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Yang J, Wang DF, Huang JH, Zhu QH, Luo LY, Lu R, Xie XL, Salehian-Dehkordi H, Esmailizadeh A, Liu GE, Li MH. Structural variant landscapes reveal convergent signatures of evolution in sheep and goats. Genome Biol 2024; 25:148. [PMID: 38845023 PMCID: PMC11155191 DOI: 10.1186/s13059-024-03288-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 05/21/2024] [Indexed: 06/10/2024] Open
Abstract
BACKGROUND Sheep and goats have undergone domestication and improvement to produce similar phenotypes, which have been greatly impacted by structural variants (SVs). Here, we report a high-quality chromosome-level reference genome of Asiatic mouflon, and implement a comprehensive analysis of SVs in 897 genomes of worldwide wild and domestic populations of sheep and goats to reveal genetic signatures underlying convergent evolution. RESULTS We characterize the SV landscapes in terms of genetic diversity, chromosomal distribution and their links with genes, QTLs and transposable elements, and examine their impacts on regulatory elements. We identify several novel SVs and annotate corresponding genes (e.g., BMPR1B, BMPR2, RALYL, COL21A1, and LRP1B) associated with important production traits such as fertility, meat and milk production, and wool/hair fineness. We detect signatures of selection involving the parallel evolution of orthologous SV-associated genes during domestication, local environmental adaptation, and improvement. In particular, we find that fecundity traits experienced convergent selection targeting the gene BMPR1B, with the DEL00067921 deletion explaining ~10.4% of the phenotypic variation observed in goats. CONCLUSIONS Our results provide new insights into the convergent evolution of SVs and serve as a rich resource for the future improvement of sheep, goats, and related livestock.
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Affiliation(s)
- Ji Yang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Jia-Hui Huang
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qiang-Hui Zhu
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ling-Yun Luo
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Ran Lu
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Xing-Long Xie
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Hosein Salehian-Dehkordi
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences (UCAS), Beijing, 100049, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, 76169-133, Iran
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Beltsville, MD, 20705, USA
| | - Meng-Hua Li
- State Key Laboratory of Animal Biotech Breeding, China Agricultural University, Beijing, 100193, China.
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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2
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Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024; 908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Department of Animal Science, Werabe University, P.O. Box 46, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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3
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Wang C, Chen C, Lei B, Qin S, Zhang Y, Li K, Zhang S, Liu Y. Constructing eRNA-mediated gene regulatory networks to explore the genetic basis of muscle and fat-relevant traits in pigs. Genet Sel Evol 2024; 56:28. [PMID: 38594607 PMCID: PMC11003151 DOI: 10.1186/s12711-024-00897-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 04/03/2024] [Indexed: 04/11/2024] Open
Abstract
BACKGROUND Enhancer RNAs (eRNAs) play a crucial role in transcriptional regulation. While significant progress has been made in understanding epigenetic regulation mediated by eRNAs, research on the construction of eRNA-mediated gene regulatory networks (eGRN) and the identification of critical network components that influence complex traits is lacking. RESULTS Here, employing the pig as a model, we conducted a comprehensive study using H3K27ac histone ChIP-seq and RNA-seq data to construct eRNA expression profiles from multiple tissues of two distinct pig breeds, namely Enshi Black (ES) and Duroc. In addition to revealing the regulatory landscape of eRNAs at the tissue level, we developed an innovative network construction and refinement method by integrating RNA-seq, ChIP-seq, genome-wide association study (GWAS) signals and enhancer-modulating effects of single nucleotide polymorphisms (SNPs) measured by self-transcribing active regulatory region sequencing (STARR-seq) experiments. Using this approach, we unraveled eGRN that significantly influence the growth and development of muscle and fat tissues, and identified several novel genes that affect adipocyte differentiation in a cell line model. CONCLUSIONS Our work not only provides novel insights into the genetic basis of economic pig traits, but also offers a generalizable approach to elucidate the eRNA-mediated transcriptional regulation underlying a wide spectrum of complex traits for diverse organisms.
