1
|
Yi M, Asgenbaatar N, Wang X, Ulaangerel T, Shen Y, Wen X, Du M, Dong X, Dugarjav M, Bou G. Different expression patterns of DNA methyltransferases during horse testis development. Gene 2024; 920:148531. [PMID: 38705424 DOI: 10.1016/j.gene.2024.148531] [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: 02/22/2024] [Revised: 04/28/2024] [Accepted: 05/02/2024] [Indexed: 05/07/2024]
Abstract
DNA methyltransferases (DNMTs) are important epigenetic modification during spermatogenesis. To further evaluate the pattern of DNMTs in horse testes during development, we investigated the expression and localization of DNMT1, DNMT3a and DNMT3b at different time points. The qRT-PCR results showed that DNMT1 expression was maintained in testes tissue from 6-month-old (0.5y) to 2-year-old (2y) of age and decreased after 3-year-old (3y) (P < 0.01). The expression levels of DNMT3a and DNMT3b peaked in testes tissue at 3y (P < 0.01). At 4-year-old (4y), the expression of DNMT3a and DNMT3b was decreased and became similar to that at 0.5y. Immunofluorescence of DNMT1, DNMT3a and DNMT3b on testis samples confirmed the differential expression and localization of these three DNA methylation transferases during horse development. Further molecular biological studies are needed to understand the implications of the expression patterns of these DNMTs in horse testes.
Collapse
Affiliation(s)
- Minna Yi
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Nairag Asgenbaatar
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China; Da Bei Nong group rumination technology rumination acadamy Haidian District, Beijing, China
| | - Xisheng Wang
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China; Collaborative Innovation Center for Birth Defect Research and Transformation of Shandong Province, Jining Medical University, Jining, China
| | - Tseweendolmaa Ulaangerel
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Yingchao Shen
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Xin Wen
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Ming Du
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaoling Dong
- Da Bei Nong group rumination technology rumination acadamy Haidian District, Beijing, China; China Agricultural University, Beijing, China
| | - Manglai Dugarjav
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China.
| | - Gerelchimeg Bou
- Inner Mongolia Key Laboratory of Equine Science Research and Technology Innovation, Inner Mongolia Agricultural University, Hohhot, China.
| |
Collapse
|
2
|
Yue C, Wang J, Shen Y, Zhang J, Liu J, Xiao A, Liu Y, Eer H, Zhang QE. Whole-genome DNA methylation profiling reveals epigenetic signatures in developing muscle in Tan and Hu sheep and their offspring. Front Vet Sci 2023; 10:1186040. [PMID: 37388464 PMCID: PMC10301830 DOI: 10.3389/fvets.2023.1186040] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 05/24/2023] [Indexed: 07/01/2023] Open
Abstract
Introduction The Tan sheep is a popular local breed in China because of its tenderness and flavor. The Hu sheep breed is also famous for its high litter size, and its muscle growth rate is faster than that of Tan sheep. However, the epigenetic mechanism behind these muscle-related phenotypes is unknown. Methods In this study, the longissimus dorsi tissue from 18 6 month-old Tan sheep, Hu sheep, and Tan-Hu F2 generation (6 sheep per population) were collected. After genomic DNA extraction, whole-genome bisulfite sequencing (WGBS) and bioinformatics analysis were performed to construct genome-wide DNA methylome maps for the Tan sheep, Hu sheep and their Tan-Hu F2 generation. Results Distinct genome-wide DNA methylation patterns were observed between Tan sheep and Hu sheep. Moreover, DNA methylated regions were significantly increased in the skeletal muscle from Tan sheep vs. the F2 generation compared to the Hu sheep vs. F2 generation and the Tan sheep vs. Hu sheep. Compared with Hu sheep, the methylation levels of actin alpha 1 (ACTA1), myosin heavy chain 11 (MYH11), Wiskott-Aldrich syndrome protein (WAS), vav guanine nucleotide exchange factor 1 (VAV1), fibronectin 1 (FN1) and Rho-associated protein kinase 2 (ROCK2) genes were markedly distinct in the Tan sheep. Furthermore, Gene Ontology analysis indicated that these genes were involved in myotube differentiation, myotube cell development, smooth muscle cell differentiation and striated muscle cell differentiation. Conclusion The findings from this study, in addition to data from previous research, demonstrated that the ACTA1, MYH11, WAS, VAV1, FN1, and ROCK2 genes may exert regulatory effects on muscle development.
