Global DNA Methylation in the Limbic System of Cattle

Cantrell, Bonnie; Lachance, Hannah; Murdoch, Brenda M.; Sjoquist, Julia; Funston, R. N.; Weaber, R. L.; McKay, Stephanie

doi:10.3390/epigenomes3020008

Cited by 8 publications

(3 citation statements)

References 27 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Cerebellum samples demonstrated a higher level of both CG and non-CG methylation compared to the liver and spleen. Brain tissues are known to differ from other tissues in methylation patterns in other species, and furthermore, the cerebellum has been shown to be different than other brain tissues ( Gibbs et al, 2010 ; Cantrell et al, 2019 ).…”

Section: Discussionmentioning

confidence: 99%

Characterizing Genetic Regulatory Elements in Ovine Tissues

et al. 2021

View full text Add to dashboard Cite

The Ovine Functional Annotation of Animal Genomes (FAANG) project, part of the broader livestock species FAANG initiative, aims to identify and characterize gene regulatory elements in domestic sheep. Regulatory element annotation is essential for identifying genetic variants that affect health and production traits in this important agricultural species, as greater than 90% of variants underlying genetic effects are estimated to lie outside of transcribed regions. Histone modifications that distinguish active or repressed chromatin states, CTCF binding, and DNA methylation were used to characterize regulatory elements in liver, spleen, and cerebellum tissues from four yearling sheep. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed for H3K4me3, H3K27ac, H3K4me1, H3K27me3, and CTCF. Nine chromatin states including active promoters, active enhancers, poised enhancers, repressed enhancers, and insulators were characterized in each tissue using ChromHMM. Whole-genome bisulfite sequencing (WGBS) was performed to determine the complement of whole-genome DNA methylation with the ChIP-seq data. Hypermethylated and hypomethylated regions were identified across tissues, and these locations were compared with chromatin states to better distinguish and validate regulatory elements in these tissues. Interestingly, chromatin states with the poised enhancer mark H3K4me1 in the spleen and cerebellum and CTCF in the liver displayed the greatest number of hypermethylated sites. Not surprisingly, active enhancers in the liver and spleen, and promoters in the cerebellum, displayed the greatest number of hypomethylated sites. Overall, chromatin states defined by histone marks and CTCF occupied approximately 22% of the genome in all three tissues. Furthermore, the liver and spleen displayed in common the greatest percent of active promoter (65%) and active enhancer (81%) states, and the liver and cerebellum displayed in common the greatest percent of poised enhancer (53%), repressed enhancer (68%), hypermethylated sites (75%), and hypomethylated sites (73%). In addition, both known and de novo CTCF-binding motifs were identified in all three tissues, with the highest number of unique motifs identified in the cerebellum. In summary, this study has identified the regulatory regions of genes in three tissues that play key roles in defining health and economically important traits and has set the precedent for the characterization of regulatory elements in ovine tissues using the Rambouillet reference genome.

show abstract

Section: Discussionmentioning

confidence: 99%

Characterizing Genetic Regulatory Elements in Ovine Tissues

et al. 2021

View full text Add to dashboard Cite

show abstract

“…Furthermore, it can provide insights to improve farm management to guide future epigenetic experimental studies. Environmental conditions regulating gene expression are well known for many traits, including docility ( Cantrell et al, 2019 ). Hence, the listed environmental factors affecting yearling temperament can also be indicative of a programmer of epigenetics modifications.…”

Section: Discussionmentioning

confidence: 99%

Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits

Alvarenga

Oliveira

Miller³

et al. 2022

Front. Genet.

View full text Add to dashboard Cite

Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen’s safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1–6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal–human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.

show abstract

“…The presence of DNMTs is much lower in post-mitotic cells compared with cells undergoing mitosis, which suggests that DNA methylation is stable in post-mitotic cells ( Moore et al, 2013 ). Still, certain tissues do exhibit distinct measures of variable methylation ( Cantrell et al, 2019 ). One example is brains, where neurons are particularly unique and DNMTs continue to be present at substantial levels in post-mitotic cells, suggesting a unique role of methylation in the brain ( Moore et al, 2013 ).…”

Section: Introduction To Epigenetics In Livestockmentioning

confidence: 99%