Evidence map›Paper›PMID 25274302›Full record

ArticleNature2014

Programmable RNA recognition and cleavage by CRISPR/Cas9.

Mitchell R O'Connell, Benjamin L Oakes, Samuel H Sternberg, Alexandra East-Seletsky, Matias Kaplan, Jennifer A Doudna

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 313 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
313citing papers in PubMed, 1 pooled it
28.3field-weighted citation impact, top 1% of its field
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

313 citing papers in PubMed, 1 synthesis or guideline pooled it, 634 citations in OpenAlex.

  1. Engineering CRISPR guide RNAs for programmable RNA sensors.Biochemical Society transactions · 2023
    Pooled it
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  20. Treating genetic blood disorders in the era of CRISPR-mediated genome editing.Molecular therapy : the journal of the American Society of Gene Therapy · 2025
    Review

253 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

6 authors at 2 institutions in 1 country.

Mitchell R O'ConnellDepartment of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.
Benjamin L OakesDepartment of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.
Samuel H SternbergDepartment of Chemistry, University of California, Berkeley, California 94720, USA.
Alexandra East-SeletskyDepartment of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA.
Matias Kaplan1] Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA [2] Department of Agricultural and Biological Engineering, University of Florida, Gainesville, Florida 32611, USA.
Jennifer A Doudna1] Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, USA [2] Department of Chemistry, University of California, Berkeley, California 94720, USA [3] Howard Hughes Medical Institute, University of California, Berkeley, California 94720, USA [4] Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
University of California, Berkeley · USHoward Hughes Medical Institute · US

Funding

THE MOLECULAR BASIS OF CELL FUNCTIONT32GM007232 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI BILDER, DAVID, UNAL, ELCIN · 1985 to 2022
$36.4M
PROJECT 3P50GM102706 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI CATE, JAMIE H · 2012 to 2016
$9.5M
Univ of Calif Berkeley Chemistry-Biology Interface ProgramT32GM066698 · NIGMS · UNIVERSITY OF CALIFORNIA BERKELEY · PI CHANG, CHRISTOPHER J., FRANCIS, MATTHEW B · 2004 to 2023
$7.5M
Howard Hughes Medical InstituteNIGMS NIH HHS P50 GM102706NIGMS NIH HHS P50GM102706-03NIGMS NIH HHS T32 GM007232NIGMS NIH HHS T32 GM066698
6 · The paper itself

Abstract

The CRISPR-associated protein Cas9 is an RNA-guided DNA endonuclease that uses RNA-DNA complementarity to identify target sites for sequence-specific double-stranded DNA (dsDNA) cleavage. In its native context, Cas9 acts on DNA substrates exclusively because both binding and catalysis require recognition of a short DNA sequence, known as the protospacer adjacent motif (PAM), next to and on the strand opposite the twenty-nucleotide target site in dsDNA. Cas9 has proven to be a versatile tool for genome engineering and gene regulation in a large range of prokaryotic and eukaryotic cell types, and in whole organisms, but it has been thought to be incapable of targeting RNA. Here we show that Cas9 binds with high affinity to single-stranded RNA (ssRNA) targets matching the Cas9-associated guide RNA sequence when the PAM is presented in trans as a separate DNA oligonucleotide. Furthermore, PAM-presenting oligonucleotides (PAMmers) stimulate site-specific endonucleolytic cleavage of ssRNA targets, similar to PAM-mediated stimulation of Cas9-catalysed DNA cleavage. Using specially designed PAMmers, Cas9 can be specifically directed to bind or cut RNA targets while avoiding corresponding DNA sequences, and we demonstrate that this strategy enables the isolation of a specific endogenous messenger RNA from cells. These results reveal a fundamental connection between PAM binding and substrate selection by Cas9, and highlight the utility of Cas9 for programmable transcript recognition without the need for tags.

Indexed as

Base SequenceCell ExtractsClustered Regularly Interspaced Short Palindromic RepeatsCRISPR-Associated ProteinsCRISPR-Cas SystemsDNAGenetic EngineeringGlyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)HeLa CellsHumansNucleotide MotifsOligonucleotidesRNARNA, Guide, CRISPR-Cas SystemsRNA, MessengerSubstrate SpecificityCell ExtractsCRISPR-Associated ProteinsDNAGlyceraldehyde-3-Phosphate Dehydrogenase (Phosphorylating)OligonucleotidesRNARNA, Guide, CRISPR-Cas SystemsRNA, Messenger

Identifiers

PMID25274302
PMCPMC4268322
OpenAlexW2030974598

What OpenQuestion holds

Textmetadata
LicenceTDM
Read underepoch 390

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.