Evidence map›Paper›PMID 42282796›Full record

ArticlebioRxiv : the preprint server for biology2026

POCKET-seq enables genome-wide profiling of on- and off-target transcriptional regulation events by dCas9-KRAB during CRISPR interference experiments.

Christine M Joyce, Griffin D Kramer, Jonathan T Vu, Katherine U Tavasoli, Brooke M Gardner, Chris D Richardson

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing 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

0 citing papers in PubMed.

No citing paper in PubMed yet.

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

6 authors.

Christine M JoyceDepartment of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
Griffin D KramerDepartment of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.
Jonathan T VuBiomolecular Science and Engineering Program, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.ORCID 0000-0002-4950-7967
Katherine U TavasoliDepartment of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.ORCID 0009-0006-4421-6390
Brooke M GardnerDepartment of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.ORCID 0000-0001-7999-8827
Chris D RichardsonDepartment of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA.ORCID 0000-0003-3122-4851

Funding

Investigating the mechanisms of peroxisome homeostasisR35GM146784 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI Brooke Meghan Gardner · 2022 to 2026
$2.1M
Defining DNA resection and protein localization changes that occur during DSB repairR35GM142975 · NIGMS · UNIVERSITY OF CALIFORNIA SANTA BARBARA · PI RICHARDSON, CHRIS · 2021 to 2025
$1.9M
NIGMS NIH HHS R35 GM142975NIGMS NIH HHS R35 GM146784
6 · The paper itself

Abstract

CRISPR interference screens use catalytically inactive dCas9 fused to a repressor domain to enable genetic perturbations at the transcriptomic level. Interpretation of results involves identification of guide RNAs associated with the screen phenotype, followed by secondary analysis. During validation of a genetic screen, we observed different phenotypes from non-overlapping guide RNAs targeting one gene. Here, we developed POCKET-seq to map the binding of dCas9 genome-wide. We show that off-target binding occurs frequently and can generate false-positive interactions when it occurs near the promoter of genes associated with the screen phenotype. POCKET-seq classifies these false-positive and true-positive interactions using gene ontology.

Indexed as

ChIP-seqCRISPR interferenceCRISPR screendCas9-KRABgene ontologyoff-target

Identifiers

PMID42282796
PMCPMC13252386

What OpenQuestion holds

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LicenceCC BY
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Registered trials

None linked

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.