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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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Research: Environmentally induced plasticity of programmed DNA elimination boosts somatic variability in Paramecium tetraurelia
- Valerio Vitali,
- Rebecca Hagen,
- and Francesco Catania
Genome Res. October 2019 29: 1693-1704; Published in Advance September 23, 2019, doi:10.1101/gr.245332.118
...that environmentally induced developmental thermoplasticity contributes to genotypic diversification in Paramecium.The DNA that is perpetuated by the germline is not always carried over to the soma in its entirety. In a broad range of eukaryotes, germline DNA sequences are reproducibly discarded at each round...
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Research: The role of transposon activity in shaping cis-regulatory element evolution after whole-genome duplication
- Øystein Monsen,
- Lars Grønvold,
- Alex Datsomor,
- Thomas Harvey,
- James Kijas,
- Alexander Suh,
- Torgeir R. Hvidsten,
- and Simen Rød Sandve
Genome Res. March 2025 35: 475-488; Published in Advance February 12, 2025, doi:10.1101/gr.278931.124
...TE annotation from Lien et al. (2016). The total TE annotation covered 51.92% of the . Consistent with previous findings (Goodier and Davidson 1994; Lien et al. 2016), the dominating TE group was DNA transposons from the Tc1-Mariner superfamily with more than 655,000 copies, covering 327 million base...
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Research: KRAB zinc-finger proteins regulate endogenous retroviruses to sculpt germline transcriptomes and genome evolution
- Kai Otsuka,
- Akihiko Sakashita,
- So Maezawa,
- Richard M. Schultz,
- and Satoshi H. Namekawa
Genome Res. March 2025 35: 417-431; Published in Advance March 12, 2025, doi:10.1101/gr.279924.124
...takes place. During meiosis, H3K9me3 is established on the X Chromosome by SETDB1 and its germline-specific partner ATF7IP2, but this action of SETDB1–ATF7IP2 is regulated downstream from the DNA damage response (DDR) pathway (Hirota et al. 2018; Alavattam et al. 2024), which is the master regulator...
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Research: Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models
- Yiqiao Zheng,
- Gary D. Stormo,
- and Shiming Chen
Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
...Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models Yiqiao Zheng1,2,5, Gary D. Stormo3 and Shiming Chen2,4 1Molecular Genetics and Genomics Graduate Program, Division of Biology & Biomedical Sciences, Washington...
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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
....wang@ucdenver.edu, richard.davis@ucdenver.eduAbstractProgrammed DNA elimination is a developmentally regulated process leading to the reproducible loss of specific genomic sequences. DNA elimination occurs in unicellular ciliates and a variety of metazoans, including invertebrates and vertebrates. In metazoa, DNA...
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Resource: A systems view on DNA damage response kinetics in Tetrahymena
- Emily Nischwitz,
- Vivien Schoonenberg,
- Rachel Mullner,
- Albert Fradera-Sola,
- Susanne Zimbelmann,
- Joshua J Smith,
- and Falk Butter
Genome Res. January 28, 2026 gr.281000.125; Published in Advance January 28, 2026, doi:10.1101/gr.281000.125
...). In addition to this dynamicity filter, 126 to select transcripts generally differentially regulated in response to the DNA damaging agents, 127 we filtered based on log2 fold change (L2FC), requiring the expression change over the time 128 course to reach a magnitude of at least 1 L2FC, and a significance...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...-translational modifications, play a crucial role in regulating programs integral to a cell's identity, like gene expression and DNA replication. However, the transcriptional, chromatin, and replication timing profiles of adult stem cells in vivo remain poorly understood. Containing germline stem cells (GSCs) and somatic cyst...
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Method: Analytical validation of germline small variant detection using long-read HiFi genome sequencing
- Nathan Hammond,
- Linda Liao,
- Pun Wai Tong,
- Zena Ng,
- Thuy-Mi P. Nguyen,
- Chandler Ho,
- Yao Yang,
- and Stuart A. Scott
Genome Res. June 2025 35: 1391-1399; Published in Advance April 11, 2025, doi:10.1101/gr.278836.123
...provide the infrastructure for long-read HiFi sequencing-based detection of germline variation, which supports the use of this innovative technology for clinical diagnostic testing.MethodsAnalytical validation specimensHigh molecular weight (HMW) reference material DNA samples were acquired from...
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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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