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Affiliation(s)
- Chao Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Choulin Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Bowen Lei
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Shenghua Qin
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
| | - Yuanyuan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- School of Life Sciences, Henan University, Kaifeng, 475004, People's Republic of China
- Shenzhen Research Institute of Henan University, Shenzhen, 518000, People's Republic of China
| | - Kui Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China
| | - Song Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China.
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China.
| | - Yuwen Liu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Key Laboratory of Livestock and Poultry Multi-Omics of MARA, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China.
- Innovation Group of Pig Genome Design and Breeding, Research Centre for Animal Genome, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, People's Republic of China.
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, Foshan, 528226, People's Republic of China.
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Xu J, Wen Y, Li X, Peng W, Zhang Z, Liu X, Yang P, Chen N, Lei C, Zhang J, Wang E, Chen H, Huang Y. Bovine enhancer-regulated circSGCB acts as a ceRNA to regulate skeletal muscle development via enhancing KLF3 expression. Int J Biol Macromol 2024; 261:129779. [PMID: 38290628 DOI: 10.1016/j.ijbiomac.2024.129779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/07/2024] [Accepted: 01/24/2024] [Indexed: 02/01/2024]
Abstract
Skeletal muscle growth and development in livestock and poultry play a pivotal role in determining the quality and yield of meat production. However, the mechanisms of myogenesis are remained unclear due to it finely regulated by a complex network of biological macromolecules. In this study, leveraging previous sequencing data, we investigated a differentially expressed circular RNA (circSGCB) present in fetal and adult muscle tissues among various ruminant species, including cattle, goat, and sheep. Our analysis revealed that circSGCB is a single exon circRNA, potentially regulated by an adjacent bovine enhancer. Functional analysis through loss-of-function tests demonstrated that circSGCB exerts inhibitory effects on bovine myoblast proliferation while promoting myocytes generation. Furthermore, we discovered that circSGCB primarily localizes to the cytoplasm, where it functions as a molecular sponge by binding to bta-miR-27a-3p. This interaction releases the mRNAs of KLF3 gene and further activates downstream functional pathways. In vivo, studies provided evidence that up-regulation of KLF3 contributes to muscle regeneration. These findings collectively suggest that circSGCB operates via a competing endogenous RNA (ceRNA) mechanism to regulate KLF3, thereby influencing myogenesis in ruminants and highlights it may as potential molecular targets for enhancing meat production in livestock and poultry industries.
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Affiliation(s)
- Jiawei Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yifan Wen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmiao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Peng
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
| | - Zijing Zhang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Xian Liu
- Henan Provincial Animal Husbandry General Station, Zhengzhou, Henan 450008, China
| | - Peng Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ningbo Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jun Zhang
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China
| | - Eryao Wang
- Institute of Animal Husbandry and Veterinary Science, Henan Academy of Agricultural Sciences, Zhengzhou, Henan 450002, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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5
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Zhang Q, Li Q, Wang Y, Zhang Y, Peng R, Wang Z, Zhu B, Xu L, Gao X, Chen Y, Gao H, Hu J, Qian C, Ma M, Duan R, Li J, Zhang L. Characterization of Chromatin Accessibility in Fetal Bovine Chondrocytes. Animals (Basel) 2023; 13:1875. [PMID: 37889831 PMCID: PMC10251841 DOI: 10.3390/ani13111875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/28/2023] [Accepted: 05/29/2023] [Indexed: 10/29/2023] Open
Abstract
Despite significant advances of the bovine epigenome investigation, new evidence for the epigenetic basis of fetal cartilage development remains lacking. In this study, the chondrocytes were isolated from long bone tissues of bovine fetuses at 90 days. The Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq) and transcriptome sequencing (RNA-seq) were used to characterize gene expression and chromatin accessibility profile in bovine chondrocytes. A total of 9686 open chromatin regions in bovine fetal chondrocytes were identified and 45% of the peaks were enriched in the promoter regions. Then, all peaks were annotated to the nearest gene for Gene Ontology (GO) and Kyoto Encylopaedia of Genes and Genomes (KEGG) analysis. Growth and development-related processes such as amide biosynthesis process (GO: 0043604) and translation regulation (GO: 006417) were enriched in the GO analysis. The KEGG analysis enriched endoplasmic reticulum protein processing signal pathway, TGF-β signaling pathway and cell cycle pathway, which are closely related to protein synthesis and processing during cell proliferation. Active transcription factors (TFs) were enriched by ATAC-seq, and were fully verified with gene expression levels obtained by RNA-seq. Among the top50 TFs from footprint analysis, known or potential cartilage development-related transcription factors FOS, FOSL2 and NFY were found. Overall, our data provide a theoretical basis for further determining the regulatory mechanism of cartilage development in bovine.
