Evidence map›Paper›PMID 40994625›Full record

ArticlebioRxiv : the preprint server for biology2025

The functional organization of chromosome territories in single nuclei during zygotic genome activation.

Akshada Shankar Ganesh, Taylor M Orban, Romir Raj, Peter I Fatzinger, Anna Johnson, Sean M Riccard, Akhmed Zhanaidarov, Mayu Inaba, Jelena Erceg

Abstract readPreprint
PubMed Full text at PMC Publisher
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.

Akshada Shankar GaneshDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Taylor M OrbanDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Romir RajDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Peter I FatzingerDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Anna JohnsonDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Sean M RiccardDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Akhmed ZhanaidarovDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.
Mayu InabaDepartment of Cell Biology, University of Connecticut Health Center, Farmington, CT 06032, USA.
Jelena ErcegDepartment of Molecular and Cell Biology, University of Connecticut, Storrs, CT 06269, USA.

Funding

Nanotube-mediated regulation of niche-stem cell signalingR35GM128678 · NIGMS · UNIVERSITY OF CONNECTICUT SCH OF MED/DNT · PI Mayu Inaba-Oguro · 2018 to 2026
$3.3M
Genome Folding and Regulation in Diploid Multicellular OrganismsR35GM146922 · NIGMS · UNIVERSITY OF CONNECTICUT STORRS · PI Jelena Erceg · 2022 to 2026
$2.0M
NIGMS NIH HHS R35 GM128678NIGMS NIH HHS R35 GM146922
6 · The paper itself

Abstract

Chromosome territories (CTs) are intricately organized and regulated within the nucleus. Despite remarkable advances in our understanding of genome packaging and gene expression, the interplay among CTs, pairing of parental homologous chromosomes, and genome function during development remains elusive. Here, we employ an Oligopaints-based high-resolution imaging approach to examine variable CT organization in single nuclei during the developmental process of zygotic genome activation. We reveal large-scale chromosome changes with extensive homolog pairing at the whole-chromosome level that decreases locally due to spatial variability in chromosome conformations. In the absence of one homolog copy, the dynamics of CT compaction and RNA polymerase II recruitment are supported by transcriptional changes in haploid embryos. Finally, global inhibition of transcription results in decreased CT opening and no significant impact on CT pairing levels. These findings enhance our understanding of parental genome folding and regulation, which may inform strategies for chromosome-based diseases.

Indexed as

chromosome territories (CTs)haploidhomolog pairingRNA polymerase IItranscriptionzygotic genome activation (ZGA)

Identifiers

PMID40994625
PMCPMC12456445

What OpenQuestion holds

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Registered trials

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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.