Evidence map›Paper›PMID 40011704›Full record

ArticleNature microbiology2025

CRISPRi-ART enables functional genomics of diverse bacteriophages using RNA-binding dCas13d.

Benjamin A Adler, Muntathar J Al-Shimary, Jaymin R Patel, Emily G Armbruster, David Colognori, Emeric J Charles, Kate V Miller, Arushi Lahiri, Michael L Cui, Agnès Oromí-Bosch and 13 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature microbiology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
17citing papers in PubMed, 1 pooled it
–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

17 citing papers in PubMed, 1 synthesis or guideline pooled it.

  1. Pooled it
  2. Article
  3. Article
  4. Cap-Independent Translation Regulation of VEGF Using CRISPR-dCas13d.bioRxiv : the preprint server for biology · 2026
    Article
  5. Review
  6. Article
  7. The biology of jumbo phages.Nature communications · 2026
    Review
  8. Article
  9. Article
  10. Bacteriophage genome-wide transposon mutagenesis.bioRxiv : the preprint server for biology · 2025
    Article
  11. Review
  12. Article
  13. Article
  14. Article
  15. Phage-based delivery of CRISPR-associated transposases for targeted bacterial editing.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  16. Review
  17. 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

23 authors.

Benjamin A Adler *California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-7488-3040
Muntathar J Al-Shimary *Innovative Genomics Institute, University of California, Berkeley, CA, USA.
Jaymin R PatelInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Emily G ArmbrusterSchool of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0003-0377-1209
David ColognoriCalifornia Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
Emeric J CharlesInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Kate V MillerInnovative Genomics Institute, University of California, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-5315-4172
Arushi LahiriDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Michael L CuiInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Agnès Oromí-BoschInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Angela VoelkerInnovative Genomics Institute, University of California, Berkeley, CA, USA.
Marena TrinidadInnovative Genomics Institute, University of California, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-7839-4642
Jina LeeSchool of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
Sebastien BeurnierDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.
Ron BogerCalifornia Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.ORCID http://orcid.org/0000-0002-4467-271X
Jason NomburgCalifornia Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA.
Rodolphe BarrangouDepartment of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, USA.ORCID http://orcid.org/0000-0002-0648-3504
Vivek K MutalikInnovative Genomics Institute, University of California, Berkeley, CA, USA.ORCID http://orcid.org/0000-0001-7934-0400
Joseph S SchoenigerSystems Biology Department, Sandia National Laboratories, Livermore, CA, USA.
Joseph A PoglianoSchool of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.ORCID http://orcid.org/0000-0001-8989-2655
David F SavageDepartment of Molecular and Cell Biology, University of California, Berkeley, CA, USA.ORCID http://orcid.org/0000-0003-0042-2257
Jennifer A DoudnaCalifornia Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA, USA. doudna@berkeley.edu.ORCID http://orcid.org/0000-0001-9161-999X
Brady F CressInnovative Genomics Institute, University of California, Berkeley, CA, USA. cress@berkeley.edu.ORCID http://orcid.org/0000-0002-2948-2846

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Bacteriophages constitute one of the largest reservoirs of genes of unknown function in the biosphere. Even in well-characterized phages, the functions of most genes remain unknown. Experimental approaches to study phage gene fitness and function at genome scale are lacking, partly because phages subvert many modern functional genomics tools. Here we leverage RNA-targeting dCas13d to selectively interfere with protein translation and to measure phage gene fitness at a transcriptome-wide scale. We find CRISPR Interference through Antisense RNA-Targeting (CRISPRi-ART) to be effective across phage phylogeny, from model ssRNA, ssDNA and dsDNA phages to nucleus-forming jumbo phages. Using CRISPRi-ART, we determine a conserved role of diverse rII homologues in subverting phage Lambda RexAB-mediated immunity to superinfection and identify genes critical for phage fitness. CRISPRi-ART establishes a broad-spectrum phage functional genomics platform, revealing more than 90 previously unknown genes important for phage fitness.

Indexed as

BacteriophagesCRISPR-Cas SystemsGenomicsRNA-Binding ProteinsBacteriophage lambdaGenetic FitnessGenome, ViralPhylogenyRNA-Binding Proteins

Identifiers

PMID40011704
PMCPMC11879866

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.