Evidence map›Paper›PMID 38659757›Full record

ArticlebioRxiv : the preprint server for biology2024

A fine kinetic balance of interactions directs transcription factor hubs to genes.

Samantha Fallacaro, Apratim Mukherjee, Puttachai Ratchasanmuang, Joseph Zinski, Yara I Haloush, Kareena Shankta, Mustafa Mir

Open access · greenAbstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

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

0 citing papers in PubMed, 16 citations in OpenAlex.

No citing paper in PubMed yet.

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

7 authors at 1 institution in 1 country.

Samantha FallacaroDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA.ORCID 0000-0001-7749-0034
Apratim MukherjeeDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA.ORCID 0000-0002-1762-3277
Puttachai RatchasanmuangCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.ORCID 0000-0003-1443-825X
Joseph ZinskiDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA.ORCID 0000-0002-5120-5386
Yara I HaloushCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.
Kareena ShanktaCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.
Mustafa MirDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA.ORCID 0000-0001-8280-2821
Children's Hospital of Philadelphia · US

Funding

Structural biology and molecular biophysics training programT32GM132039 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Ben E. Black, Elizabeth Rhoades · 2019 to 2026
$3.3M
Quantifying the dynamics of gene regulation and nuclear organization during embryogenesisDP2HD108775 · NICHD · CHILDREN'S HOSP OF PHILADELPHIA · PI MIR, MUSTAFA AIZED HASAN · 2021 to 2024
$2.6M
NICHD NIH HHS DP2 HD108775NIGMS NIH HHS T32 GM132039
6 · The paper itself

Abstract

Eukaryotic gene regulation relies on the binding of sequence-specific transcription factors (TFs). TFs bind chromatin transiently yet occupy their target sites by forming high-local concentration microenvironments (hubs and condensates) that increase the frequency of binding. Despite their ubiquity, such microenvironments are difficult to study in endogenous contexts due to technical limitations. Here, we use live embryo light-sheet imaging, single-molecule tracking, and genomics to overcome these limitations and investigate how hubs are localized to target genes to drive TF occupancy and transcription. By examining mutants of a hub-forming TF, Zelda, in

Identifiers

PMID38659757
PMCPMC11042322
OpenAlexW4394887657

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.