Evidence map›Paper›PMID 39676667›Full record

ArticleNucleic acids research2025

A modular toolbox for the optogenetic deactivation of transcription.

Philipp Muench, Matteo Fiumara, Nicholas Southern, Davide Coda, Sabine Aschenbrenner, Bruno Correia, Johannes Gräff, Dominik Niopek, Jan Mathony

Erratum issuedAbstract read
In one paragraph

Article in Nucleic acids research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Philipp MuenchDepartment of Biology, Technical University of Darmstadt, Schnittspahnstraße 10, Darmstadt 64287, Germany.
Matteo FiumaraLaboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), SV 2513 (Bâtiment SV) - Station 19, Lausanne CH-1015, Switzerland.
Nicholas SouthernInstitute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.
Davide CodaLaboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), SV 2513 (Bâtiment SV) - Station 19, Lausanne CH-1015, Switzerland.
Sabine AschenbrennerInstitute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.
Bruno CorreiaInstitute of Bioengineering, École Polytechnique Fédérale de Lausanne, AI 3138 (Bâtiment AI) - Station 19, Lausanne CH-1015, Switzerland.
Johannes GräffLaboratory of Neuroepigenetics, Brain Mind Institute, School of Life Sciences, École Polytechnique Fédérale de Lausanne (EPFL), SV 2513 (Bâtiment SV) - Station 19, Lausanne CH-1015, Switzerland.
Dominik NiopekInstitute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.ORCID 0000-0001-7479-530X
Jan MathonyInstitute of Pharmacy and Molecular Biotechnology (IPMB), Faculty of Engineering Sciences, Heidelberg University, Im Neuenheimer Feld 364, Heidelberg 69120, Germany.

Funding

Aventis FoundationERC/SERI CoG 101043457European Union 101041570Executive AgencyGerman Research Foundation 453202693HFSPSERI CoG 101043457Swiss National Science Foundation 310 030_197752Vallee Foundation
6 · The paper itself

Abstract

Light-controlled transcriptional activation is a commonly used optogenetic strategy that allows researchers to regulate gene expression with high spatiotemporal precision. The vast majority of existing tools are, however, limited to light-triggered induction of gene expression. Here, we inverted this mode of action and created optogenetic systems capable of efficiently terminating transcriptional activation in response to blue light. First, we designed highly compact regulators by photo-controlling the VP16 (pcVP16) transactivation peptide. Then, applying a two-hybrid strategy, we engineered LOOMINA (light off-operated modular inductor of transcriptional activation), a versatile transcriptional control platform for mammalian cells that is compatible with various effector proteins. Leveraging the flexibility of CRISPR systems, we combined LOOMINA with dCas9 to control transcription with blue light from endogenous promoters with exceptionally high dynamic ranges in multiple cell lines. Functionally and mechanistically, the versatile LOOMINA platform and the exceptionally compact pcVP16 transactivator represent valuable additions to the optogenetic repertoire for transcriptional regulation.

Indexed as

OptogeneticsTranscriptional ActivationTranscription, GeneticAnimalsCRISPR-Cas SystemsGene Expression RegulationHEK293 CellsHerpes Simplex Virus Protein Vmw65HumansLightPromoter Regions, GeneticTrans-ActivatorsHerpes Simplex Virus Protein Vmw65Trans-Activators

Identifiers

PMID39676667
PMCPMC11797043

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.