Evidence map›Paper›PMID 40014450›Full record

ArticleCell reports2025

B cell stimulation changes the structure and higher-order organization of the inactive X chromosome.

Isabel Sierra, Natalie E Toothacre, Robin H van der Weide, Claudia D Lovell, Son C Nguyen, R Jordan Barnett, Ashley L Cook, Han-Seul Ryu, Sarah Pyfrom, Harrison Wang and 4 more

Abstract read
In one paragraph

Article in Cell reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing 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

7 citing papers in PubMed.

  1. Sex-Biased Immunity: The Hidden Variable in Immuno-oncology.Clinical cancer research : an official journal of the American Association for Cancer Research · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

14 authors.

Isabel SierraDepartment of Biomedical Science, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
Natalie E ToothacreDepartment of Biomedical Science, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
Robin H van der WeideHubrecht Institute, Royal Netherlands Academy of Arts and Sciences (KNAW) and University Medical Center Utrecht, Utrecht, the Netherlands; Oncode Institute, University Medical Center Utrecht, Utrecht, the Netherlands.
Claudia D LovellDepartment of Biomedical Science, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
Son C NguyenDepartment of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
R Jordan BarnettDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
Ashley L CookDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
Han-Seul RyuDepartment of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA.
Sarah PyfromDepartment of Biomedical Science, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
Harrison WangDepartment of Biomedical Science, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Daniel BeitingDepartment of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
Jennifer E Philips-CreminsDepartment of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
Eric F JoyceDepartment of Genetics, Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA.
Montserrat C AngueraDepartment of Biomedical Science, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA USA. Electronic address: anguera@vet.upenn.edu.

Funding

From 3D genomes to neural connectomes: Higher-order chromatin mechanisms encoding long-term memoryDP1MH129957 · NIMH · WASHINGTON UNIVERSITY · PI PHILLIPS-CREMINS, JENNIFER ELIZABETH · 2021 to 2025
$5.7M
Engineering and Imaging 3D genome structure-function dynamics across time scalesU01DK127405 · NIDDK · UNIVERSITY OF PENNSYLVANIA · PI BLOBEL, GERD A, PHILLIPS-CREMINS, JENNIFER ELIZABETH · 2020 to 2024
$5.7M
Gene regulation mechanisms involving the inactive X in B cells during lupus diseaseR01AI134834 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI Montserrat C Anguera · 2018 to 2026
$4.2M
Regulation of chromatin folding in space and timeR35GM128903 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI Eric F. Joyce · 2018 to 2026
$4.2M
Single-cell dissection of chromatin architecture mechanisms connecting pathologic instability and transcriptional silencingU01DA052715 · NIDA · UNIVERSITY OF PENNSYLVANIA · PI JAIN, RAJAN, JOYCE, ERIC F. · 2020 to 2024
$3.1M
Connecting 3D genome misfolding to transcriptional silencing in fragile X syndromeR01MH120269 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI PHILLIPS-CREMINS, JENNIFER ELIZABETH · 2019 to 2024
$3.1M
Elucidating the 3-D epigenetic determinants of activity-dependent gene expression in mammalian neuronsR01NS114226 · NINDS · UNIVERSITY OF PENNSYLVANIA · PI PHILLIPS-CREMINS, JENNIFER ELIZABETH, SHEPHERD, JASON D · 2020 to 2024
$2.3M
Role for nuclear matrix proteins and DNA methylation for XCI maintenance in female lymphocytesR01AI168047 · NIAID · UNIVERSITY OF PENNSYLVANIA · PI Montserrat C Anguera · 2023 to 2026
$2.2M
Connecting 3D genome misfolding to transcriptional silencing in fragile X syndromeR37MH120269 · NIMH · WASHINGTON UNIVERSITY · PI Jennifer Elizabeth Phillips-Cremins · 2025 to 2026
$1.0M
Elucidating the Role of Dynamic X-Chromosome Inactivation Maintenance in the Pathogenesis of Systemic SclerosisR21AR081588 · NIAMS · UNIVERSITY OF PENNSYLVANIA · PI ANGUERA, MONTSERRAT C · 2022 to 2023
$393k
Investigating the nuclear organization of the inactive X in female lymphocytesF31GM136073 · NIGMS · UNIVERSITY OF PENNSYLVANIA · PI SIERRA, ISABEL · 2020 to 2022
$108k
NIAID NIH HHS R01 AI134834NIAID NIH HHS R01 AI168047NIAMS NIH HHS R21 AR081588NIDA NIH HHS U01 DA052715NIDDK NIH HHS U01 DK127405NIGMS NIH HHS F31 GM136073NIGMS NIH HHS R35 GM128903NIMH NIH HHS DP1 MH129957NIMH NIH HHS R01 MH120269NIMH NIH HHS R37 MH120269NINDS NIH HHS R01 NS114226
6 · The paper itself

Abstract

X chromosome inactivation (XCI) equalizes X-linked gene expression between sexes. B cells exhibit dynamic XCI, with Xist RNA/heterochromatic marks absent on the inactive X (Xi) in naive B cells but returning following mitogenic stimulation. The impact of dynamic XCI on Xi structure and maintenance was previously unknown. Here, we find dosage compensation of the Xi with state-specific XCI escape genes in naive and in vitro-activated B cells. Allele-specific OligoPaints indicate similar Xi and active X (Xa) territories in B cells that are less compact than in fibroblasts. Allele-specific Hi-C reveals a lack of TAD-like structures on the Xi of naive B cells and stimulation-induced alterations in TAD-like boundary strength independent of gene expression. Notably, Xist deletion in B cells changes TAD boundaries and large-scale Xi compaction. Altogether, our results uncover B cell-specific Xi plasticity, which could underlie sex-biased biological mechanisms.

Indexed as

B-LymphocytesX ChromosomeX Chromosome InactivationAnimalsFemaleFibroblastsGene Expression RegulationLymphocyte ActivationMaleMiceallele-specific Hi-CB cellsB cell stimulationchromosome compartmentschromosome structureCP: ImmunologyCP: Molecular biologyinactive X chromosomeTAD remodelingtopological associated domainsX chromosome inactivationXCI escape genesXCI maintenanceXist RNA

Identifiers

PMID40014450
PMCPMC11998099

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.