Evidence map›Paper›PMID 25533786›Full record

ArticleCell2015

Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds.

Jesse G Zalatan, Michael E Lee, Ricardo Almeida, Luke A Gilbert, Evan H Whitehead, Marie La Russa, Jordan C Tsai, Jonathan S Weissman, John E Dueber, Lei S Qi and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 479 papers.

0numbers the graph read from it
0cells of the map it votes in
479citing 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

479 citing papers in PubMed.

  1. Article
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  10. Article
  11. Review
  12. Elucidating the design principles for engineering plant organ size.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  13. Review
  14. Advances in Engineered Virus-Like Particles for Genome Editing and Therapy.BioDrugs : clinical immunotherapeutics, biopharmaceuticals and gene therapy · 2026
    Review
  15. Epigenetic editing: from concept to clinic.Nature reviews. Drug discovery · 2026
    Review
  16. Article
  17. Article
  18. Article
  19. Article
  20. Review

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Jesse G ZalatanDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA.
Michael E LeeDepartment of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Ricardo AlmeidaDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA.
Luke A GilbertDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
Evan H WhiteheadDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, University of California San Francisco, San Francisco, CA 94158, USA.
Marie La RussaDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, University of California San Francisco, San Francisco, CA 94158, USA; Biomedical Sciences Graduate Program, University of California San Francisco, San Francisco, CA 94158, USA.
Jordan C TsaiDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA.
Jonathan S WeissmanDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; Center for RNA Systems Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA.
John E DueberDepartment of Bioengineering, University of California, Berkeley, Berkeley, CA 94720, USA; Energy Biosciences Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
Lei S QiDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, University of California San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA. Electronic address: slqi@stanford.edu.
Wendell A LimDepartment of Cellular and Molecular Pharmacology, University of California San Francisco, San Francisco, CA 94158, USA; Howard Hughes Medical Institute, University of California San Francisco, San Francisco, CA 94158, USA; UCSF Center for Systems and Synthetic Biology, University of California San Francisco, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, San Francisco, CA 94158, USA. Electronic address: wendell.lim@ucsf.edu.

Funding

Rewiring Therapeutic Cells: User-Controlled T Cells and Stem CellsP50GM081879 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, WENDELL A · 2010 to 2017
$19.0M
PREDOCTORAL TRAINING IN BIOMEDICAL SCIENCEST32GM008568 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI ANSEL, KARL MARK · 1995 to 2019
$6.3M
Harnessing CRISPR for Targeted and Inducible Epigenomic ReprogrammingR01DA036858 · NIDA · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI LIM, WENDELL A, QI, LEI STANLEY · 2013 to 2017
$2.9M
A novel RNA-guided platform for sequence-specific cell reprogrammingDP5OD017887 · OD · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI QI, LEI STANLEY · 2013 to 2017
$2.0M
Howard Hughes Medical InstituteNIDA NIH HHS R01 DA036858NIGMS NIH HHS P50 GM081879NIGMS NIH HHS P50GM081879NIGMS NIH HHS T32 GM008568NIH HHS DP5 OD017887
6 · The paper itself

Abstract

Eukaryotic cells execute complex transcriptional programs in which specific loci throughout the genome are regulated in distinct ways by targeted regulatory assemblies. We have applied this principle to generate synthetic CRISPR-based transcriptional programs in yeast and human cells. By extending guide RNAs to include effector protein recruitment sites, we construct modular scaffold RNAs that encode both target locus and regulatory action. Sets of scaffold RNAs can be used to generate synthetic multigene transcriptional programs in which some genes are activated and others are repressed. We apply this approach to flexibly redirect flux through a complex branched metabolic pathway in yeast. Moreover, these programs can be executed by inducing expression of the dCas9 protein, which acts as a single master regulatory control point. CRISPR-associated RNA scaffolds provide a powerful way to construct synthetic gene expression programs for a wide range of applications, including rewiring cell fates or engineering metabolic pathways.

Indexed as

CRISPR-Cas SystemsGene ExpressionGenetic TechniquesHEK293 CellsHumansMetabolic EngineeringRNA, Guide, CRISPR-Cas SystemsSaccharomyces cerevisiaeStreptococcus pyogenesRNA, Guide, CRISPR-Cas Systems

Identifiers

PMID25533786
PMCPMC4297522

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.