CoChat
Sign Up
PreprintCited by 5Genomics and Chromatin DynamicsChromosomal and Genetic VariationsProtist diversity and phylogeny

The DOI matches its Crossref record; 1 of the 1 references it cites were found in a registry or an index.

ISWI1 complex proteins facilitate developmental genome editing in Paramecium

Open access
Singh, Aditi, Häußermann, Lilia, Emmerich, Christiane, Nischwitz, Emily, Seah, Brandon KB, Butter, Falk, Nowacki, Mariusz, Swart, Estienne C.·2023·Genome Research
DOI 10.1101/2023.08.09.552620PMC PMC11789628

Preprint — published as 10.1101/gr.278402.123 · Paper page

Open this paper in CoChat — free accountOpen PDF

Abstract

Chromatin remodeling is required for essential cellular processes, including DNA replication, DNA repair, and transcription regulation. The ciliate germline and soma are partitioned into two distinct nuclei within the same cell. During a massive editing process that forms a somatic genome, ciliates eliminate thousands of DNA sequences from a germline genome copy in the form of internal eliminated sequences (IESs). Recently we showed that the chromatin remodeler ISWI1 is required for somatic genome development in the ciliate Paramecium tetraurelia . Here we describe two paralogous proteins, ICOP1 and ICOP2, essential for DNA elimination. ICOP1 and ICOP2 are highly divergent from known proteins; the only domain detected showed distant homology to the WSD motif. We show that both ICOP1 and ICOP2 interact with the chromatin remodeler ISWI1. Upon ICOP knockdown, changes in alternative IES 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 ICOP1 and ICOP2 are needed for chromatin remodeling and accurate DNA elimination in Paramecium .

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1101/2023.08.09.552620

Cites

1 of 1 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Research works printed but not linked: 64

