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Research: Developmental timing of programmed DNA elimination in Paramecium tetraurelia recapitulates germline transposon evolutionary dynamics
- Coralie Zangarelli,
- Olivier Arnaiz,
- Mickaël Bourge,
- Kevin Gorrichon,
- Yan Jaszczyszyn,
- Nathalie Mathy,
- Loïc Escoriza,
- Mireille Bétermier,
- and Vinciane Régnier
Genome Res. November/December 2022 32: 2028-2042; Published in Advance November 23, 2022, doi:10.1101/gr.277027.122
...of mature MACs (about 800C to 1600C in Paramecium tetraurelia) (Preer 1976). Concomitantly with amplification, programmed DNA elimination (PDE) removes ∼30% of germline DNA from the new MAC , going from a 98- to 151-Mbp haploid size in the MIC to 72–75 Mbp in the mature MAC (Aury et al. 2006; Guérin et al...
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Research: ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh,
- Lilia Häußermann,
- Christiane Emmerich,
- Emily Nischwitz,
- Brandon K.B. Seah,
- Falk Butter,
- Mariusz Nowacki,
- and Estienne C. Swart
Genome Res. January 2025 35: 93-108; Published in Advance November 14, 2024, doi:10.1101/gr.278402.123
...eliminate tens of thousands of DNA sequences from a germline copy. Recently, we showed that the chromatin remodeler ISWI1 is required for somatic development in the ciliate Paramecium tetraurelia. Here, we describe two high similarity paralogous proteins, ICOPa and ICOPb, essential for their editing. ICOPa...
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Method: Genealogy-based trait association with LOCATER boosts power at loci with allelic heterogeneity
- Xinxin Wang,
- Ryan Christ,
- Erica Young,
- Chul Joo Kang,
- Indraniel Das,
- Edward A. Belter, Jr.,
- Markku Laakso,
- Louis J.M. Aslett,
- David Steinsaltz,
- Nathan O. Stitziel,
- and Ira M. Hall
Genome Res. April 16, 2026 ; Published in Advance April 16, 2026, doi:10.1101/gr.280372.124
...-specific haplotype tree. Here, we develop a -wide LOCATER analysis pipeline and apply it to a sequencing study of 6795 Finnish individuals with 101 cardiometabolic traits and 18.9 million autosomal variants. We identify 351 significant trait associations at 47 distinct genomic loci and find that LOCATER boosts...
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Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
- Xuyan Liu,
- Lin Xia,
- Yixin Qiao,
- Yang Li,
- Yan Huang,
- Bingyan Yue,
- Xi Liang,
- Xin Yang,
- Honghui Zhang,
- Jiaxun Zhang,
- Xiao Chen,
- Dan Xie,
- and Jifeng Liu
Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
...by introducing DNA double-strand breaks(Yoshida et al. 2020; 231 Degawa et al. 1994; Aw et al. 2021). 232 233 To investigate the functional impact of somatic deletions in smoking-related LSCC, 234 we focused on the 42 somatic DEL regions (after merging adjacent windows, as 235 described in Methods: Sample...
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Research: GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency in Paramecium
- Stefano Gnan,
- Mélody Matelot,
- Marion Weiman,
- Olivier Arnaiz,
- Frédéric Guérin,
- Linda Sperling,
- Mireille Bétermier,
- Claude Thermes,
- Chun-Long Chen,
- and Sandra Duharcourt
Genome Res. April 2022 32: 699-709; Published in Advance March 9, 2022, doi:10.1101/gr.276125.121
...with high splicing efficiency. Our data reveal a complex link between GC content, nucleosome positioning, and intron evolution in Paramecium.In eukaryotes, genomic DNA is compacted by histones into chromatin. The basic unit of chromatin is the nucleosome, which comprises a histone octamer made of the four...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien A.C. Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J. Smith,
- and Falk Butter
Genome Res. January 28, 2026 ; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...-Loeffler-Institut, 17493 Greifswald, Germany; 3School of Health Sciences-Biomedical Sciences Program, Missouri State University, Springfield, Missouri 65897, USA A tightly regulated DNA damage response is critical to the overall integrity of the . Here, we combine transcriptomics and proteomics to study DNA damage...
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Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
- Shaoqiang Hu,
- Xiangguo Zeng,
- Yuguo Liu,
- Yongping Li,
- Minghao Qu,
- Wen-Biao Jiao,
- Yongchao Han,
- and Chunying Kang
Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
...al. 2015). Genome-wide increases in DNA methylation levels, particularly at CHH sites, were detected in cultured samples during somatic embryogenesis in soybean (Ji et al. 2019). In sweet orange, the global CHH methylation levels were significantly decreased at the callus induction stage...
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Research: Broad domains of histone marks in the highly compact Paramecium macronuclear genome
- Franziska Drews,
- Abdulrahman Salhab,
- Sivarajan Karunanithi,
- Miriam Cheaib,
- Martin Jung,
- Marcel H. Schulz,
- and Martin Simon
Genome Res. April 2022 32: 710-725; Published in Advance March 9, 2022, doi:10.1101/gr.276126.121
...Render [https://biorender.com]).ResultsUnusual properties of the macronuclear The mechanisms of DNA elimination described above during development of the Paramecium MAC result in a highly compact with striking differences in comparison to Schizosaccharomyces pombe and individual metazoans (Fig. 2A...
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Research: Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations
- Xiu Fan,
- Qili Qian,
- Wenran Li,
- Tianzi Liu,
- Changqing Zeng,
- Peilin Jia,
- Huandong Lin,
- Xin Gao,
- Li Jin,
- Mingfeng Xia,
- Sijia Wang,
- and Fan Liu
Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
...and stochastic accumulation of epigenetic changes, such as DNA methylation variability, with advancing age. Although increasingly recognized for its potential role in aging biology, its extent, biological significance, and population specificity remain insufficiently characterized. Here, we present the first...
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Research: Comparative genome analysis of programmed DNA elimination in nematodes
- Jianbin Wang,
- Shenghan Gao,
- Yulia Mostovoy,
- Yuanyuan Kang,
- Maxim Zagoskin,
- Yongqiao Sun,
- Bing Zhang,
- Laura K. White,
- Alice Easton,
- Thomas B. Nutman,
- Pui-Yan Kwok,
- Songnian Hu,
- Martin K. Nielsen,
- and Richard E. Davis
Genome Res. December 2017 27: 2001-2014; Published in Advance November 8, 2017, doi:10.1101/gr.225730.117
...elimination (Wang and Davis 2014b). Programmed DNA elimination occurs in unicellular ciliates where it is involved in generating the macronucleus (the somatic ) from the micronucleus (the germline ) during sexual reproduction (Chalker and Yao 2011; Bracht et al. 2013). Many metazoans, including some nematodes...

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