinska A, Kastaniotis AJ, Kufel J (2019) Non-canonical translation initiation in yeast generates a cryptic pool of mitochondrial proteins. Nucleic Acids Res 47, 5777-5791.

Kwasnik A, Wang VY, Krzyszton M, Gozdek A, Zakrzewska-Placzek M, Stepniak K, Poznanski J, Tong L, Kufel J (2019) Arabidopsis DXO1 links RNA turnover and chloroplast function independently of its enzymatic activity. Nucleic Acids Res 47, 4751-4764.

Kufel J, Grzechnik P (2019) Small Nucleolar RNAs Tell a Different Tale. Trends Genet 35, 104-117.

2018

Grzechnik P, Szczepaniak SA, Dhir S, Pastucha A, Parslow H, Matuszek Z, Mischo HE, Kufel J, Proudfoot NJ (2018) Nuclear fate of yeast snoRNA is determined by co-transcriptional Rnt1 cleavage. Nat Commun 9, 1783.

Wawer I, Golisz A, Sulkowska A, Kawa D, Kulik A, Kufel J (2018) mRNA Decapping and 5′-3′ Decay Contribute to the Regulation of ABA Signaling in Arabidopsis thaliana. Front Plant Sci 9, 312.

Krzyszton M, Zakrzewska-Placzek M, Kwasnik A, Dojer N, Karlowski W, Kufel J (2018) Defective XRN3-mediated transcription termination in Arabidopsis affects the expression of protein-coding genes. Plant J 93, 1017-1031.

2017

Tomecki R, Sikorski PJ, Zakrzewska-Placzek M (2017) Comparison of preribosomal RNA processing pathways in yeast, plant and human cells – focus of coordinated action of endo- and exoribonucleases. FEBS Lett. 591, 1801-1850.

2016

Wawiórka L, Molestak E, Szajwaj M, Michalec-Wawiórka B, Boguszewska B, Borkiewicz L, Liudkovska V, Kufel J, Tchórzewski M (2016) Functional analysis of the uL11 protein impact on translational machinery. Cell Cycle 15, 1060-1072.

Stirpe M, Palermo V, Ferrari M, Mroczek S, Kufel J, Falcone C, Mazzoni C (2016) Increased levels of RNA oxidation enhance the reversion frequency in aging pro-apoptotic yeast mutants. Apoptosis 22, 200-206.

2010 – 2015

Sikorski PJ, Zuber H, Philippe L, Sement FM, Canaday J, Kufel J, Gagliardi D, Lange H (2015) Distinct 18S rRNA precursors are targets of the exosome complex, the exoribonuclease RRP6L2 and the terminal nucleotidyl-transferase TRL in Arabidopsis thaliana. Plant J 83, 991-1004.

Skowronek E, Grzechnik P, Späth B, Marchfelder A, Kufel J (2014) tRNA 3′ processing in yeast involves tRNase Z, Rex1, and Rrp6. RNA 20, 115-30.

Kerényi F, Wawer I, Sikorski PJ, Kufel J, Silhavy D (2013) Phosphorylation of the N- and C-terminal UPF1 domains plays a critical role in plant nonsense-mediated mRNA decay. Plant J 76, 836-48.

Nyikó T, Kerényi F, Szabadkai L, Benkovics AH, Major P, Sonkoly B, Mérai Z, Barta E, Niemiec E, Kufel J, Silhavy D (2013) Plant nonsense-mediated mRNA decay is controlled by different autoregulatory circuits and can be induced by an EJC-like complex. Nucleic Acids Res 41, 6715-28.

Golisz A, Sikorski PJ, Kruszka K, Kufel J (2013) Arabidopsis thaliana LSM proteins function in mRNA splicing and degradation. Nucleic Acids Res 41, 6232-49.

Krzyszton M, Zakrzewska-Placzek M, Koper M, Kufel J (2012) Rat1 and Xrn2: The diverse functions of  the nuclear Rat1/Xrn2 exonuclease. Enzymes 31, 131-63.

Szczepaniak SA, Zuberek J, Darzynkiewicz E, Kufel J, Jemielity J (2012) Affinity resins containing enzymatically resistant mRNA cap analogs–a new tool for the analysis of cap-binding proteins. RNA 18, 1421-32.

Alexander RA, Barrass JD, Dichtl B, Kos M, Obtulowicz T, Robert M-C, Koper M, Karkusiewicz I, Mariconti L, Tollervey D, Dicht B, Kufel J, Bertrand E, Beggs JD (2010) RiboSys, a quantitative approach to study gene expression in Saccharomyces cerevisiae. RNA 16, 2570-2578.

Zakrzewska-Placzek M, Souret FF, Sobczyk GJ, Green PJ, Kufel J (2010) Arabidopsis thaliana XRN2 is required for primary cleavage in the pre-ribosomal RNA. Nucleic Acids Res 38, 4487-502.

2002 – 2010

Mroczek S, Kufel J (2008) Apoptotic signals induce specific degradation of ribosomal RNA in yeast. Nucleic Acids Res 36, 2874-2888.

Grzechnik P, Kufel J (2008) Polyadenylation linked to transcription termination directs the processing of snoRNA precursors in yeast. Mol Cell 32, 247-58.

El Hage A, Koper M, Kufel J, Tollervey D (2008) Efficient termination of transcription by RNA polymerase I requires the 5′ exonuclease Rat1 in yeast. Genes Dev 22, 1069-81.

Houalla R, Devaux F, Fatica A, Kufel J, Barrass D, Torchet C, Tollervey D (2006) Microarray detection of novel nuclear RNA substrates for the exosome. Yeast 23, 439-54.

Kufel J, Bousquet-Antonelli C, Beggs JD, Tollervey D (2004) Nuclear pre-mRNA decapping and 5′ degradation in yeast require the Lsm2-8p complex. Mol Cell Biol 24, 9646-9657.

Kufel J, Allmang C, Verdone L, Beggs J, Tollervey D (2003) A complex pathway for 3′ processing of the yeast U3 snoRNA. Nucleic Acids Res 31, 6788-6797.

Kufel J, Allmang C, Petfalski E, Beggs J, Tollervey D (2003) Lsm Proteins are required for normal processing and stability of ribosomal RNAs. J Biol Chem 278, 2147-2156.

Bousquet-Antonelli C, Milligan L, Thompson E, Kufel J, Tollervey D (2002) Processing of 3′-extended read-through transcripts by the exosome can generate functional mRNAs. Mol Cell 9, 1285-1296.