2018

Michelini, Flavia; Jalihal, Ameya P.; Francia, Sofia; Meers,Chance; Neeb, Zachary T.;  Rossiello, Francesca Gioia, Ubaldo; Aguado, Julio;  Jones-Weinert, Corey;  Luke, Brian;  BiamontiGiuseppe Nowacki, Mariusz; Storici, Francesca; CarninciPiero 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

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

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 Biol., pp. 1-12. Landes Bioscience

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