Skip to content
DraconiticResearch
Search Sources API
203,234 studies31 sourcesUpdated 52 min ago
Peer-reviewedCC BY-NC-NDNature communications

A temporal single cell atlas of dynamic chromatin accessibility during murine lung maturation.

  • Xin Wang1,2
  • Yuhao Deng2
  • Yanru Zhang2
  • Yurong Chen3
  • Hang Li4
  • Min Zhang2
  • Zhizhuo Cao2
  • Shaojun Zhang5
  • Fang Wang6
6 affiliations
  1. 1Department of Oncology, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
  2. 2Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China.
  3. 3Department of Gynecological Radiotherapy, Harbin Medical University Cancer Hospital, Harbin Medical University, Harbin, China.
  4. 4Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China.
  5. 5Medical Research Institute, Guangdong Provincial People's Hospital (Guangdong Academy of Medical Sciences), Southern Medical University, Guangzhou, China. [email protected].
  6. 6Institute of Precision Medicine, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China. [email protected].
Read full textPDFDOICite

Abstract

Lung maturation involves intricate cellular differentiation and structural remodeling, yet the underlying epigenetic dynamics remain poorly characterized at single-cell resolution. Here we present HTL-ATAC-seq, an ultra-high-throughput, ligation-based single-cell ATAC-seq approach. Applying HTL-ATAC-seq to mouse lung tissue across 15 continuous postnatal time points, we construct a temporal chromatin accessibility atlas of 1,185,619 nuclei, identifying 129 distinct cell subclusters and 713,987 candidate chromatin regulatory elements. Temporal analysis reveals three distinct cellular maturation stages and 12 dynamic chromatin accessibility patterns, capturing the transition from structural morphogenesis to immune maturation. We uncover distinct transcription factor regulatory patterns between alveolar type 1 and 2 cells and identify a putative Sprr1a enhancer specifically active in alveolar type 1 cells. Finally, we identify time- and cell-type-specific cis-regulatory elements associated with lung disease-related gene sets. In this work, we provide a comprehensive resource for understanding the epigenetic mechanisms underlying lung maturation and lung disease-associated regulatory programs.

Related

  1. integrating single-cell transcriptomics and chromatin accessibility profiling to decipher the molecular landscape of Hepatocellular carcinoma
    Kaile Pan, Lijian Chen, Yitao Zheng
    PLOS OnePeer-reviewedCC BY 4.0Full textMolecular biology & gene regulationPLOS
  2. CIRCE: a scalable Python package to predict cis-regulatory DNA interactions from single-cell chromatin accessibility data
    Rémi Trimbour, Julio Saez-Rodriguez, Laura Cantini
    BioinformaticsPeer-reviewedCC BY 4.0Full textMolecular biology & gene regulationHAL
  3. Cis-TERN: a graph-based method to integrate single-cell chromatin accessibility with gene expression data to infer the pseudotime ordering of cells
    Ameya Gokhale, Pawel F Przytycki
    Bioinformatics AdvancesPeer-reviewedCC BY 4.0Full textMolecular biology & gene regulationPMC
  4. AI and computational methods for reconstructing cell-state-specific gene regulatory networks from single-cell transcriptome and chromatin accessibility data in cancer: methods, applications, and perspectives
    Jinying Wang, Fenjuan Chen
    Frontiers in geneticsPeer-reviewedCC BYFull textMolecular biology & gene regulationEurope PMCEurope PMCPMC
  5. scLAP: A Liver-Adapted Contrastive Shared-Latent Framework for Pseudo-Pairing Single-Cell Transcriptomes and Chromatin Accessibility Profiles
    Hongfei Li, Jiechen Wang, Huan Yang
    International Journal of Molecular SciencesPeer-reviewedCC BY 4.0General biochemistryCrossref

Cite

BibTeXRIS
BibTeX
@article{wang2026temporal,
  title = {{A temporal single cell atlas of dynamic chromatin accessibility during murine lung maturation.}},
  author = {Xin Wang and Yuhao Deng and Yanru Zhang and Yurong Chen and Hang Li and Min Zhang and Zhizhuo Cao and Shaojun Zhang and Fang Wang},
  journal = {Nature communications},
  year = {2026},
  month = sep,
  doi = {10.1038/s41467-026-77870-w},
  url = {https://europepmc.org/article/MED/42901895},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - A temporal single cell atlas of dynamic chromatin accessibility during murine lung maturation.
AU  - Xin Wang
AU  - Yuhao Deng
AU  - Yanru Zhang
AU  - Yurong Chen
AU  - Hang Li
AU  - Min Zhang
AU  - Zhizhuo Cao
AU  - Shaojun Zhang
AU  - Fang Wang
PY  - 2026
DA  - 2026/09/18
JO  - Nature communications
DO  - 10.1038/s41467-026-77870-w
UR  - https://europepmc.org/article/MED/42901895
AB  - Lung maturation involves intricate cellular differentiation and structural remodeling, yet the underlying epigenetic dynamics remain poorly characterized at single-cell resolution. Here we present HTL-ATAC-seq, an ultra-high-throughput, ligation-based single-cell ATAC-seq approach. Applying HTL-ATAC-seq to mouse lung tissue across 15 continuous postnatal time points, we construct a temporal chromatin accessibility atlas of 1,185,619 nuclei, identifying 129 distinct cell subclusters and 713,987 candidate chromatin regulatory elements. Temporal analysis reveals three distinct cellular maturation stages and 12 dynamic chromatin accessibility patterns, capturing the transition from structural morphogenesis to immune maturation. We uncover distinct transcription factor regulatory patterns between alveolar type 1 and 2 cells and identify a putative Sprr1a enhancer specifically active in alveolar type 1 cells. Finally, we identify time- and cell-type-specific cis-regulatory elements associated with lung disease-related gene sets. In this work, we provide a comprehensive resource for understanding the epigenetic mechanisms underlying lung maturation and lung disease-associated regulatory programs.
SN  - 2041-1723
ER  -