Evidence map›Paper›PMID 38844479›Full record

ArticleNature communications2024

Pre-hypertrophic chondrogenic enhancer landscape of limb and axial skeleton development.

Fabrice Darbellay, Anna Ramisch, Lucille Lopez-Delisle, Michael Kosicki, Antonella Rauseo, Zahra Jouini, Axel Visel, Guillaume Andrey

Abstract read
In one paragraph

Article in Nature communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.

0numbers the graph read from it
0cells of the map it votes in
10citing 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

10 citing papers in PubMed.

  1. Review
  2. Review
  3. Evolution of repressive sequences within an enhancer contributed to morphological diversity in crucifer plants.Proceedings of the National Academy of Sciences of the United States of America · 2025
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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Fabrice DarbellayDepartment of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland.ORCID http://orcid.org/0000-0001-6942-3325
Anna RamischDepartment of Basic Neurosciences, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland.ORCID http://orcid.org/0000-0002-0641-4330
Lucille Lopez-DelisleSchool of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015, Lausanne, Switzerland.ORCID http://orcid.org/0000-0002-1964-4960
Michael KosickiEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA.
Antonella RauseoDepartment of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland.
Zahra JouiniDepartment of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland.ORCID http://orcid.org/0009-0004-8188-7789
Axel ViselEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley Laboratory, Berkeley, CA, 94720, USA.ORCID http://orcid.org/0000-0002-4130-7784
Guillaume AndreyDepartment of Genetic Medicine and Development, Faculty of Medicine, University of Geneva, 1211, Geneva, Switzerland. guillaume.andrey@unige.ch.ORCID http://orcid.org/0000-0002-0911-4907

Funding

Generation of an In Vivo Human Genome Transcriptional Enhancer DatasetR01HG003988 · NHGRI · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI Len Alexander Pennacchio · 2006 to 2026
$24.1M
A Single-Cell Resolution Enhancer Atlas of Craniofacial DevelopmentR01DE028599 · NIDCR · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI VISEL, AXEL · 2019 to 2023
$4.2M
NHGRI NIH HHS R01 HG003988NIDCR NIH HHS R01 DE028599Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation) PP00P3_210996
6 · The paper itself

Abstract

Chondrocyte differentiation controls skeleton development and stature. Here we provide a comprehensive map of chondrocyte-specific enhancers and show that they provide a mechanistic framework through which non-coding genetic variants can influence skeletal development and human stature. Working with fetal chondrocytes isolated from mice bearing a Col2a1 fluorescent regulatory sensor, we identify 780 genes and 2'704 putative enhancers specifically active in chondrocytes using a combination of RNA-seq, ATAC-seq and H3K27ac ChIP-seq. Most of these enhancers (74%) show pan-chondrogenic activity, with smaller populations being restricted to limb (18%) or trunk (8%) chondrocytes only. Notably, genetic variations overlapping these enhancers better explain height differences than those overlapping non-chondrogenic enhancers. Finally, targeted deletions of identified enhancers at the Fgfr3, Col2a1, Hhip and, Nkx3-2 loci confirm their role in regulating cognate genes. This enhancer map provides a framework for understanding how genes and non-coding variations influence bone development and diseases.

Indexed as

ChondrocytesChondrogenesisEnhancer Elements, GeneticReceptor, Fibroblast Growth Factor, Type 3AnimalsBone DevelopmentCell DifferentiationCollagen Type IIExtremitiesFemaleGene Expression Regulation, DevelopmentalHumansMaleMiceTranscription FactorsCol2a1 protein, mouseCollagen Type IIFgfr3 protein, mouseReceptor, Fibroblast Growth Factor, Type 3Transcription Factors

Identifiers

PMID38844479
PMCPMC11156918

What Socratic holds

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LicenceCC BY
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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 Socratic graph.