Evidence map›Paper›PMID 39948644›Full record

ArticleGenome biology2025

Unveiling the role of chromosome structure morphology on gene function through chromosome conformation analysis.

Yuxiang Zhan, Asli Yildirim, Lorenzo Boninsegna, Frank Alber

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.

0numbers the graph read from it
0cells of the map it votes in
4citing 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

4 citing papers in PubMed.

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

Corrections and comments

5 · Who and what money

Authors and funding

4 authors.

Yuxiang ZhanDepartment of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Asli YildirimDepartment of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Lorenzo BoninsegnaDepartment of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA.
Frank AlberDepartment of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA, 90095, USA. falber@g.ucla.edu.ORCID http://orcid.org/0000-0003-1981-8390

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Single-cell chromosome conformations vary significantly among individual cells. We introduce a two-step dimensionality reduction method for density-based, unsupervised clustering of single-cell 3D chromosome structures from simulations or multiplexed 3D-FISH imaging. Our method clusters up to half of all structures into 5-12 prevalent conformational states per chromosome. These states are distinguished by subdivisions into chromosome territory domains, whose boundary locations influence subnuclear positions and speckle associations of certain genes and establish long-range structural variations of more than 10 Mb. Territory domain boundaries are found at few sequence locations, shared among cell types and often situated at syntenic breakpoints.

Indexed as

ChromosomesChromosome StructuresNucleic Acid ConformationHumansIn Situ Hybridization, FluorescenceSingle-Cell AnalysisCell-to-cell heterogeneityChromosome structureConformational statesDimension reductionGene transcriptionGenome structure variationGenomics

Identifiers

PMID39948644
PMCPMC11827233

What Socratic 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 Socratic graph.