Evidence map›Paper›PMID 39468082›Full record

ArticleNature communications2024

Structural variation of types IV-A1- and IV-A3-mediated CRISPR interference.

R Čepaitė, N Klein, A Mikšys, S Camara-Wilpert, V Ragožius, F Benz, A Skorupskaitė, H Becker, G Žvejytė, N Steube and 5 more

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Article
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Emerging tools in plant genome editing.Frontiers in genome editing · 2025
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

R Čepaitė *LSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
N Klein *Department of Biology, Philipps-Universität Marburg, Marburg, Germany.ORCID 0009-0001-1579-4929
A Mikšys *LSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.ORCID 0000-0002-6951-6449
S Camara-WilpertDepartment of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.
V RagožiusLSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.ORCID 0009-0001-4279-0093
F BenzSynthetic Biology, Institut Pasteur, Université Paris Cité, CNRS UMR6047, Paris, France.ORCID 0000-0002-6679-6502
A SkorupskaitėLSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.ORCID 0000-0002-4124-4453
H BeckerDepartment of Biology, Philipps-Universität Marburg, Marburg, Germany.ORCID 0009-0008-8886-2866
G ŽvejytėLSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania.ORCID 0009-0005-9509-4429
N SteubeEvolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.ORCID 0000-0001-7661-1893
G K A HochbergEvolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany.ORCID 0000-0002-7155-0451
L RandauDepartment of Biology, Philipps-Universität Marburg, Marburg, Germany.ORCID 0000-0002-2780-2076
R Pinilla-RedondoDepartment of Biology, Section of Microbiology, University of Copenhagen, Copenhagen, Denmark.ORCID 0000-0003-3521-460X
L MalinauskaitėLSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania. lina.malinauskaite@biontech.co.uk.ORCID 0000-0003-3232-0415
P PauschLSC-EMBL Partnership Institute for Genome Editing Technologies, Life Sciences Center, Vilnius University, Vilnius, Lithuania. patrick.pausch@gmc.vu.lt.ORCID 0000-0001-8947-9107

Funding

European Molecular Biology Organization (EMBO) 5342-2023Lietuvos Mokslo Taryba (Research Council of Lithuania) S-MIP-22-10
6 · The paper itself

Abstract

CRISPR-Cas mediated DNA-interference typically relies on sequence-specific binding and nucleolytic degradation of foreign genetic material. Type IV-A CRISPR-Cas systems diverge from this general mechanism, using a nuclease-independent interference pathway to suppress gene expression for gene regulation and plasmid competition. To understand how the type IV-A system associated effector complex achieves this interference, we determine cryo-EM structures of two evolutionarily distinct type IV-A complexes (types IV-A1 and IV-A3) bound to cognate DNA-targets in the presence and absence of the type IV-A signature DinG effector helicase. The structures reveal how the effector complexes recognize the protospacer adjacent motif and target-strand DNA to form an R-loop structure. Additionally, we reveal differences between types IV-A1 and IV-A3 in DNA interactions and structural motifs that allow for in trans recruitment of DinG. Our study provides a detailed view of type IV-A mediated DNA-interference and presents a structural foundation for engineering type IV-A-based genome editing tools.

Indexed as

CRISPR-Cas SystemsCryoelectron MicroscopyBacterial ProteinsClustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Associated ProteinsDNADNA HelicasesEscherichia coliEscherichia coli ProteinsGene EditingR-Loop StructuresBacterial ProteinsCRISPR-Associated ProteinsDNADNA HelicasesEscherichia coli Proteins

Identifiers

PMID39468082
PMCPMC11519345

What OpenQuestion holds

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.