ISWI1 complex proteins facilitate developmental genome editing in Paramecium
- Aditi Singh1,5,
- Lilia Häußermann1,5,
- Christiane Emmerich1,
- Emily Nischwitz2,
- Brandon K.B. Seah1,
- Falk Butter2,3,
- Mariusz Nowacki4 and
- Estienne C. Swart1
- 1Max Planck Institute for Biology, 72076 Tübingen, Germany;
- 2Institute of Molecular Biology, 55128 Mainz, Germany;
- 3Institute of Molecular Virology and Cell Biology (IMVZ), Friedrich Loeffler Institut, 17493 Greifswald, Germany;
- 4Institute of Cell Biology, University of Bern, 3012 Bern, Switzerland
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↵5 These authors contributed equally to this work.
Abstract
One of the most extensive forms of natural genome editing occurs in ciliates, a group of microbial eukaryotes. Ciliate germline and somatic genomes are contained in distinct nuclei within the same cell. During the massive reorganization process of somatic genome development, ciliates eliminate tens of thousands of DNA sequences from a germline genome copy. Recently, we showed that the chromatin remodeler ISWI1 is required for somatic genome development in the ciliate Paramecium tetraurelia. Here, we describe two high similarity paralogous proteins, ICOPa and ICOPb, essential for their genome editing. ICOPa and ICOPb are highly divergent from known proteins; the only domain detected showed distant homology with the WSD (WHIM2 + WHIM3) motif. We show that both ICOPa and ICOPb interact with the chromatin remodeler ISWI1. Upon ICOP knockdown, changes in alternative DNA excision boundaries and nucleosome densities are similar to those observed for ISWI1 knockdown. We thus propose that a complex comprising ISWI1 and either or both ICOPa and ICOPb are needed for Paramecium’s precise genome editing.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.278402.123.
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Freely available online through the Genome Research Open Access option.
- Received August 17, 2023.
- Accepted October 15, 2024.
This article, published in Genome Research, is available under a Creative Commons License (Attribution 4.0 International), as described at http://creativecommons.org/licenses/by/4.0/.