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Affiliation(s)
- Qi Zhang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Qian Li
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Yahui Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Yapeng Zhang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Ruiqi Peng
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Zezhao Wang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Bo Zhu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Lingyang Xu
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Xue Gao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Yan Chen
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Huijiang Gao
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Junwei Hu
- Academy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, China; (J.H.); (C.Q.); (M.M.); (R.D.)
| | - Cong Qian
- Academy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, China; (J.H.); (C.Q.); (M.M.); (R.D.)
| | - Minghao Ma
- Academy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, China; (J.H.); (C.Q.); (M.M.); (R.D.)
| | - Rui Duan
- Academy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, China; (J.H.); (C.Q.); (M.M.); (R.D.)
| | - Junya Li
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
| | - Lupei Zhang
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (Q.Z.); (Q.L.); (Y.W.); (Y.Z.); (R.P.); (Z.W.); (B.Z.); (L.X.); (X.G.); (Y.C.); (H.G.)
- Academy of Pingliang Red Cattle, 492 South Ring Road, Kongtong District, Pingliang 744000, China; (J.H.); (C.Q.); (M.M.); (R.D.)
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6
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Boschiero C, Gao Y, Baldwin RL, Ma L, Li CJ, Liu GE. Differentially CTCF-Binding Sites in Cattle Rumen Tissue during Weaning. Int J Mol Sci 2022; 23:ijms23169070. [PMID: 36012336 PMCID: PMC9408924 DOI: 10.3390/ijms23169070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022] Open
Abstract
The weaning transition in calves is characterized by major structural changes such as an increase in the rumen capacity and surface area due to diet changes. Studies evaluating rumen development in calves are vital to identify genetic mechanisms affected by weaning. This study aimed to provide a genome-wide characterization of CTCF-binding sites and differentially CTCF-binding sites (DCBS) in rumen tissue during the weaning transition of four Holstein calves to uncover regulatory elements in rumen epithelial tissue using ChIP-seq. Our study generated 67,280 CTCF peaks for the before weaning (BW) and 39,891 for after weaning (AW). Then, 7401 DCBS were identified for the AW vs. BW comparison representing 0.15% of the cattle genome, comprising ~54% of induced DCBS and ~46% of repressed DCBS. Most of the induced and repressed DCBS were in distal intergenic regions, showing a potential role as insulators. Gene ontology enrichment revealed many shared GO terms for the induced and the repressed DCBS, mainly related to cellular migration, proliferation, growth, differentiation, cellular adhesion, digestive tract morphogenesis, and response to TGFβ. In addition, shared KEGG pathways were obtained for adherens junction and focal adhesion. Interestingly, other relevant KEGG pathways were observed for the induced DCBS like gastric acid secretion, salivary secretion, bacterial invasion of epithelial cells, apelin signaling, and mucin-type O-glycan biosynthesis. IPA analysis further revealed pathways with potential roles in rumen development during weaning, including TGFβ, Integrin-linked kinase, and Integrin signaling. When DCBS were further integrated with RNA-seq data, 36 putative target genes were identified for the repressed DCBS, including KRT84, COL9A2, MATN3, TSPAN1, and AJM1. This study successfully identified DCBS in cattle rumen tissue after weaning on a genome-wide scale and revealed several candidate target genes that may have a role in rumen development, such as TGFβ, integrins, keratins, and SMADs. The information generated in this preliminary study provides new insights into bovine genome regulation and chromatin landscape.
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Affiliation(s)
- Clarissa Boschiero
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Correspondence: (C.-j.L.); (G.E.L.); Tel.: +1-301-504-7216 (C.-j.L.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (C.-j.L. & G.E.L.)
