A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs
Abstract Background Topologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries...
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2025-05-01
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| Online Access: | https://doi.org/10.1186/s12864-025-11490-4 |
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| author | Hongwei Yin Qianyi Zhao Liu Yang Guoqiang Yi Wenye Yao Lingzhao Fang Lijing Bai |
| author_facet | Hongwei Yin Qianyi Zhao Liu Yang Guoqiang Yi Wenye Yao Lingzhao Fang Lijing Bai |
| author_sort | Hongwei Yin |
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| description | Abstract Background Topologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries can lead to aberrant expression of neighboring genes. In our study, we analyzed high-throughput chromatin conformation capture (Hi-C) datasets from publicly available sources, integrating 71 datasets across five tissues in six pig breeds. Results Our comprehensive analysis revealed 65,843 TADs in pigs, and we found that TAD boundaries are enriched for expression Quantitative Trait Loci (eQTL), splicing Quantitative Trait Loci (sQTL), Loss-of-Function variants (LoFs), and other regulatory variants. Genes within conserved TADs are associated with fundamental biological functions, while those in dynamic TADs may have tissue-specific roles. Specifically, we observed differential expression of the NCOA2 gene within dynamic TADs. This gene is highly expressed in adipose tissue, where it plays a crucial role in regulating lipid metabolism and maintaining energy homeostasis. Additionally, differential expression of the BMPER gene within dynamic TADs is associated with its role in modulating the activities of bone morphogenetic proteins (BMPs)—critical growth factors involved in bone and cartilage development. Conclusion Our investigations have shed light on the pivotal roles of TADs in governing gene expression and even influencing traits. Our study has unveiled a holistic interplay between chromatin interactions and gene regulation across various tissues and pig breeds. Furthermore, we anticipate that incorporating markers, such as structural variants (SVs), and phenotypes will enhance our understanding of their intricate interactions. |
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| language | English |
| publishDate | 2025-05-01 |
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| series | BMC Genomics |
| spelling | doaj-art-c5920aadb6624df0bf5ca93fb23fe31a2025-08-20T02:32:04ZengBMCBMC Genomics1471-21642025-05-0126111310.1186/s12864-025-11490-4A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigsHongwei Yin0Qianyi Zhao1Liu Yang2Guoqiang Yi3Wenye Yao4Lingzhao Fang5Lijing Bai6Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesCenter for Quantitative Genetics and Genomics (QGG), Aarhus UniversityShenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural SciencesAbstract Background Topologically associating domains (TADs) are functional units that organize chromosomes into 3D structures of interacting chromatin, and play a crucial role in regulating gene expression by constraining enhancer-promoter contacts. Evidence suggests that deletion of TAD boundaries can lead to aberrant expression of neighboring genes. In our study, we analyzed high-throughput chromatin conformation capture (Hi-C) datasets from publicly available sources, integrating 71 datasets across five tissues in six pig breeds. Results Our comprehensive analysis revealed 65,843 TADs in pigs, and we found that TAD boundaries are enriched for expression Quantitative Trait Loci (eQTL), splicing Quantitative Trait Loci (sQTL), Loss-of-Function variants (LoFs), and other regulatory variants. Genes within conserved TADs are associated with fundamental biological functions, while those in dynamic TADs may have tissue-specific roles. Specifically, we observed differential expression of the NCOA2 gene within dynamic TADs. This gene is highly expressed in adipose tissue, where it plays a crucial role in regulating lipid metabolism and maintaining energy homeostasis. Additionally, differential expression of the BMPER gene within dynamic TADs is associated with its role in modulating the activities of bone morphogenetic proteins (BMPs)—critical growth factors involved in bone and cartilage development. Conclusion Our investigations have shed light on the pivotal roles of TADs in governing gene expression and even influencing traits. Our study has unveiled a holistic interplay between chromatin interactions and gene regulation across various tissues and pig breeds. Furthermore, we anticipate that incorporating markers, such as structural variants (SVs), and phenotypes will enhance our understanding of their intricate interactions.https://doi.org/10.1186/s12864-025-11490-4PigTADsGene expressionBiological functions |
| spellingShingle | Hongwei Yin Qianyi Zhao Liu Yang Guoqiang Yi Wenye Yao Lingzhao Fang Lijing Bai A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs BMC Genomics Pig TADs Gene expression Biological functions |
| title | A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs |
| title_full | A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs |
| title_fullStr | A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs |
| title_full_unstemmed | A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs |
| title_short | A multi-tissue and -breed catalogue of chromatin conformations and their implications in gene regulation in pigs |
| title_sort | multi tissue and breed catalogue of chromatin conformations and their implications in gene regulation in pigs |
| topic | Pig TADs Gene expression Biological functions |
| url | https://doi.org/10.1186/s12864-025-11490-4 |
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