Evidence map›Paper›PMID 29358654›Full record

ArticleNature genetics2018

Genetic determinants and epigenetic effects of pioneer-factor occupancy.

Julie Donaghey, Sudhir Thakurela, Jocelyn Charlton, Jennifer S Chen, Zachary D Smith, Hongcang Gu, Ramona Pop, Kendell Clement, Elena K Stamenova, Rahul Karnik and 7 more

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

Article in Nature genetics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 116 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
116citing papers in PubMed, 1 pooled it
9.0field-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

116 citing papers in PubMed, 1 synthesis or guideline pooled it, 185 citations in OpenAlex.

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

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

17 authors at 3 institutions in 3 countries.

Julie DonagheyBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Sudhir ThakurelaBroad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID http://orcid.org/0000-0003-1285-8680
Jocelyn CharltonDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Jennifer S ChenDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Zachary D SmithBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Hongcang GuBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Ramona PopDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.
Kendell ClementBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Elena K StamenovaBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Rahul KarnikBroad Institute of MIT and Harvard, Cambridge, MA, USA.
David R KelleyDepartment of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.ORCID http://orcid.org/0000-0001-7782-3548
Casey A GiffordBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Davide CacchiarelliBroad Institute of MIT and Harvard, Cambridge, MA, USA.
John L RinnBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Andreas GnirkeBroad Institute of MIT and Harvard, Cambridge, MA, USA.
Michael J ZillerDepartment for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany.
Alexander MeissnerBroad Institute of MIT and Harvard, Cambridge, MA, USA. meissner@molgen.mpg.de.ORCID http://orcid.org/0000-0001-8646-7469
Broad Institute · USHarvard University · USMax Planck Institute of Psychiatry · DE

Funding

Center for Cell CircuitsP50HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI REGEV, AVIV · 2011 to 2015
$15.6M
Center for Cell CircuitsRM1HG006193 · NHGRI · BROAD INSTITUTE, INC. · PI BLAINEY, PAUL CLARK, HACOHEN, NIR · 2016 to 2020
$14.9M
NHGRI NIH HHS P50 HG006193NHGRI NIH HHS RM1 HG006193
6 · The paper itself

Abstract

Transcription factors (TFs) direct developmental transitions by binding to target DNA sequences, influencing gene expression and establishing complex gene-regultory networks. To systematically determine the molecular components that enable or constrain TF activity, we investigated the genomic occupancy of FOXA2, GATA4 and OCT4 in several cell types. Despite their classification as pioneer factors, all three TFs exhibit cell-type-specific binding, even when supraphysiologically and ectopically expressed. However, FOXA2 and GATA4 can be distinguished by low enrichment at loci that are highly occupied by these factors in alternative cell types. We find that expression of additional cofactors increases enrichment at a subset of these sites. Finally, FOXA2 occupancy and changes to DNA accessibility can occur in G

Indexed as

A549 CellsBinding SitesCell LineageCells, CulturedComputational BiologyDNAEpigenesis, GeneticEpistasis, GeneticGATA4 Transcription FactorGene Expression RegulationGene Regulatory NetworksGenes, SwitchHEK293 CellsHepatocyte Nuclear Factor 3-betaHep G2 CellsHumansDNAFOXA2 protein, humanGATA4 protein, humanGATA4 Transcription FactorHepatocyte Nuclear Factor 3-betaOctamer Transcription Factor-3POU5F1 protein, humanTranscription Factors

Identifiers

PMID29358654
PMCPMC6517675
OpenAlexW2785791409

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.