Nowacki, Mariusz

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2024

Stefanov, Bozhidar-Adrian; Ajuh, Elvis; Allen, Sarah; Nowacki, Mariusz (2024). Eukaryotic release factor 1 from Euplotes promotes frameshifting at premature stop codons in human cells. iScience, 27(4) Elsevier 10.1016/j.isci.2024.109413

Liu, Yongqiang; Niu, Junhua; Ye, Fei; Solberg, Therese; Lu, Borong; Wang, Chundi; Nowacki, Mariusz; Gao, Shan (2024). Dynamic DNA N 6-adenine methylation (6mA) governs the encystment process, showcased in the unicellular eukaryote Pseudocohnilembus persalinus. Genome research, 34(2), pp. 256-271. Cold Spring Harbor, N.Y 10.1101/gr.278796.123

Zhang, Fukai; Bechara, Sebastian; Nowacki, Mariusz (2024). Structural maintenance of chromosomes (SMC) proteins are required for DNA elimination in Paramecium. Life science alliance, 7(2) EMBO Press 10.26508/lsa.202302281

2023

Solberg, Therese; Mason, Victor; Wang, Chundi; Nowacki, Mariusz (2023). Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium. Cell reports, 42(3), p. 112213. Cell Press 10.1016/j.celrep.2023.112213

2022

Singh, Aditi; Maurer-Alcalá, Xyrus X; Solberg, Therese; Haeussermann, Lilia; Gisler, Silvan; Ignarski, Michael; Swart, Estienne C; Nowacki, Mariusz (2022). Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium. The EMBO journal, 41(22), e111839. EMBO Press 10.15252/embj.2022111839

Wang, Chundi; Solberg, Therese; Maurer-Alcalá, Xyrus X; Swart, Estienne C; Gao, Feng; Nowacki, Mariusz (2022). A small RNA-guided PRC2 complex eliminates DNA as an extreme form of transposon silencing. Cell reports, 40(8), p. 111263. Cell Press 10.1016/j.celrep.2022.111263

Bechara, Sebastian; Kabbani, Lyna; Maurer Alcala, Xyrus; Nowacki, Mariusz (2022). Identification of novel, functional long non-coding RNAs involved in programmed, large scale genome rearrangements. RNA, 28(8), pp. 1110-1127. Cold Spring Harbor Laboratory Press 10.1261/rna.079134.122

Rzeszutek, Iwona; Swart, Estienne C; Pabian-Jewuła, Sylwia; Russo, Antonietta; Nowacki, Mariusz (2022). Early developmental, meiosis-specific proteins - Spo11, Msh4-1, and Msh5 - Affect subsequent genome reorganization in Paramecium tetraurelia. Biochimica et biophysica acta. Molecular cell research, 1869(6), p. 119239. Elsevier 10.1016/j.bbamcr.2022.119239

2020

Allen, Sarah E.; Nowacki, Mariusz (2020). Roles of non-coding RNAs in ciliate genome architecture. Journal of molecular biology, 432(15), pp. 4186-4198. Elsevier 10.1016/j.jmb.2019.12.042

2019

Maurer-Alcalá, Xyrus X.; Nowacki, Mariusz (2019). Evolutionary origins and impacts of genome architecture in ciliates. Annals of the New York Academy of Sciences, 1447(1), pp. 110-118. New York Academy of Sciences 10.1111/nyas.14108

2018

Bischerour, Julien; Bhullar, Simran; Denby Wilkes, Cyril; Régnier, Vinciane; Mathy, Nathalie; Dubois, Emeline; Singh, Aditi; Swart, Estienne Carl; Arnaiz, Olivier; Sperling, Linda; Nowacki, Mariusz; Bétermier, Mireille (2018). Six domesticated PiggyBac transposases together carry out programmed DNA elimination in . eLife, 7 eLife Sciences Publications 10.7554/eLife.37927

Nowacki, Mariusz; Höhener, Cristina; Hug, Iris Sandra (2018). Dicer-like Enzymes with Sequence Cleavage Preferences. Cell, 173(1), 234-247.e7. Cell Press 10.1016/j.cell.2018.02.029

Neeb, Zachary Thomas; Nowacki, Mariusz (2018). RNA-mediated transgenerational inheritance in ciliates and plants. Chromosoma, 127(1), pp. 19-27. Springer 10.1007/s00412-017-0655-4

Michelini, Flavia; Jalihal, Ameya P.; Francia, Sofia; Meers, Chance; Neeb, Zachary Thomas; Rossiello, Francesca; Gioia, Ubaldo; Aguado, Julio; Jones-Weinert, Corey; Luke, Brian; Biamonti, Giuseppe; Nowacki, Mariusz; Storici, Francesca; Carninci, Piero; Walter, Nils G.; Fagagna, Fabrizio d’Adda di (2018). From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chemical reviews, 118(8), pp. 4365-4403. American Chemical Society 10.1021/acs.chemrev.7b00487

