Evidence map›Paper›PMID 39764062›Full record

ArticlebioRxiv : the preprint server for biology2025

Single-cell analysis of the epigenome and 3D chromatin architecture in the human retina.

Ying Yuan, Pooja Biswas, Nathan R Zemke, Kelsey Dang, Yue Wu, Matteo D'Antonio, Yang Xie, Qian Yang, Keyi Dong, Pik Ki Lau and 16 more

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

26 authors.

Ying YuanDepartment of Material Science, UC San Diego, La Jolla, CA 92037, USA.
Pooja BiswasOphthalmology, Shiley Eye Institute, UC San Diego, La Jolla, CA 92037, USA.
Nathan R ZemkeCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Kelsey DangCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Yue WuDepartment of Biological Science, UC San Diego, La Jolla, CA 92037, USA.
Matteo D'AntonioDepartment of Biomedical Informatics, UC San Diego, La Jolla, CA 92037, USA.
Yang XieDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92037, USA.
Qian YangCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Keyi DongCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Pik Ki LauCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Daofeng LiDepartment of Genetics, Washington University School of Medicine in St.Louis, St. Louis, MO 63130, USA.ORCID 0000-0001-7492-3703
Chad SengDepartment of Genetics, Washington University School of Medicine in St.Louis, St. Louis, MO 63130, USA.
Weronika BartosikCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Justin BuchananCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Lin LinCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Ryan LancioneCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Kangli WangDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92037, USA.
Seoyeon LeeDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92037, USA.
Zane GibbsDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92037, USA.
Joseph EckerGenomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA,USA.
Kelly FrazerDepartment of Pediatrics, University of California, San Diego, La Jolla, CA, USA.
Ting WangDepartment of Genetics, Washington University School of Medicine in St.Louis, St. Louis, MO 63130, USA.
Sebastian PreisslCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Allen WangCenter for Epigenomics, UC San Diego, La Jolla, CA 92037, USA.
Radha AyyagariOphthalmology, Shiley Eye Institute, UC San Diego, La Jolla, CA 92037, USA.
Bing RenDepartment of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA 92037, USA.

Funding

Vision BiostatisticsP30EY022589 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Radha Ayyagari · 2012 to 2026
$10.3M
Center for Integrated Multi-modal and Multi-scale Nucleome ResearchUM1HG011585 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI DULAC, CATHERINE, LEIN, ED · 2020 to 2024
$6.7M
Molecular Basis of Hereditary Retinal DegenerationsR01EY021237 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AYYAGARI, RADHA · 2011 to 2020
$5.6M
Unraveling the molecular pathology of retinal degeneration through single cell genomicsR01EY031663 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AYYAGARI, RADHA, FRAZER, KELLY A · 2021 to 2025
$3.3M
Molecular mechanism underlying late-onset retinal/macular degenerationR01EY030591 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI AYYAGARI, RADHA · 2020 to 2023
$1.9M
Translational Vision Research Training at UCSDT32EY026590 · NEI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI ZANGWILL, LINDA M · 2016 to 2025
$854k
NEI NIH HHS P30 EY022589NEI NIH HHS R01 EY021237NEI NIH HHS R01 EY030591NEI NIH HHS R01 EY031663NEI NIH HHS T32 EY026590NHGRI NIH HHS UM1 HG011585
6 · The paper itself

Abstract

Most genetic risk variants linked to ocular diseases are non-protein coding and presumably contribute to disease through dysregulation of gene expression, however, deeper understanding of their mechanisms of action has been impeded by an incomplete annotation of the transcriptional regulatory elements across different retinal cell types. To address this knowledge gap, we carried out single-cell multiomics assays to investigate gene expression, chromatin accessibility, DNA methylome and 3D chromatin architecture in human retina, macula, and retinal pigment epithelium (RPE)/choroid. We identified 420,824 unique candidate regulatory elements and characterized their chromatin states in 23 sub-classes of retinal cells. Comparative analysis of chromatin landscapes between human and mouse retina cells further revealed both evolutionarily conserved and divergent retinal gene-regulatory programs. Leveraging the rapid advancements in deep-learning techniques, we developed sequence-based predictors to interpret non-coding risk variants of retina diseases. Our study establishes retina-wide, single-cell transcriptome, epigenome, and 3D genome atlases, and provides a resource for studying the gene regulatory programs of the human retina and relevant diseases.

Identifiers

PMID39764062
PMCPMC11703273

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC
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.