Evidence map›Paper›PMID 34930411›Full record

ArticleGenome biology2021

Quantitative-enhancer-FACS-seq (QeFS) reveals epistatic interactions among motifs within transcriptional enhancers in developing Drosophila tissue.

Colin T Waters, Stephen S Gisselbrecht, Yuliya A Sytnikova, Tiziana M Cafarelli, David E Hill, Martha L Bulyk

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
0.2field-weighted citation impact, top 46% 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

3 citing papers in PubMed, 5 citations in OpenAlex.

  1. Article
  2. Review
  3. Article
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 at 2 institutions in 1 country.

Colin T Waters *Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
Stephen S Gisselbrecht *Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.ORCID 0000-0001-8723-902X
Yuliya A SytnikovaDivision of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
Tiziana M CafarelliCenter for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
David E HillCenter for Cancer Systems Biology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA.
Martha L BulykDivision of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA. mlbulyk@genetics.med.harvard.edu.
Brigham and Women's Hospital · USHarvard University · US

Funding

Training Program in Bioinformatics and Integrative GenomicsT32HG002295 · NHGRI · MASSACHUSETTS INSTITUTE OF TECHNOLOGY · PI Peter J Park · 2001 to 2026
$15.8M
High-Throughput Identification of Tissue/Cell-Type-Specific Cis Regulatory ModuleR01HG005287 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI BULYK, MARTHA L · 2010 to 2016
$3.4M
Transcriptional silencers inDrosophilaR01HG009723 · NHGRI · BRIGHAM AND WOMEN'S HOSPITAL · PI BULYK, MARTHA L · 2017 to 2020
$2.7M
NHGRI NIH HHS R01 HG005287NHGRI NIH HHS R01 HG009723NHGRI NIH HHS T32 HG002295NIH HHS R01 HG005287NIH HHS R01 HG009723
6 · The paper itself

Abstract

Understanding the contributions of transcription factor DNA binding sites to transcriptional enhancers is a significant challenge. We developed Quantitative enhancer-FACS-Seq for highly parallel quantification of enhancer activities from a genomically integrated reporter in Drosophila melanogaster embryos. We investigate the contributions of the DNA binding motifs of four poorly characterized TFs to the activities of twelve embryonic mesodermal enhancers. We measure quantitative changes in enhancer activity and discover a range of epistatic interactions among the motifs, both synergistic and alleviating. We find that understanding the regulatory consequences of TF binding motifs requires that they be investigated in combination across enhancer contexts.

Indexed as

Enhancer Elements, GeneticTranscription, GeneticAnimalsBinding SitesDNADNA-Binding ProteinsDrosophilaDrosophila melanogasterDrosophila ProteinsGene Expression Regulation, DevelopmentalMesodermTranscription FactorsDNADNA-Binding ProteinsDrosophila ProteinsTranscription FactorsDrosophila embryonic mesodermEnhancersEpistasisReporter assayTranscription factor binding sites

Identifiers

PMID34930411
PMCPMC8686523
OpenAlexW4200195028

What OpenQuestion holds

Textmetadata
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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.