Evidence map›Paper›PMID 41365655›Full record

ArticleGenome research2026

Genome-wide nucleosome and transcription factor responses to genetic perturbations reveal chromatin-mediated mechanisms of transcriptional regulation.

Kevin Moyung, Yulong Li, Heather K MacAlpine, Alexander J Hartemink, David M MacAlpine

Abstract read
In one paragraph

Article in Genome research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

5 authors.

Kevin MoyungProgram in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA.ORCID 0000-0001-8068-7620
Yulong LiDepartment of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.
Heather K MacAlpineDepartment of Pharmacology and Cancer Biology, Duke University Medical Center, Durham, North Carolina 27710, USA.
Alexander J HarteminkProgram in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; david.macalpine@duke.edu amink@cs.duke.edu.ORCID 0000-0002-1292-2606
David M MacAlpineProgram in Computational Biology and Bioinformatics, Duke University, Durham, North Carolina 27708, USA; david.macalpine@duke.edu amink@cs.duke.edu.

Funding

Chromatin-mediated mechanisms of genome integrityR35GM127062 · NIGMS · DUKE UNIVERSITY · PI David M MacAlpine · 2018 to 2026
$3.7M
Methods to Elucidate the Dynamics of Transcriptional Regulation and ChromatinR35GM141795 · NIGMS · DUKE UNIVERSITY · PI HARTEMINK, ALEXANDER J · 2021 to 2025
$2.1M
NIGMS NIH HHS R35 GM127062NIGMS NIH HHS R35 GM141795
6 · The paper itself

Abstract

Epigenetic mechanisms contribute to gene regulation by altering chromatin accessibility through changes in transcription factor (TF) and nucleosome occupancy across the genome. Despite numerous studies focusing on changes in gene expression, the intricate chromatin-mediated regulatory code remains largely uncharted on a comprehensive scale. We address this by employing a factor-agnostic, reverse-genetics approach that uses MNase-seq to capture genome-wide TF and nucleosome occupancies in response to the individual deletion of 201 transcriptional regulators in

Indexed as

ChromatinGene Expression Regulation, FungalNucleosomesTranscription FactorsTranscription, GeneticEpigenesis, GeneticGene Regulatory NetworksGenome, FungalSaccharomyces cerevisiaeSaccharomyces cerevisiae ProteinsChromatinNucleosomesSaccharomyces cerevisiae ProteinsTranscription Factors

Identifiers

PMID41365655
PMCPMC12758391

What Socratic holds

Textmetadata
LicenceCC BY-NC
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.