Multimodal Exploration Offers Novel Insights into the Transcriptomic and Epigenomic Landscape of the Human Submandibular Glands
Abstract
1. Introduction
2. Materials and Methods
2.1. Collection of Human Submandibular Gland Tissue
2.2. Immunostaining and Imaging
2.3. Generation of the Human SMG Gene Signature
2.4. Salivary Gland Sample Preparation for ChIP-Seq Analysis
2.5. Histone ChIP-Seq
2.6. Histone ChIP-Seq Alignment and Peak Calling
2.7. Clustering of Cis-Regulatory Elements
2.8. Identification of Super-Enhancers in the Human SMG
2.9. Identification of Differential Super-Enhancer Loci Across the SMG and Other Human Tissues
3. Results
3.1. Generation of a Submandibular Gland-Specific Gene Signature
3.2. Enriched and Diverse Expression of Important Transcription Factor Families in Human SMGs
3.3. Generation of a Global Epigenome Map of the Human SMG
3.4. SMG-Specific H3K27Ac Peaks Mark Genes Critical to Salivary Gland Function
3.5. Super-Enhancers in the SMG Likely Regulate Important Genes
3.6. Conserved Super-Enhancers Mark Genes Critical to Salivary Gland Function
4. Discussion
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
SMGs | Submandibular Gland |
lncRNA | Long non-coding RNA |
ChIP-seq | Chromatin Immunoprecipitation Sequencing |
SGs | Salivary Glands |
PG | Parotid Gland |
SLG | Sublingual Gland |
NGS | Next-generation Sequencing |
scRNA-seq | Single-cell RNA-sequencing |
TFs | Transcription Factors |
ANTE | Atlas of Normal Tissue Expression |
PCA | Principal Component Analysis |
IDs | Intercalated Ducts |
ETS | Erythroblast Transformation-specific |
FOX | Forkhead Box |
SIX | Sine oculis |
IDR | Irreproducible Discovery Rate |
TSS | Transcriptional Start Site |
CRMs | Cis-regulatory Modules |
SE | Super-enhancers |
ROSE | Rank Order of Super Enhancer |
KRT | Keratin |
GSEA | Gene Set Enrichment Analysis |
GTEx | Genotype-Tissue Expression |
ENCODE | Encyclopedia of DNA Elements |
GREAT | Genomic Regions Enrichment of Annotations Tool |
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Horeth, E.; Wrynn, T.; Osinski, J.M.; Glathar, A.; Bard, J.; Burke, M.S.; Popat, S.; Loree, T.; Nagai, M.; Phillips, R.; et al. Multimodal Exploration Offers Novel Insights into the Transcriptomic and Epigenomic Landscape of the Human Submandibular Glands. Cells 2025, 14, 1561. https://doi.org/10.3390/cells14191561
Horeth E, Wrynn T, Osinski JM, Glathar A, Bard J, Burke MS, Popat S, Loree T, Nagai M, Phillips R, et al. Multimodal Exploration Offers Novel Insights into the Transcriptomic and Epigenomic Landscape of the Human Submandibular Glands. Cells. 2025; 14(19):1561. https://doi.org/10.3390/cells14191561
Chicago/Turabian StyleHoreth, Erich, Theresa Wrynn, Jason M. Osinski, Alexandra Glathar, Jonathan Bard, Mark S. Burke, Saurin Popat, Thom Loree, Michael Nagai, Robert Phillips, and et al. 2025. "Multimodal Exploration Offers Novel Insights into the Transcriptomic and Epigenomic Landscape of the Human Submandibular Glands" Cells 14, no. 19: 1561. https://doi.org/10.3390/cells14191561
APA StyleHoreth, E., Wrynn, T., Osinski, J. M., Glathar, A., Bard, J., Burke, M. S., Popat, S., Loree, T., Nagai, M., Phillips, R., Tapia, J. L., Frustino, J., Kramer, J. M., Sinha, S., & Romano, R.-A. (2025). Multimodal Exploration Offers Novel Insights into the Transcriptomic and Epigenomic Landscape of the Human Submandibular Glands. Cells, 14(19), 1561. https://doi.org/10.3390/cells14191561