Evidence map›Paper›PMID 25775043›Full record

ArticleNature methods2015

Functional annotation of native enhancers with a Cas9-histone demethylase fusion.

Nicola A Kearns, Hannah Pham, Barbara Tabak, Ryan M Genga, Noah J Silverstein, Manuel Garber, René Maehr

Abstract read
In one paragraph

Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 356 papers.

0numbers the graph read from it
0cells of the map it votes in
356citing 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

356 citing papers in PubMed.

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  9. Advances and clinical potential of epigenome editing.Cellular and molecular life sciences : CMLS · 2026
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  11. Article
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  17. Epigenome editing based treatment: Progresses and challenges.Molecular therapy : the journal of the American Society of Gene Therapy · 2026
    Review
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  20. Review

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors.

Nicola A Kearns *Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Hannah Pham *Diabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Barbara TabakProgram in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Ryan M GengaDiabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Noah J SilversteinProgram in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
Manuel GarberProgram in Molecular Medicine, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.
René MaehrDiabetes Center of Excellence, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.

Funding

Rules of gene expression modeled on human dendritic cell response to pathogensU01HG007910 · NHGRI · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GARBER, MANUEL, LUBAN, JEREMY · 2015 to 2017
$6.1M
Dietary effects on the sperm epigenomeR01HD080224 · NICHD · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI RANDO, OLIVER J · 2014 to 2022
$5.9M
Humanized Mouse Avatars for T1DUC4DK104218 · NIDDK · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI BREHM, MICHAEL ALLEN, DALEY, GEORGE Q · 2014 to 2014
$4.1M
Using pluripotent stem cells to study gene dosage-dependent immunodeficiencyR56AI114525 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI MAEHR, RENE · 2015 to 2015
$514k
Functionally dissecting the transcriptional regulatory network of the innate immune response using CRISPR-effectorsR21AI119885 · NIAID · UNIV OF MASSACHUSETTS MED SCH WORCESTER · PI GARBER, MANUEL, MAEHR, RENE · 2015 to 2016
$461k
NHGRI NIH HHS U01 HG007910NIAID NIH HHS R21 AI119885NIAID NIH HHS R56 AI114525NICHD NIH HHS 1R01HD080224-01A1NICHD NIH HHS R01 HD080224NIDDK NIH HHS UC4 DK104218
6 · The paper itself

Abstract

Understanding of mammalian enhancers is limited by the lack of a technology to rapidly and thoroughly test the cell type-specific function. Here, we use a nuclease-deficient Cas9 (dCas9)-histone demethylase fusion to functionally characterize previously described and new enhancer elements for their roles in the embryonic stem cell state. Further, we distinguish the mechanism of action of dCas9-LSD1 at enhancers from previous dCas9-effectors.

Indexed as

AnimalsBacterial ProteinsCaspase 9Cells, CulturedEmbryonic Stem CellsEnhancer Elements, GeneticGene Expression Regulation, EnzymologicGenes, ReporterHistone DemethylasesHistonesMiceNeisseria meningitidisRecombinant ProteinsBacterial ProteinsCaspase 9Histone DemethylasesHistonesRecombinant Proteins

Identifiers

PMID25775043
PMCPMC4414811

What OpenQuestion holds

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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.