Evidence map›Paper›PMID 39554055›Full record

ArticlebioRxiv : the preprint server for biology2024

Single-cell DNA methylome and 3D genome atlas of the human subcutaneous adipose tissue.

Zeyuan Johnson Chen, Sankha Subhra Das, Asha Kar, Seung Hyuk T Lee, Kevin D Abuhanna, Marcus Alvarez, Mihir G Sukhatme, Kyla Z Gelev, Matthew G Heffel, Yi Zhang and 9 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. 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

19 authors.

Zeyuan Johnson ChenDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0002-9564-6271
Sankha Subhra DasDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Asha KarDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Seung Hyuk T LeeDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Kevin D AbuhannaDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Marcus AlvarezDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Mihir G SukhatmeDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Kyla Z GelevDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Matthew G HeffelDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Yi ZhangDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Oren AvramDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA.ORCID 0000-0003-1984-2139
Elior RahmaniDepartment of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Sriram SankararamanDepartment of Computer Science, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Sini HeinonenObesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Hilkka PeltoniemiEira Hospital, Helsinki, Finland.
Eran HalperinDepartment of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Kirsi H PietiläinenObesity Research Unit, Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
Chongyuan LuoDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Päivi PajukantaDepartment of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.

Funding

Leveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotencyU01HG012079 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Chongyuan Luo, Kathrin Plath · 2021 to 2026
$6.9M
Multimodal omics approach to identify health to cardiometabolic disease transitionsR01HL170604 · NHLBI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Paivi Pajukanta · 2023 to 2026
$2.8M
Methods for Genomic Analysis in Heterogeneous TissuesR01HG010505 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI HALPERIN, ERAN · 2019 to 2022
$2.6M
Genetics of adipose cell-type expression and cardiometabolic traitsR01DK132775 · NIDDK · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI MOHLKE, KAREN L., PAJUKANTA, PAIVI · 2022 to 2025
$2.4M
NHGRI NIH HHS R01 HG010505NHGRI NIH HHS U01 HG012079NHLBI NIH HHS R01 HL170604NIDDK NIH HHS R01 DK132775
6 · The paper itself

Abstract

Human subcutaneous adipose tissue (SAT) contains a diverse array of cell-types; however, the epigenomic landscape among the SAT cell-types has remained elusive. Our integrative analysis of single-cell resolution DNA methylation and chromatin conformation profiles (snm3C-seq), coupled with matching RNA expression (snRNA-seq), systematically cataloged the epigenomic, 3D topology, and transcriptomic dynamics across the SAT cell-types. We discovered that the SAT CG methylation (mCG) landscape is characterized by pronounced hyper-methylation in myeloid cells and hypo-methylation in adipocytes and adipose stem and progenitor cells (ASPCs), driving nearly half of the 705,063 detected differentially methylated regions (DMRs). In addition to the enriched cell-type-specific transcription factor binding motifs, we identified

Identifiers

PMID39554055
PMCPMC11566006

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.