Next Article in Journal
Translating Molecular Psychiatry: From Biomarkers to Personalized Therapies—A Narrative Review
Next Article in Special Issue
The Association Between Hematological Profiles and Whole-Blood Transcriptome Genes Identified Using Quantitative Analysis with Average Daily Gain and Feed Efficiency in Forage-Fed Beef Heifers
Previous Article in Journal
Neighborhood-Regularized Matrix Factorization for lncRNA–Disease Association Identification
Previous Article in Special Issue
Mechanisms of Adipose Tissue Metabolism in Naturally Grazing Sheep at Different Growth Stages: Insights from mRNA and miRNA Profiles
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
IJMS
Volume 26
Issue 9
10.3390/ijms26094284
ijms-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Exploring Tissue- and Sex-Specific DNA Methylation in Cattle Using a Pan-Mammalian Infinium Array

by
Zhenbin Hu
1,
Clarissa Boschiero
1,
Mahesh Neupane
1,
Nayan Bhowmik
1,
Liu Yang
1,
Levi Kilian
2,
James Mel DeJarnette
2,
Mehdi Sargolzaei
2,
Bo Harstine
2,
Cong-Jun Li
1,
Wenbin Tuo
3,
Ransom L. Baldwin VI
1,
Curtis P. Van Tassell
1,
Charles G. Sattler
2 and
George E. Liu
1,*
1
Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
2
Select Sires Inc., 11740 U.S. 42 North, Plain City, OH 43064, USA
3
Animal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA
*
Author to whom correspondence should be addressed.
Int. J. Mol. Sci. 2025, 26(9), 4284; https://doi.org/10.3390/ijms26094284
Submission received: 20 March 2025 / Revised: 24 April 2025 / Accepted: 29 April 2025 / Published: 1 May 2025
(This article belongs to the Special Issue Molecular Genetics and Genomics of Ruminants)
Browse Figures
Versions Notes

Abstract

DNA methylation is crucial in gene expression regulation and tissue differentiation in livestock. However, genome-wide methylation patterns among tissues remain underexplored in cattle, one of the world’s most important farm animals. This study investigates sex- and tissue-specific DNA methylation in cattle using CpG site methylation data generated by an Infinium DNA Methylation array (HorvathMammalMethyl-Chip40) across seven tissues. Our analysis revealed significant tissue-specific methylation differences, with reproductive tissues/cells, such as the sperm, exhibiting distinct profiles compared to somatic tissues like hair and blood. Principal component analysis (PCA) highlighted tissue differentiation as the primary driver of methylation variability. We also identified 222 CpG sites with significant sex-based methylation differences, particularly on the X chromosome, suggesting the potential epigenetic regulation of sex-specific traits. The Gene Ontology (GO) enrichment analysis indicated that these methylation patterns may influence biological processes such as epithelial cell proliferation and blood vessel remodeling. Overall, this study provides important insights into sex- and tissue-specific epigenetic regulation in cattle, with implications for improving livestock breeding strategies through integrating epigenetic data.
Keywords: cattle; DNA methylation; tissue-specific DNA methylation; sex-specific DNA methylation; HorvathMammalMethyl-Chip40 cattle; DNA methylation; tissue-specific DNA methylation; sex-specific DNA methylation; HorvathMammalMethyl-Chip40

Share and Cite

MDPI and ACS Style

Hu, Z.; Boschiero, C.; Neupane, M.; Bhowmik, N.; Yang, L.; Kilian, L.; DeJarnette, J.M.; Sargolzaei, M.; Harstine, B.; Li, C.-J.; et al. Exploring Tissue- and Sex-Specific DNA Methylation in Cattle Using a Pan-Mammalian Infinium Array. Int. J. Mol. Sci. 2025, 26, 4284. https://doi.org/10.3390/ijms26094284

AMA Style

Hu Z, Boschiero C, Neupane M, Bhowmik N, Yang L, Kilian L, DeJarnette JM, Sargolzaei M, Harstine B, Li C-J, et al. Exploring Tissue- and Sex-Specific DNA Methylation in Cattle Using a Pan-Mammalian Infinium Array. International Journal of Molecular Sciences. 2025; 26(9):4284. https://doi.org/10.3390/ijms26094284

Chicago/Turabian Style

Hu, Zhenbin, Clarissa Boschiero, Mahesh Neupane, Nayan Bhowmik, Liu Yang, Levi Kilian, James Mel DeJarnette, Mehdi Sargolzaei, Bo Harstine, Cong-Jun Li, and et al. 2025. "Exploring Tissue- and Sex-Specific DNA Methylation in Cattle Using a Pan-Mammalian Infinium Array" International Journal of Molecular Sciences 26, no. 9: 4284. https://doi.org/10.3390/ijms26094284

APA Style

Hu, Z., Boschiero, C., Neupane, M., Bhowmik, N., Yang, L., Kilian, L., DeJarnette, J. M., Sargolzaei, M., Harstine, B., Li, C.-J., Tuo, W., Baldwin, R. L., VI, Van Tassell, C. P., Sattler, C. G., & Liu, G. E. (2025). Exploring Tissue- and Sex-Specific DNA Methylation in Cattle Using a Pan-Mammalian Infinium Array. International Journal of Molecular Sciences, 26(9), 4284. https://doi.org/10.3390/ijms26094284

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop