A comparative investigation on H3K27ac enhancer activities in the brain and liver tissues between wild boars and domesticated pigs

Zhou, Zhimin; Jiang, Tao; Zhu, Yuanjun; Ling, Ziqi; Yang, Bin; Huang, Lusheng

doi:10.1111/eva.13461

Cited by 3 publications

(2 citation statements)

References 64 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Some studies [ 45 , 46 , 47 , 48 ] have utilized two enhancer-associated histone modifications, H3K27ac and H3K4me1 [ 7 , 49 , 50 , 51 ]. However, these studies come with high implementation costs, are limited by tissue/cell types and genetic backgrounds, and still require substantial effort and funding to determine whether these regions indeed possess actual enhancer functionality, as demonstrated through regulatory assays in transgenic mice [ 52 ].…”

Section: Introductionmentioning

confidence: 99%

PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks

Wang,

Zhang,

Chen

et al. 2023

Animals

View full text Add to dashboard Cite

Understanding the mechanisms of gene expression regulation is crucial in animal breeding. Cis-regulatory DNA sequences, such as enhancers, play a key role in regulating gene expression. Identifying enhancers is challenging, despite the use of experimental techniques and computational methods. Enhancer prediction in the pig genome is particularly significant due to the costliness of high-throughput experimental techniques. The study constructed a high-quality database of pig enhancers by integrating information from multiple sources. A deep learning prediction framework called PorcineAI-enhancer was developed for the prediction of pig enhancers. This framework employs convolutional neural networks for feature extraction and classification. PorcineAI-enhancer showed excellent performance in predicting pig enhancers, validated on an independent test dataset. The model demonstrated reliable prediction capability for unknown enhancer sequences and performed remarkably well on tissue-specific enhancer sequences.The study developed a deep learning prediction framework, PorcineAI-enhancer, for predicting pig enhancers. The model demonstrated significant predictive performance and potential for tissue-specific enhancers. This research provides valuable resources for future studies on gene expression regulation in pigs.

show abstract

Section: Introductionmentioning

confidence: 99%

PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks

Wang,

Zhang,

Chen

et al. 2023

Animals

View full text Add to dashboard Cite

show abstract

“…The genetic background of pig traits may be useful for annotating human enhancers and diseases (43). The SEs of some tissues (e.g., liver, brain, muscle, and adipose) have been reported in previous studies (44)(45)(46)(47). To advance our understanding of SEs and their possible functions in pigs, we systematically identified SEs in 14 pig tissues by integrating ChIP-seq data labeled with H3K27ac signals and five types of enhancer annotations (48).…”

Section: Introductionmentioning

confidence: 99%

A body map of super-enhancers and their function in pig

Yang,

Li,

Meng

et al. 2023

Front. Vet. Sci.

View full text Add to dashboard Cite

IntroductionSuper-enhancers (SEs) are clusters of enhancers that act synergistically to drive the high-level expression of genes involved in cell identity and function. Although SEs have been extensively investigated in humans and mice, they have not been well characterized in pigs.MethodsHere, we identified 42,380 SEs in 14 pig tissues using chromatin immunoprecipitation sequencing, and statistics of its overall situation, studied the composition and characteristics of SE, and explored the influence of SEs characteristics on gene expression.ResultsWe observed that approximately 40% of normal enhancers (NEs) form SEs. Compared to NEs, we found that SEs were more likely to be enriched with an activated enhancer and show activated functions. Interestingly, SEs showed X chromosome depletion and short interspersed nuclear element enrichment, implying that SEs play an important role in sex traits and repeat evolution. Additionally, SE-associated genes exhibited higher expression levels and stronger conservation than NE-associated genes. However, genes with the largest SEs had higher expression levels than those with the smallest SEs, indicating that SE size may influence gene expression. Moreover, we observed a negative correlation between SE gene distance and gene expression, indicating that the proximity of SEs can affect gene activity. Gene ontology enrichment and motif analysis revealed that SEs have strong tissue-specific activity. For example, the CORO2B gene with a brain-specific SE shows strong brain-specific expression, and the phenylalanine hydroxylase gene with liver-specific SEs shows strong liver-specific expression.DiscussionIn this study, we illustrated a body map of SEs and explored their functions in pigs, providing information on the composition and tissue-specific patterns of SEs. This study can serve as a valuable resource of gene regulatory and comparative analyses to the scientific community and provides a theoretical reference for genetic control mechanisms of important traits in pigs.

show abstract

Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics

Du,

Zhuo,

et al. 2024

Preprint

View full text Add to dashboard Cite

Pigs are among the most essential sources of high-quality protein in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs limits the presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deep-sequenced genomes across Eurasia. Moreover, a section-wide gene repertoire was constructed, which indicated that core genes were more evolutionarily conserved than variable genes. Subsequently, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of the TBX19 gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. Our constructed pig pangenome and the identified SVs provide rich resources for future functional genomic research on pigs.

show abstract

A comparative investigation on H3K27ac enhancer activities in the brain and liver tissues between wild boars and domesticated pigs

Cited by 3 publications

References 64 publications

PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks

PorcineAI-Enhancer: Prediction of Pig Enhancer Sequences Using Convolutional Neural Networks

A body map of super-enhancers and their function in pig

Pangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics

Contact Info

Product

Resources

About