Evidence map›Paper›PMID 42098160›Full record

ArticleNature communications2026

Enhancer placement impacts transcriptional dynamics in Drosophila embryos.

Emilia A Leyes Porello, Jiayi Wu, Samantha Fallacaro, Emma Dreispiel Juan, Robert T Trudeau, J Andres Vidal, Shufan Lin, César Nieto, Abhyudai Singh, Mustafa Mir and 1 more

Abstract read
In one paragraph

Article in Nature communications, 2026. 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. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

11 authors.

Emilia A Leyes PorelloDepartment of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0002-2917-3883
Jiayi WuDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0009-0001-4980-1111
Samantha FallacaroDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0001-7749-0034
Emma Dreispiel JuanDepartment of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0009-0007-3189-3381
Robert T TrudeauDepartment of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0001-5659-9540
J Andres VidalDepartment of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA.
Shufan LinDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA, USA.
César NietoElectrical and Computer Engineering, University of Delaware, Newark, DE, USA.
Abhyudai SinghElectrical and Computer Engineering, University of Delaware, Newark, DE, USA.ORCID http://orcid.org/0000-0002-1451-2838
Mustafa MirDepartment of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.ORCID http://orcid.org/0000-0001-8280-2821
Bomyi LimDepartment of Chemical and Biomolecular Engineering, University of Pennsylvania, Philadelphia, PA, USA. bomyilim@seas.upenn.edu.ORCID http://orcid.org/0000-0002-3058-9181

Funding

Design principles and dynamic gene control in embryonic developmentR35GM133425 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Bomyi Lim · 2019 to 2026
$2.9M
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
Generalized fluctuation test for deciphering phenotypic switching within cell populationsR35GM148351 · NIGMS · UNIVERSITY OF DELAWARE · PI Abhyudai Singh · 2023 to 2026
$1.6M
National Science Foundation (NSF) DGE-2236662NICHD NIH HHS DP2 HD108775NIGMS NIH HHS R35 GM133425NIGMS NIH HHS R35 GM148351U.S. Department of Health & Human Services | National Institutes of Health (NIH) DP2HD108775U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM133425U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS) R35GM148351
6 · The paper itself

Abstract

The functional role of enhancer-promoter configurations in transcription regulation remains poorly understood, despite the wide range of linear genomic distance and relative enhancer positioning observed in endogenous contexts. While canonical models suggest that enhancers operate independently of genomic position, technical limitations have obscured insights on transcriptional kinetics. Here, we employ single-cell MS2/MCP-based live imaging in Drosophila embryos to systematically analyze transcriptional dynamics driven by sub-10kb enhancer-promoter arrangements. Kinetic analyses reveal that while linear enhancer-promoter distance moderately tunes transcriptional output, downstream enhancer positioning reduces mRNA output by 70%. Each configuration modulates distinct transcriptional parameters: linear distance governs initiation kinetics, while relative enhancer positioning dictates transcriptional active state stability. These effects are consistent across varied enhancer and reporter sequences, revealing configuration-dependent cis-regulatory element arrangement as an intrinsic mechanism for transcriptional fine-tuning. This work directly correlates enhancer-promoter configuration with a distinct transcription property for the first time and establishes a framework to dissect the interplay between genome architecture and transcription regulation.

Indexed as

Drosophila melanogasterEnhancer Elements, GeneticGene Expression Regulation, DevelopmentalTranscription, GeneticAnimalsEmbryo, NonmammalianKineticsPromoter Regions, GeneticRNA, MessengerRNA, Messenger

Identifiers

PMID42098160
PMCPMC13365399

What Socratic 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 Socratic graph.