Evidence map›Paper›PMID 37162887›Full record

ArticlebioRxiv : the preprint server for biology2023

Competition between transcription and loop extrusion modulates promoter and enhancer dynamics.

Angeliki Platania, Cathie Erb, Mariano Barbieri, Bastien Molcrette, Erwan Grandgirard, Marit Ac de Kort, Karen Meaburn, Tiegh Taylor, Virlana M Shchuka, Silvia Kocanova and 8 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Review
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

18 authors.

Angeliki PlataniaDepartment of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France.
Cathie ErbDepartment of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France.
Mariano BarbieriTranslational Epigenetics Group, Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany.
Bastien MolcretteDepartment of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France.
Erwan GrandgirardDepartment of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France.
Marit Ac de KortDivision of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands.
Karen MeaburnGenome Damage and Stability Centre, Sussex University, School of Life Sciences, University of Sussex, Brighton, UK.
Tiegh TaylorDepartment of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada.
Virlana M ShchukaDepartment of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada.
Silvia KocanovaMolecular Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI) University of Toulouse Paul Sabatier, CNRS, 31062 Toulouse, France.
Guilherme Monteiro OliveiraDepartment of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France.
Jennifer A MitchellDepartment of Cell and Systems Biology, University of Toronto, Toronto, Ontario M55 3G5, Canada.
Evi SoutoglouGenome Damage and Stability Centre, Sussex University, School of Life Sciences, University of Sussex, Brighton, UK.
Tineke L LenstraDivision of Gene Regulation, the Netherlands Cancer Institute, Oncode Institute, 1066CX Amsterdam, the Netherlands.
Nacho MolinaDepartment of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France.
Argyris PapantonisTranslational Epigenetics Group, Institute of Pathology, University Medical Centre Göttingen, Göttingen, Germany.
Kerstin BystrickyMolecular Cellular and Developmental Biology unit (MCD), Centre de Biologie Integrative (CBI) University of Toulouse Paul Sabatier, CNRS, 31062 Toulouse, France.
Tom SextonDepartment of Functional Genomics and Cancer, Institute of Genetics and Molecular and Cellular Biology (IGBMC), UMR7104, Centre National de la Recherche Scientifique, U1258, Institut National de la Santé et de la Recherche Médicale, University of Strasbourg, 6704 Illkirch, France.

Funding

Computational approaches for comparative regulatory genomics to decipher long-range gene regulationR01HG010045 · NHGRI · UNIVERSITY OF WISCONSIN-MADISON · PI ROY, SUSHMITA · 2018 to 2021
$1.4M
NHGRI NIH HHS R01 HG010045
6 · The paper itself

Abstract

The spatiotemporal configuration of genes with distal regulatory elements, and the impact of chromatin mobility on transcription, remain unclear. Loop extrusion is an attractive model for bringing genetic elements together, but how this functionally interacts with transcription is also largely unknown. We combine live tracking of genomic loci and nascent transcripts with molecular dynamics simulations to assess the 4D arrangement of the

Indexed as

anomalous diffusionChromatin dynamicsenhancerlive imagingmolecular dynamicstranscription

Identifiers

PMID37162887
PMCPMC10168261

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
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.