Collapse
Affiliation(s)
- Caijuan Yue
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jiakang Wang
- College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - Yifei Shen
- Institute of Marxism, China University of Geosciences, Wuhan, Hubei, China
| | - Junli Zhang
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Jian Liu
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Aiping Xiao
- Animal Husbandry Extension Station, Yinchuan, Ningxia, China
| | - Yisha Liu
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
| | - Hehua Eer
- Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, Ningxia, China
| | - Qiao-e Zhang
- College of Animal Science and Technology, Ningxia University, Yinchuan, Ningxia, China
| |
Collapse
|
3
|
Orellana-Guerrero D, Uribe-Salazar JM, El-Sheikh Ali H, Scoggin KE, Ball B, Daels P, Finno CJ, Dini P. Dynamics of the Equine Placental DNA Methylome and Transcriptome from Mid- to Late Gestation. Int J Mol Sci 2023; 24:ijms24087084. [PMID: 37108254 PMCID: PMC10139181 DOI: 10.3390/ijms24087084] [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: 03/04/2023] [Revised: 04/04/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
The placenta is a temporary organ that is essential for the survival of the fetus, with a lifelong effect on the health of both the offspring and the dam. The functions of the placenta are controlled by its dynamic gene expression during gestation. In this study, we aimed to investigate the equine placental DNA methylome as one of the fundamental mechanisms that controls the gene expression dynamic. Chorioallantois samples from four (4M), six (6M), and ten (10M) months of gestation were used to map the methylation pattern of the placenta. Globally, methylation levels increased toward the end of gestation. We identified 921 differentially methylated regions (DMRs) between 4M and 6M, 1225 DMRs between 4M and 10M, and 1026 DMRs between 6M and 10M. A total of 817 genes carried DMRs comparing 4M and 6M, 978 comparing 4M and 10M, and 804 comparing 6M and 10M. We compared the transcriptomes between the samples and found 1381 differentially expressed genes (DEGs) when comparing 4M and 6M, 1428 DEGs between 4M and 10M, and 741 DEGs between 6M and 10M. Finally, we overlapped the DEGs and genes carrying DMRs (DMRs-DEGs). Genes exhibiting (a) higher expression, low methylation and (b) low expression, high methylation at different time points were identified. The majority of these DMRs-DEGs were located in introns (48.4%), promoters (25.8%), and exons (17.7%) and were involved in changes in the extracellular matrix; regulation of epithelial cell migration; vascularization; and regulation of minerals, glucose, and metabolites, among other factors. Overall, this is the first report highlighting the dynamics in the equine placenta methylome during normal pregnancy. The findings presented serve as a foundation for future studies on the impact of abnormal methylation on the outcomes of equine pregnancies.
Collapse
Affiliation(s)
- Daniela Orellana-Guerrero
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | | | - Hossam El-Sheikh Ali
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
- College of Veterinary Medicine, Mansoura University, Mansoura 35516, Egypt
| | - Kirsten E Scoggin
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Barry Ball
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA
| | - Peter Daels
- Faculty of Veterinary Medicine, Ghent University, 9820 Merelbeke, Belgium
| | - Carrie J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Pouya Dini
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| |
Collapse
|
4
|
Liu L, Zhang Y, Ma H, Cao H, Liu W. Integrating genome-wide methylation and transcriptome-wide analyses to reveal the genetic mechanism of milk traits in Kazakh horses. Gene 2023; 856:147143. [PMID: 36574934 DOI: 10.1016/j.gene.2022.147143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/06/2022] [Accepted: 12/21/2022] [Indexed: 12/25/2022]
Abstract
Horse Milk has important quantitative characteristics and high economic value. However, the DNA methylation regulators involved in horse milk traits have not been clarified. To explore the important role of genome-wide DNA methylation in regulating equine milk yield, this study systematically investigated the genome-wide DNA methylation profiles of Kazakh horse blood by comparing a high-production group (HP, average daily milk yield of 7.5 kg) and low-production group (LP, average daily milk yield of 3.2 kg) using deep whole-genome bisulfite sequencing. First, both groups showed similar proportions of methylation at CpG sites. Subsequently, we identified 26,677 differential methylated regions (DMRs) of CG, 15 DMRs of CHG, 480 DMRs of CHH and 8268 DMR-related genes (DMGs). GO and KEGG analyses revealed that some DMGs were involved in regulating milk and milk component formation. By combining the WGBS-seq and the previous RNA-seq data, a total of 94 overlapping genes were obtained. Finally, we found that 9 DMGs are likely involved in milk production by Kazakh horses.
