2023

Therese Solberg, Victor Mason, Chundi Wang, Mariusz Nowacki (2023).Developmental mRNA clearance by PIWI-bound endo-siRNAs in Paramecium. Cell Rep. 42, 112213

Highlights:

  • Discovery of a small-RNA-mediated mRNA clearance pathway in a unicellular eukaryote
  • Endo-siRNAs display a strict strand bias and are antisense to their target mRNAs
  • Endo-siRNAs are Dicer dependent and bound by a PIWI-clade Argonaute protein, Ptiwi08
  • Untranslated mRNAs are likely targeted for degradation by the Ptiwi08 pathway

2022

Aditi Singh; Xyrus X Maurer-Alcalá; Therese Solberg; Lilia Häußermann; Silvan Gisler; Michael Ignarski; Estienne C Swart; Mariusz Nowacki (2022). Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium. The EMBO Journal. doi:  10.15252/embj.2022111839

Highlights:

  • Paramecium ISWI homolog ISWI1 is differentially upregulated during macronuclear development and affects DNA elimination.
  • ISWI1 knockdown leads to alternative excision of IESs, including excision at the “forbidden peak” ~35 bp from the IESs, a region which is excluded from excision in wildtype.
  • Ptiwi01 and Ptiwi09 interact with ISWI1 during sexual development.
  • Knockdown of ISWI1 or the transposase PGM alters the distribution of nucleosome densities.
Chundi, Wang; 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 Rep. doi: 10.1016/j.celrep.2022.111263

Highlights:

  • PRC2 couples Piwi-bound small RNAs to transposon elimination in the new soma
  • Elimination of new and ancient transposon sequences depends on PRC2
  • Loss of PRC2 leads to retention and de-repression of transposons
  • Only new transposons require heterochromatin and small RNAs for their removal
Bechara, Sebastian T.; Kabbani, Lyna E.S.; Maurer-Alcalá, Xyrus X.; Nowacki, Mariusz (2022). Identification of novel, functional, long noncoding RNAs involved in programmed, large-scale genome rearrangements. RNA doi: 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. Biochim Biophys Acta Mol Cell Res. doi: 10.1016/j.bbamcr.2022.119239.

2020

Rzeszutek, Iwona; Maurer-Alcalá, Xyrus X.; Nowacki, Mariusz (2020). Programmed genome rearrangements in ciliates. Cell Mol Life Sci. doi: 10.1007/s00018-020-03555-2.

Allen, Sarah E. and Nowacki, Mariusz (2020). Roles of Noncoding RNAs in Ciliate Genome Architecture. J Mol Biol doi: 10.1016/j.jmb.2019.12.042.

Faktorova, D et al. (2020). Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nature Methods doi: 10.1038/s41592-020-0796-x

2019

Maurer-Alcalá, Xyrus X. and Nowacki, Mariusz (2019). Evolutionary origins and impacts of genome architecture. Ann N Y Acad Sci. doi: 10.1111/nyas.14108.

2018

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(12): e0209707.

Bischerour, Julien; Bhullar, Simran; Denby Wilkes, Cyril; Régnier, Vinciane; Mathy, Nathalie; Dubois, Emeline; Singh, Aditi; Swart, Estienne C.; Arnaiz, Olivier; Sperling, Linda; Nowacki, Mariusz; Bétermier, Mireille (2018). Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium. eLife 7: e37927.

Michelini, Flavia; Jalihal, Ameya P.; Francia, Sofia; Meers,Chance; Neeb, Zachary T.;  Rossiello, Francesca;  Gioia, Ubaldo; Aguado, Julio;  Jones-Weinert, Corey;  Luke, Brian;  Biamonti, Giuseppe;  Nowacki, Mariusz; Storici, Francesca; Carninci, Piero;  Walter, Nils G.;  d’Adda di Fagagna, Fabrizio (2018). From “Cellular” RNA to “Smart” RNA: Multiple Roles of RNA in Genome Stability and Beyond. Chem. Rev., 118 (8) pp. 4365-4403

Hoehener, Cristina; Hug, Iris; Nowacki, Mariusz (2018). Dicer-like Enzymes with Sequence Cleavage Preferences. Cell, 173 (1) pp. 234-247.

Highlights:

  • Dicer-like proteins can cleave dsRNA in a sequence-specific manner
  • Dicer-like proteins produce small RNAs with 5′ and 3′ sequence bias
  • Small RNA sequence bias enables precise targeting of transposon-derived IESs
  • Dcl5 recognizes IES-IES junction sequence motifs

Neeb, Zachary T. and Nowacki, Mariusz (2018). RNA-mediated transgenerational inheritance in ciliates and plants. Chromosoma, 127 (1), pp. 19-27.

