Evidence map›Paper›PMID 36493778›Full record

ArticleStem cell reports2023

Dynamic chromatin organization and regulatory interactions in human endothelial cell differentiation.

Kris G Alavattam, Katie A Mitzelfelt, Giancarlo Bonora, Paul A Fields, Xiulan Yang, Han Sheng Chiu, Lil Pabon, Alessandro Bertero, Nathan J Palpant, William S Noble and 1 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Stem cell reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
0.4field-weighted citation impact, top 40% of its field
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

5 citing papers in PubMed, 6 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Article
  5. Neutrophil nucleus: shaping the past and the future.Journal of leukocyte biology · 2023
    Article
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

11 authors at 2 institutions in 2 countries.

Kris G AlavattamDepartment of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Department of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Avenue NE, Seattle, WA 98195, USA.
Katie A MitzelfeltDepartment of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
Giancarlo BonoraDepartment of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Avenue NE, Seattle, WA 98195, USA.
Paul A FieldsDepartment of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
Xiulan YangDepartment of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
Han Sheng ChiuInstitute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD 4072, Australia.
Lil PabonDepartment of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Sana Biotechnology, Seattle, WA 98102, USA.
Alessandro BerteroDepartment of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA.
Nathan J PalpantInstitute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia; Centre for Cardiac and Vascular Biology, The University of Queensland, Brisbane, QLD 4072, Australia; School of Biomedical Sciences, The University of Queensland, Brisbane, QLD 4072, Australia.
William S NobleDepartment of Genome Sciences, University of Washington, William H. Foege Hall, 3720 15th Avenue NE, Seattle, WA 98195, USA; Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA 98195, USA. Electronic address: wnoble@uw.edu.
Charles E MurryDepartment of Laboratory Medicine and Pathology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Center for Cardiovascular Biology, University of Washington, 850 Republican Street, Brotman Building, Seattle, WA 98109, USA; Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA 98109, USA; Sana Biotechnology, Seattle, WA 98102, USA; Department of Medicine/Cardiology, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA; Department of Bioengineering, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, USA. Electronic address: murry@uw.edu.
University of Washington · USThe University of Queensland · AU

Funding

University of Washington Center for Nuclear Organization and FunctionU54DK107979 · NIDDK · UNIVERSITY OF WASHINGTON · PI NOBLE, WILLIAM STAFFORD, SHENDURE, JAY ASHOK · 2015 to 2019
$11.8M
UW 4-Dimensional Genomic Organization of Mammalian Embryogenesis CenterUM1HG011586 · NHGRI · UNIVERSITY OF WASHINGTON · PI DISTECHE, CHRISTINE M., NOBLE, WILLIAM STAFFORD · 2020 to 2024
$10.3M
Mechanisms of Cell-Based Heart RegenerationR01HL146868 · NHLBI · UNIVERSITY OF WASHINGTON · PI MURRY, CHARLES E, SNIADECKI, NATHAN JOHN · 2019 to 2022
$3.5M
Metabolic and Transcriptional Reprogramming of Cardiac MaturationR01HL148081 · NHLBI · UNIVERSITY OF WASHINGTON · PI MURRY, CHARLES E · 2021 to 2024
$2.5M
NHGRI NIH HHS UM1 HG011586NHLBI NIH HHS R01 HL146868NHLBI NIH HHS R01 HL148081NIDDK NIH HHS U54 DK107979
6 · The paper itself

Abstract

Vascular endothelial cells are a mesoderm-derived lineage with many essential functions, including angiogenesis and coagulation. The gene-regulatory mechanisms underpinning endothelial specialization are largely unknown, as are the roles of chromatin organization in regulating endothelial cell transcription. To investigate the relationships between chromatin organization and gene expression, we induced endothelial cell differentiation from human pluripotent stem cells and performed Hi-C and RNA-sequencing assays at specific time points. Long-range intrachromosomal contacts increase over the course of differentiation, accompanied by widespread heteroeuchromatic compartment transitions that are tightly associated with transcription. Dynamic topologically associating domain boundaries strengthen and converge on an endothelial cell state, and function to regulate gene expression. Chromatin pairwise point interactions (DNA loops) increase in frequency during differentiation and are linked to the expression of genes essential to vascular biology. Chromatin dynamics guide transcription in endothelial cell development and promote the divergence of endothelial cells from cardiomyocytes.

Indexed as

ChromatinEndothelial CellsCell DifferentiationGene Expression RegulationHumansChromatincardiomyocyteschromatindifferentiationendotheliumgenome organizationtranscription

Identifiers

PMID36493778
PMCPMC9860068
OpenAlexW4311025129

What OpenQuestion 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 OpenQuestion graph.