Collapse
Affiliation(s)
- Lingling Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Yunting Zhang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Haiyu Ma
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Hang Cao
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China.
| |
Collapse
|
5
|
The Innovative Informatics Approaches of High-Throughput Technologies in Livestock: Spearheading the Sustainability and Resiliency of Agrigenomics Research. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111893. [PMID: 36431028 PMCID: PMC9695872 DOI: 10.3390/life12111893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 11/09/2022] [Accepted: 11/14/2022] [Indexed: 11/17/2022]
Abstract
For more than a decade, next-generation sequencing (NGS) has been emerging as the mainstay of agrigenomics research. High-throughput technologies have made it feasible to facilitate research at the scale and cost required for using this data in livestock research. Scale frameworks of sequencing for agricultural and livestock improvement, management, and conservation are partly attributable to innovative informatics methodologies and advancements in sequencing practices. Genome-wide sequence-based investigations are often conducted worldwide, and several databases have been created to discover the connections between worldwide scientific accomplishments. Such studies are beginning to provide revolutionary insights into a new era of genomic prediction and selection capabilities of various domesticated livestock species. In this concise review, we provide selected examples of the current state of sequencing methods, many of which are already being used in animal genomic studies, and summarize the state of the positive attributes of genome-based research for cattle (Bos taurus), sheep (Ovis aries), pigs (Sus scrofa domesticus), horses (Equus caballus), chickens (Gallus gallus domesticus), and ducks (Anas platyrhyncos). This review also emphasizes the advantageous features of sequencing technologies in monitoring and detecting infectious zoonotic diseases. In the coming years, the continued advancement of sequencing technologies in livestock agrigenomics will significantly influence the sustained momentum toward regulatory approaches that encourage innovation to ensure continued access to a safe, abundant, and affordable food supplies for future generations.
Collapse
|
6
|
Pires VS, de O. Ganzella FA, Minozzo GA, Dias de Castro LL, Moncada AD, Klassen G, Ramos EA, Molento MB. Epigenetic regulation of SLC11a1 gene in horses infected with cyathostomins. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
7
|
Liu Y, Xu Q, Kang X, Wang K, Wang J, Feng D, Bai Y, Fang M. Dynamic changes of genomic methylation profiles at different growth stages in Chinese Tan sheep. J Anim Sci Biotechnol 2021; 12:118. [PMID: 34727982 PMCID: PMC8561971 DOI: 10.1186/s40104-021-00632-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 08/31/2021] [Indexed: 01/02/2023] Open
Abstract
Background Tan sheep, an important local sheep breed in China, is famous for their fur quality. One-month-old Tan sheep have white, curly hair with beautiful flower spikes, commonly known as “nine bends”, which has high economic value. However, the “nine bends” characteristic gradually disappears with age; consequently, the economic value of the Tan sheep decreases. Age-related changes in DNA methylation have been reported and may be responsible for age-induced changes in gene expression. Until now, no genome-wide surveys have been conducted to identify potential DNA methylation sites involved in different sheep growth stages. In this study we investigated the dynamic changes of genome-wide DNA methylation profiles in Tan sheep using DNA from skin and deep whole-genome bisulfite sequencing, and compared the DNA methylation levels at three different growth stages: 1, 24, and 48 months old (mon1, mon24, and mon48, respectively). Results In this study, 11 skin samples from three growth stages (four for mon1, four for mon24, and three for mon48) were used for DNA methylation analysis and gene expression profiling. There were 52, 288 and 236 differentially methylated genes (DMGs) identified between mon1 and mon24, mon1 and mon48, and mon24 and mon48, respectively. Of the differentially methylated regions, 1.11%, 7.61%, and 7.65% were in the promoter in mon1 vs. mon24, mon24 vs. mon48, and mon1 vs. mon48, respectively. DMGs were enriched in the MAPK and WNT signaling pathways, which are related to age growth and hair follicle morphogenesis processes. There were 51 DMGs associated with age growth and curly fleece formation. Four DMGs between mon1 and mon48 (KRT71, CD44, ROR2 and ZDHHC13) were further validated by bisulfite sequencing. Conclusions This study revealed dynamic changes in the genomic methylation profiles of mon1, mon24, and mon48 sheep, and the percentages of methylated cytosines were 3.38%, 2.85% and 4.17%, respectively. Of the DMGs, KRT71 and CD44 were highly methylated in mon1, and ROR2 and ZDHHC13 were highly methylated in mon48. These findings provide foundational information that may be used to develop strategies for potentially retaining the lamb fur and thus improving the economic value of Tan sheep. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00632-9.
