Evidence map›Paper›PMID 38266195›Full record

ArticleMolecular biology and evolution2024

Cross-Species Comparative DNA Methylation Reveals Novel Insights into Complex Trait Genetics among Cattle, Sheep, and Goats.

Siqian Chen, Shuli Liu, Shaolei Shi, Hongwei Yin, Yongjie Tang, Jinning Zhang, Wenlong Li, Gang Liu, Kaixing Qu, Xiangdong Ding and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Molecular biology and evolution, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
6.1field-weighted citation impact, top 4% of its field
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

12 citing papers in PubMed, 11 citations in OpenAlex.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Emerging opportunities for DNA methylation biomarkers in cattle improvement.The Journal of reproduction and development · 2026
    Review
  6. Review
  7. Article
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  9. Article
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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 at 6 institutions in 2 countries.

Siqian ChenNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Shuli LiuWestlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang 310024, China.
Shaolei ShiNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Hongwei YinAgriculture Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
Yongjie TangNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Jinning ZhangNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Wenlong LiNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Gang LiuNational Animal Husbandry Service, Beijing 100125, China.
Kaixing QuAcademy of Science and Technology, Chuxiong Normal University, Chuxiong 675000, China.
Xiangdong DingNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Yachun WangNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Jianfeng LiuNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.ORCID 0000-0002-5766-7864
Shengli ZhangNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Lingzhao FangCenter for Quantitative Genetics and Genomics (QGG), Aarhus University, Aarhus, Denmark.
Ying YuNational Engineering Laboratory for Animal Breeding, State Key Laboratory of Animal Biotech Breeding, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
Ministry of Agriculture and Rural Affairs · CNAarhus University · DKAgricultural Genomics Institute at Shenzhen · CNChuxiong Normal University · CNNational Animal Husbandry Service · CNWestlake University · CN

Funding

National Key R&D Program of China 2021YFD1200903National Natural Science Foundation of China 32072718Seed Fund
6 · The paper itself

Abstract

The cross-species characterization of evolutionary changes in the functional genome can facilitate the translation of genetic findings across species and the interpretation of the evolutionary basis underlying complex phenotypes. Yet, this has not been fully explored between cattle, sheep, goats, and other mammals. Here, we systematically characterized the evolutionary dynamics of DNA methylation and gene expression in 3 somatic tissues (i.e. brain, liver, and skeletal muscle) and sperm across 7 mammalian species, including 3 ruminant livestock species (cattle, sheep, and goats), humans, pigs, mice, and dogs, by generating and integrating 160 DNA methylation and transcriptomic data sets. We demonstrate dynamic changes of DNA hypomethylated regions and hypermethylated regions in tissue-type manner across cattle, sheep, and goats. Specifically, based on the phylo-epigenetic model of DNA methylome, we identified a total of 25,074 hypomethylated region extension events specific to cattle, which participated in rewiring tissue-specific regulatory network. Furthermore, by integrating genome-wide association studies of 50 cattle traits, we provided novel insights into the genetic and evolutionary basis of complex phenotypes in cattle. Overall, our study provides a valuable resource for exploring the evolutionary dynamics of the functional genome and highlights the importance of cross-species characterization of multiomics data sets for the evolutionary interpretation of complex phenotypes in cattle livestock.

Indexed as

CattleDNA MethylationGoatsSheepAnimalsDogsGenome-Wide Association StudyHumansMaleMiceMultifactorial InheritanceSwineDNA hypermethylationDNA hypomethylationepigenetic regulationGWAS enrichmentmultitissue transcriptome

Identifiers

PMID38266195
PMCPMC10834038
OpenAlexW4391161201

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.