Bhullar, Simran; Denby Wilkes, Cyril; Arnaiz, Olivier; Nowacki, Mariusz; Sperling, Linda; Meyer, Eric (2018). A mating-type mutagenesis screen identifies a zinc-finger protein required for specific DNA excision events in Paramecium. Nucleic acids research, 46(18), pp. 9550-9562. Oxford University Press 10.1093/nar/gky772

Singh, Aditi; Vancura, Adrienne; Woycicki, Rafal K.; Hogan, Daniel J; Hendrick, Alan G; Nowacki, Mariusz (2018). Determination of the presence of 5-methylcytosine in Paramecium tetraurelia. PLoS ONE, 13(10), e0206667. Public Library of Science 10.1371/journal.pone.0206667

2017

Allen, Sarah Elizabeth; Hug, Iris Sandra; Pabian, Sylwia Weronika; Rzeszutek, Iwona Maria; Höhener, Cristina; Nowacki, Mariusz (2017). Circular Concatemers of Ultra-Short DNA Segments Produce Regulatory RNAs. Cell, 168(6), 990-999.e7. Cell Press 10.1016/j.cell.2017.02.020

Allen, Sarah Elizabeth; Nowacki, Mariusz (2017). Necessity Is the Mother of Invention: Ciliates, Transposons, and Transgenerational Inheritance. Trends in genetics, 33(3), pp. 197-207. Elsevier Current Trends 10.1016/j.tig.2017.01.005

Slabodnick, Mark M; Ruby, J Graham; Reiff, Sarah B; Swart, Estienne Carl; Gosai, Sager; Prabakaran, Sudhakaran; Witkowska, Ewa; Larue, Graham E; Fisher, Susan; Freeman, Robert M; Gunawardena, Jeremy; Chu, William; Stover, Naomi A; Gregory, Brian D; Nowacki, Mariusz; Derisi, Joseph; Roy, Scott William; Marshall, Wallace F; Sood, Pranidhi (2017). The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Current Biology, 27(4), pp. 569-575. Cell Press 10.1016/j.cub.2016.12.057

Furrer, Dominique; Swart, Estienne Carl; Kraft, Matthias Fabian; Sandoval, Pamela Yohanna de Lourdes; Nowacki, Mariusz (2017). Two Sets of Piwi Proteins Are Involved in Distinct sRNA Pathways Leading to Elimination of Germline-Specific DNA. Cell reports, 20(2), pp. 505-520. Cell Press 10.1016/j.celrep.2017.06.050

2016

Swart, Estienne Carl; Serra, Valentina; Petroni, Giulio; Nowacki, Mariusz (2016). Genetic Codes with No Dedicated Stop Codon: Context-Dependent Translation Termination. Cell, 166(3), pp. 691-702. Cell Press 10.1016/j.cell.2016.06.020

Bracht, John R; Wang, Xing; Shetty, Keerthi; Chen, Xiao; Uttarotai, Grace J; Callihan, Evan C; McCloud, Sierra S; Clay, Derek M; Wang, Jingmei; Nowacki, Mariusz; Landweber, Laura F (2016). Chromosome fusions triggered by noncoding RNA. RNA biology, 14(5), pp. 620-631. Landes Bioscience 10.1080/15476286.2016.1195940

Nowacki, Mariusz; Witzany, Guenther (eds.) (2016). Biocommunication of Ciliates. Cham: Springer 10.1007/978-3-319-32211-7

Allen, Sarah Elizabeth; Nowacki, Mariusz (2016). RNA-Guided Genome Editing. In: Witzany, Guenther; Nowacki, Mariusz (eds.) Biocommunication of Ciliates (pp. 35-50). Cham: Springer 10.1007/978-3-319-32211-7_3

2015

Swart, Estienne Carl; Nowacki, Mariusz (2015). The eukaryotic way to defend and edit genomes by sRNA-targeted DNA deletion. Annals of the New York Academy of Sciences, 1341, pp. 106-114. Blackwell 10.1111/nyas.12636

2014

Ignarski, Michael; Singh, Aditi; Swart, Estienne Carl; Arambasic, Miroslav; Sandoval, Pamela Yohanna de Lourdes; Nowacki, Mariusz (2014). Paramecium tetraurelia chromatin assembly factor-1-like protein PtCAF-1 is involved in RNA-mediated control of DNA elimination. Nucleic acids research, 42(19), pp. 11952-11964. Information Retrieval Ltd. 10.1093/nar/gku874

Sandoval, Pamela Yohanna de Lourdes; Swart, Estienne Carl; Arambasic, Miroslav; Nowacki, Mariusz (2014). Functional Diversification of Dicer-like Proteins and Small RNAs Required for Genome Sculpting. Developmental cell, 28(2), pp. 174-188. Cell Press 10.1016/j.devcel.2013.12.010