2017

Furrer, Dominique I.; Swart, Estienne C.; Kraft, Matthias F.; Sandoval, Pamela Y.; Nowacki, Mariusz (2017). Two Sets of Piwi Proteins Are Involved in Distinct sRNA Pathways Leading to Elimination of Germline-Specific DNA. Cell Rep., 20 (2), pp. 505-520.

Highlights:

  • Identification of two Piwi proteins (Ptiwi10/11) associated with iesRNAs
  • Piwi proteins bind Dicer-produced sRNAs and remove passenger strands
  • Ptiwi10 is expressed from the new somatic macronucleus
  • DNA elimination activates gene transcription

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. Jr.; Gunawardena, Jeremy; Chu, William; Stover, Naomi A.; Gregory, Brian D.; Nowacki, Mariusz; Derisi, Joseph; Roy, Scott W.; Marshall, Wallace F.; Sood, Pranidhi (2017). The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. Curr. Biol., 27 (4), pp. 569-575.

Allen, Sarah Elizabeth and Nowacki, Mariusz (2017). Necessity Is the Mother of Invention: Ciliates, Transposons, and Transgenerational Inheritance. Trends Genet., 33 (3), pp. 197-207.

Allen, Sarah E; Hug, Iris; Pabian, Sylwia; Rzeszutek, Iwona; Hoehener, Cristina; Nowacki, Mariusz (2017). Circular Concatemers of Ultra-Short DNA Segments Produce Regulatory RNAs. Cell, 168 (6), pp. 990-999.

Highlights:

  • In Paramecium, pieces of deleted DNA are transcribed to form regulatory RNAs
  • Ultra-short DNA segments are concatenated and circularized, allowing transcription
  • This concatenation is carried out by Ligase IV, which also repairs DNA ends
  • Concatenation is random, which leads to diversity in the resulting sRNA population

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 (2017). Chromosome fusions triggered by noncoding RNA. RNA Biol., 14, pp. 620-631.

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.

Highlights:

  • Alternative nuclear genetic codes continue to be discovered in ciliates
  • Genetic codes with stops and all their codons encoding standard amino acids exist
  • Transcript ends may distinguish stop codons as such in ambiguous genetic codes
  • The ability to resolve genetic code ambiguity may enable genetic code evolution

2015

Swart, Estienne Carl and Nowacki, Mariusz (2015). The eukaryotic way to defend and edit genomes by sRNA-targeted DNA deletion. Ann N Y Acad Sci., 1341, pp. 106-114. Blackwell

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 Res., 42(19), pp. 11952-11964. Information Retrieval Ltd. 10.1093/nar/gku874

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 Res., 42(14), pp. 8970-8983. Information Retrieval Ltd.

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. Dev 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 Biol Evol., 6(7), pp. 1707-1723. Oxford University Press

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

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

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 Biol., 11(1), e1001473. Public Library of Science

2012

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

Arnaiz O, Mathy N, Baudry C, Malinsky S, Aury JM, Denby Wilkes C, 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, Sperling L. The Paramecium germline genome provides a niche for intragenic parasitic DNA: evolutionary dynamics of internal eliminated sequences. PLoS Genet. 2012;8(10):e1002984. doi: 10.1371/journal.pgen.1002984.

Swart EC, Nowacki M, Shum J, Stiles H, Higgins BP, Doak TG, Schotanus K, Magrini VJ, Minx P, Mardis ER, Landweber LF. The Oxytricha trifallax mitochondrial genome. Genome Biol Evol. 2012;4(2):136-54. doi: 10.1093/gbe/evr136.

2011

Nowacki, Mariusz; Shetty, Keerthi; Landweber, Laura F. (2011). RNA-Mediated Epigenetic Programming of Genome Rearrangements. Annu Rev Genomics Hum Genet., 12(1), pp. 367-389. Palo Alto, Calif.: Annual Reviews Inc.

2010

Nowacki, Mariusz; Haye, Joanna E.; Fang, Wenwen; Vijayan, Vikram; Landweber, Laura F. (2010). RNA-mediated epigenetic regulation of DNA copy number. Proc Natl Acad Sci U S A., 107(51), pp. 22140-22144. Washington, D.C.: National Academy of Sciences NAS