Evidence map›Paper›PMID 39990393›Full record

ArticlebioRxiv : the preprint server for biology2025

A single cluster of RNA Polymerase II molecules is stably associated with active genes.

Apratim Mukherjee, Manya Kapoor, Kareena Shankta, Samantha Fallacaro, Raymond D Carter, Gabriela Hayward-Lara, Puttachai Ratchasanmuang, Yara I Haloush, Mustafa Mir

Abstract readPreprint
In one paragraph

Article in bioRxiv : the preprint server for biology, 2025. 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.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

9 authors.

Apratim MukherjeeDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA.ORCID 0000-0002-1762-3277
Manya KapoorCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.ORCID 0000-0002-0352-5131
Kareena ShanktaCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.
Samantha FallacaroCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.ORCID 0000-0001-7749-0034
Raymond D CarterCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.ORCID 0000-0002-9226-9159
Gabriela Hayward-LaraCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.
Puttachai RatchasanmuangCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.ORCID 0000-0003-1443-825X
Yara I HaloushCenter for Computational and Genomic Medicine, Children's Hospital of Philadelphia; Philadelphia, PA 19104, USA.ORCID 0009-0009-1438-3421
Mustafa MirDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania; Philadelphia, PA 19104, USA.ORCID 0000-0001-8280-2821

Funding

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 HD108775
6 · The paper itself

Abstract

In eukaryotic nuclei, transcription is associated with the clustering of RNA Polymerase II (RNAPII) molecules. The mechanisms underlying cluster formation, their interactions with genes, and their impact on transcriptional activity remain heavily debated. Here we take advantage of the naturally occurring increase in transcriptional activity during Zygotic Genome Activation (ZGA) in

Identifiers

PMID39990393
PMCPMC11844394

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.