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Agricultural Research Service, U.S. Department of Agriculture, Beltsville, MD 20705, USA
- Correspondence: (C.-j.L.); (G.E.L.); Tel.: +1-301-504-7216 (C.-j.L.); +1-301-504-9843 (G.E.L.); Fax: +1-301-504-8414 (C.-j.L. & G.E.L.)
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Li Q, Wang Y, Hu X, Zhang Y, Li H, Zhang Q, Cai W, Wang Z, Zhu B, Xu L, Gao X, Chen Y, Gao H, Li J, Zhang L. Transcriptional states and chromatin accessibility during bovine myoblasts proliferation and myogenic differentiation. Cell Prolif 2022; 55:e13219. [PMID: 35362202 PMCID: PMC9136495 DOI: 10.1111/cpr.13219] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Revised: 02/17/2022] [Accepted: 02/25/2022] [Indexed: 12/14/2022] Open
Abstract
Objectives Although major advances have been made in bovine epigenome study, the epigenetic basis for fetal skeletal muscle development still remains poorly understood. The aim is to recapitulated the time course of fetal skeletal muscle development in vitro, and explore the dynamic changes of chromatin accessibility and gene expression during bovine myoblasts proliferation and differentiation. Methods PDGFR‐ cells were isolated from bovine fetal skeletal muscle, then cultured and induced myogenic differentiation in vitro in a time‐course study (P, D0, D2,and D4). The assay for transposase‐accessible chromatin sequencing (ATAC‐seq) and RNA sequencing (RNA‐seq) were performed. Results Among the enriched transcriptional factors with high variability, we determined the effects of MAFF, ZNF384, and KLF6 in myogenesis using RNA interference (RNAi). In addition, we identified both stage‐specific genes and chromatin accessibility regions to reveal the sequential order of gene expression, transcriptional regulatory, and signal pathways involved in bovine skeletal muscle development. Further investigation integrating chromatin accessibility and transcriptome data was conducted to explore cis‐regulatory regions in line with gene expression. Moreover, we combined bovine GWAS results of growth traits with regulatory regions defined by chromatin accessibility, providing a suggestive means for a more precise annotation of genetic variants of bovine growth traits. Conclusion Overall, these findings provide valuable information for understanding the stepwise regulatory mechanisms in skeletal muscle development and conducting beef cattle genetic improvement programs.
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Affiliation(s)
- Qian Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yahui Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xin Hu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yapeng Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Hongwei Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Qi Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Wentao Cai
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Zezhao Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Bo Zhu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Lingyang Xu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Xue Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Yan Chen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Huijiang Gao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Junya Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Lupei Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
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Characterization of Accessible Chromatin Regions in Cattle Rumen Epithelial Tissue during Weaning. Genes (Basel) 2022; 13:genes13030535. [PMID: 35328088 PMCID: PMC8949786 DOI: 10.3390/genes13030535] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 12/17/2022] Open
Abstract
Weaning in ruminants is characterized by the transition from a milk-based diet to a solid diet, which drives a critical gastrointestinal tract transformation. Understanding the regulatory control of this transformation during weaning can help to identify strategies to improve rumen health. This study aimed to identify regions of accessible chromatin in rumen epithelial tissue in pre- and post-weaning calves and investigate differentially accessible regions (DARs) to uncover regulatory elements in cattle rumen development using the ATAC-seq approach. A total of 126,071 peaks were identified, covering 1.15% of the cattle genome. From these accessible regions, 2766 DARs were discovered. Gene ontology enrichment resulted in GO terms related to the cell adhesion, anchoring junction, growth, cell migration, motility, and morphogenesis. In addition, putative regulatory canonical pathways were identified (TGFβ, integrin-linked kinase, integrin signaling, and regulation of the epithelial–mesenchymal transition). Canonical pathways integrated with co-expression results showed that TGFβ and ILK signaling pathways play essential roles in rumen development through the regulation of cellular adhesions. In this study, DARs during weaning were identified, revealing enhancers, transcription factors, and candidate target genes that represent potential biomarkers for the bovine rumen development, which will serve as a molecular tool for rumen development studies.
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