  1. 10.1038/nrm3288 · DOI
  2. 10.1016/j.cell.2017.02.020 · DOI
  3. 10.4161/cc.11.1.18475 · DOI
  4. 10.1371/journal.pgen.1002984 · DOI
  5. 10.4161/15384101.2014.956551 · DOI
  6. 10.1016/j.tig.2010.08.003 · DOI
  7. 10.1016/j.bbagrm.2011.12.007 · DOI
  8. 10.1101/gad.547309 · DOI
  9. 10.1101/2023.04.16.537068 · DOI
  10. 10.1101/pdb.prot5364 · DOI
  11. 10.1101/pdb.prot5361 · DOI
  12. 10.1101/pdb.prot5362 · DOI
  13. 10.1101/pdb.prot5363 · DOI
  14. Bischerour J , Bhullar S , Denby Wilkes C , Régnier V , Mathy N , Dubois E , Singh A , Swart E , Arnaiz O , Sperling L , et al. 2018. Six domesticated PiggyBac transposases together carry out programmed DNA elimination in Paramecium. eLife 7. · DOI
  15. 10.1093/nar/gkq1283 · DOI
  16. 10.1146/annurev.genet.032608.103928 · DOI · Paper page
  17. 10.1146/annurev.biochem.77.062706.153223 · DOI
  18. 10.1093/bioinformatics/btv691 · DOI
  19. 10.1139/o04-044 · DOI
  20. 2022, Paramecium epigenetics in development and proliferation, J Eukaryot Microbiol, 69, e12914, 10.1111/jeu.12914 · DOI
  21. 10.1101/gr.276126.121 · DOI
  22. 10.1155/2012/436196 · DOI
  23. 10.1101/gr.074534.107 · DOI
  24. 10.1101/2021.10.04.463034 · DOI · Paper page
  25. Finn R , Griffiths-Jones S , Bateman A . 2003. Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics Chapter 2: Unit 2.5. · DOI
  26. 10.1016/j.celrep.2017.06.050 · DOI
  27. 10.1128/MCB.24.17.7370-7379.2004 · DOI
  28. 10.1101/gr.276125.121 · DOI
  29. 10.1016/S1097-2765(03)00273-9 · DOI
  30. 10.1016/S0092-8674(00)00215-4 · DOI
  31. 10.1093/nar/gku874 · DOI
  32. 10.1371/journal.pgen.1002049 · DOI
  33. 10.1093/nar/23.11.2006 · DOI
  34. 10.1016/S1097-2765(01)00397-5 · DOI
  35. 10.1016/S0092-8674(00)80797-7 · DOI
  36. 10.1093/nar/gkn1018 · DOI
  37. 10.1093/bioinformatics/btp324 · DOI · Paper page
  38. 2009, 1000 Genome Project Data Processing Subgroup, The Sequence Alignment/Map format and SAMtools. Bioinformatics, 25, 2078
  39. 10.1038/s41586-019-1029-2 · DOI
  40. 10.1371/journal.pgen.1005383 · DOI
  41. 10.1016/j.devcel.2022.03.014 · DOI
  42. 2021, Structural insights into the interaction between transcription factors and the nucleosome, Curr Opin Struct Biol, 71, 171, 10.1016/j.sbi.2021.06.016 · DOI
  43. 10.1093/molbev/msp201 · DOI
  44. 10.1016/j.cub.2005.07.033 · DOI
  45. 10.1074/jbc.M405790200 · DOI
  46. 10.1016/0092-8674(90)90087-U · DOI
  47. 10.1016/j.cell.2013.02.011 · DOI · Paper page
  48. 10.1016/0092-8674(92)90289-O · DOI · Paper page
  49. 10.1038/nmeth.1818 · DOI · Paper page
  50. 10.1038/nmeth.2251 · DOI · Paper page
  51. 10.1107/S0907444906031003 · DOI
  52. 10.1016/j.devcel.2013.12.010 · DOI
  53. 2023, MITE infestation accommodated by genome editing in the germline genome of the ciliate Blepharisma, Proc Natl Acad Sci USA, 120, e2213985120, 10.1073/pnas.2213985120 · DOI
  54. 10.1371/journal.pbio.3001309 · DOI
  55. 2022, Chromatin remodeling is required for sRNA-guided DNA elimination in Paramecium, EMBO J, 41, e111839, 10.15252/embj.2022111839 · DOI
  56. Singh A . 2023. ISWI complex proteins facilitate genome editing and development . Edmond. https://doi.org/10.17617/3.ZBOLU8 (Accessed July 28, 2023). · DOI
  57. 10.1091/mbc.8.6.1063 · DOI
  58. 10.1007/978-1-62703-691-7_2 · DOI · Paper page
  59. 2017, Identification and analysis of functional associations among natural eukaryotic genome editing components [version 1; peer review: 1 approved, 1 approved with reservations]. F1000Res, 6, 1374
  60. 10.1007/s00412-013-0447-4 · DOI
  61. 10.1016/j.celrep.2022.111263 · DOI
  62. 10.1038/nature09947 · DOI
  63. 10.1101/gr.277027.122 · DOI
  64. 10.1016/j.jmb.2017.12.007 · DOI · Paper page

Metadata

Authors
Singh, A., Häußermann, L., Emmerich, C., Nischwitz, E., Seah, B. K., Butter, F., Nowacki, M., & Swart, E. C.
Affiliations
  • Max Planck Society (DE)
  • Max Planck Institute for Biology (DE)
  • Institute of Molecular Biology (DE)
  • Friedrich-Loeffler-Institut (DE)
  • University of Bern (CH)
Corresponding author
  • Singh, Aditi
  • Swart, Estienne C.
ORCID
Venue
Genome Research
Publisher
openRxiv
Published
2023-08-09
Volume
35
Issue
1
Pages
93-108
ISSN
1088-9051 (ISSN-L)
DOI
10.1101/2023.08.09.552620
PMC
PMC11789628
OpenAlex
W4404375541
Cited by
5
References
1
Citations by year
2025: 2 · 2024: 3
Type
posted content
Language
en
Open access
Licence
cc-by
Locations
  • Genome Research (publishedVersion)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • OpenAgrar (submittedVersion, cc-by-nc)
Funders
Max-Planck-Gesellschaft
Topics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
  • Life Sciences › Agricultural and Biological Sciences › Ecology, Evolution, Behavior and Systematics › Protist diversity and phylogeny
Keywords
germline genome, chromatin remodeling, Paramecium tetraurelia, ciliates, nucleosome density, protein complexes
MeSH terms
Gene Editing, Paramecium, Protozoan Proteins, Paramecium tetraurelia, Genome, Protozoan, Chromatin Assembly and Disassembly

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review