Aeschlimann, Samuel H.; Jönsson, Franziska; Postberg, Jan; Stover, Nicholas A.; Petera, Robert L.; Lipps, Hans-Joachim; Nowacki, Mariusz; Swart, Estienne Carl (2014). The Draft Assembly of the Radically Organized Stylonychia lemnae Macronuclear Genome. Genome biology and evolution, 6(7), pp. 1707-1723. Oxford University Press 10.1093/gbe/evu139

Swart, Estienne Carl; Wilkes, Cyril Denby; Sandoval, Pamela Yohanna de Lourdes; Arambasic, Miroslav; Sperling, Linda; Nowacki, Mariusz (2014). Genome-wide analysis of genetic and epigenetic control of programmed DNA deletion. Nucleic acids research, 42(14), pp. 8970-8983. Oxford University Press 10.1093/nar/gku619

Almouzni, Geneviève; Altucci, Lucia; Amati, Bruno; Ashley, Neil; Baulcombe, David; Beaujean, Nathalie; Bock, Christoph; Bongcam-Rudloff, Erik; Bousquet, Jean; Braun, Sigurd; Paillerets, Brigitte Bressac-de; Bussemakers, Marion; Clarke, Laura; Conesa, Ana; Estivill, Xavier; Fazeli, Alireza; Grgurević, NeŽa; Gut, Ivo; Heijmans, Bastiaan T; Hermouet, Sylvie; ... (2014). Relationship between genome and epigenome - challenges and requirements for future research BioMed Central 10.1186/1471-2164-15-487

Arambasic, Miroslav; Sandoval, Pamela Yohanna de Lourdes; Höhener, Cristina; Singh, Aditi; Swart, Estienne Carl; Nowacki, Mariusz (2014). Pdsg1 and Pdsg2, novel proteins involved in developmental genome remodelling in Paramecium. PLoS ONE, 9(11), e112899. Public Library of Science 10.1371/journal.pone.0112899

2013

Fuhrmann, Gloria; Swart, Estienne; Nowacki, Mariusz; Lipps, Hans J. (2013). RNA-dependent genome processing during nuclear differentiation: the model systems of stichotrichous ciliates. Epigenomics, 5(2), pp. 229-236. Future Medicine 10.2217/epi.13.15

Swart, Estienne C.; Bracht, John R.; Magrini, Vincent; Minx, Patrick; Chen, Xiao; Zhou, Yi; Khurana, Jaspreet S.; Goldman, Aaron D.; Nowacki, Mariusz; Schotanus, Klaas; Jung, Seolkyoung; Fulton, Robert S.; Ly, Amy; McGrath, Sean; Haub, Kevin; Wiggins, Jessica L.; Storton, Donna; Matese, John C.; Parsons, Lance; Chang, Wei-Jen; ... (2013). The Oxytricha trifallax macronuclear genome: a complex eukaryotic genome with 16,000 tiny chromosomes. PLoS biology, 11(1), e1001473. Public Library of Science 10.1371/journal.pbio.1001473

2012

Arnaiz, O; Mathy, N; Baudry, C; Malinsky, S; Aury, JM; Wilkes, CD; Garnier, O; Labadie, K; Lauderdale, BE; Le Mouël, A; Marmignon, A; Nowacki, M; Poulain, J; Prajer, M; Wincker, P; Meyer, E; Duharcourt, S; Duret, L; Bétermier, M and Sperling, L (2012). The Paramecium Germline Genome Provides a Niche for Intragenic Parasitic DNA: Evolutionary Dynamics of Internal Eliminated Sequences. PLoS genetics, 8(10), e1002984. San Francisco, Calif.: Public Library of Science 10.1371/journal.pgen.1002984

Fang, Wenwen; Wang, Xing; Bracht, John R.; Nowacki, Mariusz; Landweber, Laura F. (2012). Piwi-Interacting RNAs Protect DNA against Loss during Oxytricha Genome Rearrangement. Cell, 151(6), pp. 1243-1255. Cambridge, Mass.: Cell Press 10.1016/j.cell.2012.10.045

Swart, E.C.; Nowacki, M.; Shum, J.; Stiles, H.; Higgins, B.P.; Doak, T.G.; Schotanus, K.; Magrini, V.J.; Minx, P.; Mardis, E.R.; Landweber, L.F. (2012). The Oxytricha trifallax mitochondrial genome. Genome biology and evolution, 4(2), pp. 136-154. Oxford: Oxford University Press 10.1093/gbe/evr136

2011

Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F. (2011). RNA-Mediated Epigenetic Programming of Genome Rearrangements. Annual review of genomics and human genetics, 12(1), pp. 367-389. Palo Alto, Calif.: Annual Reviews Inc. 10.1146/annurev-genom-082410-101420

2010

Nowacki, Mariusz; Haye, Joanna E.; Fang, Wenwen; Vijayan, Vikram; Landweber, Laura F. (2010). RNA-mediated epigenetic regulation of DNA copy number. Proceedings of the National Academy of Sciences of the United States of America - PNAS, 107(51), pp. 22140-22144. Washington, D.C.: National Academy of Sciences NAS 10.1073/pnas.1012236107

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