Evidence map›Paper›PMID 40362521›Full record

ArticleInternational journal of molecular sciences2025

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

Zhenbin Hu, Clarissa Boschiero, Mahesh Neupane, Nayan Bhowmik, Liu Yang, Levi Kilian, James Mel DeJarnette, Mehdi Sargolzaei, Bo Harstine, Cong-Jun Li and 5 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in International journal of molecular sciences, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Review
  3. Emerging opportunities for DNA methylation biomarkers in cattle improvement.The Journal of reproduction and development · 2026
    Review
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors.

Zhenbin HuAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Clarissa BoschieroAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0002-6575-5266
Mahesh NeupaneAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Nayan BhowmikAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0003-3906-1460
Liu YangAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Levi KilianSelect Sires Inc., 11740 U.S. 42 North, Plain City, OH 43064, USA.
James Mel DeJarnetteSelect Sires Inc., 11740 U.S. 42 North, Plain City, OH 43064, USA.
Mehdi SargolzaeiSelect Sires Inc., 11740 U.S. 42 North, Plain City, OH 43064, USA.
Bo HarstineSelect Sires Inc., 11740 U.S. 42 North, Plain City, OH 43064, USA.ORCID 0000-0003-3000-9949
Cong-Jun LiAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.
Wenbin TuoAnimal Parasitic Diseases Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0002-3764-8981
Ransom L BaldwinAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0002-0753-4377
Curtis P Van TassellAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0002-8416-2087
Charles G SattlerSelect Sires Inc., 11740 U.S. 42 North, Plain City, OH 43064, USA.
George E LiuAnimal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD 20705, USA.ORCID 0000-0003-0192-6705

Funding

CRADA sponsored by Select Sires Inc. 58-8042-2-14USDA NIFA 2019-67015-29321USDA NIFA 2021-67015-33409US-Israel Binational Agricultural Research and Development (BARD) Fund US-4997-17
6 · The paper itself

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.

Indexed as

DNA MethylationAnimalsCattleCpG IslandsEpigenesis, GeneticFemaleMaleOligonucleotide Array Sequence AnalysisOrgan SpecificityPrincipal Component AnalysisSex CharacteristicscattleDNA methylationHorvathMammalMethyl-Chip40sex-specific DNA methylationtissue-specific DNA methylation

Identifiers

PMID40362521
PMCPMC12072048

What OpenQuestion holds

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LicenceCC BY
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.