Collapse
Affiliation(s)
- Yufang Liu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.,College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056021, People's Republic of China
| | - Qiao Xu
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China.,Biotechnology Institute, Nanchang Normal University, Nanchang, 330029, People's Republic of China
| | - Xiaolong Kang
- College of Agriculture, Ningxia University, Yinchuan, 750021, People's Republic of China
| | - Kejun Wang
- College of Animal Science and Veterinary Medicine, Henan Agricultural University, Zhengzhou, 450002, People's Republic of China
| | - Jve Wang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China
| | - Dengzhen Feng
- Biotechnology Institute, Nanchang Normal University, Nanchang, 330029, People's Republic of China
| | - Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, 056021, People's Republic of China
| | - Meiying Fang
- Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, MOA Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, No. 2 Yuanmingyuan West Rd, Beijing, 100193, People's Republic of China. .,Beijing Key Laboratory for Animal Genetic Improvement, Beijing, 100193, People's Republic of China.
| |
Collapse
|
8
|
Tian Y, Yang X, Du J, Zeng W, Wu W, Di J, Huang X, Tian K. Differential Methylation and Transcriptome Integration Analysis Identified Differential Methylation Annotation Genes and Functional Research Related to Hair Follicle Development in Sheep. Front Genet 2021; 12:735827. [PMID: 34659357 PMCID: PMC8515899 DOI: 10.3389/fgene.2021.735827] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Accepted: 08/30/2021] [Indexed: 11/13/2022] Open
Abstract
Hair follicle growth and development are a complex and long-term physiological process, which is regulated by a variety of physical factors and signal pathways. Increasing the understanding of the epigenetic regulation and function of candidate genes related to hair follicle development will help to better understand the molecular regulatory mechanisms of hair follicle development. In this study, the methylated DNA immunoprecipitation sequencing (MeDIP-seq) was used to obtain the genome-wide methylation map of the hair follicular development of Super Merino sheep in six stages (fetal skin tissue at 65d, 85d, 105d, 135d, 7d, and 30d after birth). Combined with the results of previous RNA-sequencing, 65 genes were screened out that were both differential methylation and differential expression, including EDN1, LAMC2, NR1D1, RORB, MyOZ3, and WNT2 gene. Differential methylation genes were enriched in Wnt, TNF, TGF-beta, and other signaling pathways related to hair follicle development. The bisulfite sequencing PCR results and MeDIP-seq were basically consistent, indicating that the sequencing results were accurate. As a key gene in the Wnt signaling pathway, both differential methylation and expression gene identified by MeDIP-seq and RNA-seq, further exploration of the function of WNT2 gene revealed that the DNA methylation of exon 5 (CpG11 site) promoted the expression of WNT2 gene. The overexpression vector of lentivirus pLEX-MCS-WNT2 was constructed, and WNT2 gene effectively promoted the proliferation of sheep skin fibroblasts. The results showed that WNT2 gene could promote the growth and development of skin and hair follicles. The results of this study will provide a theoretical basis for further research on sheep hair follicle development and gene regulation mechanisms.
Collapse
Affiliation(s)
- Yuezhen Tian
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xuemei Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jianwen Du
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Weidan Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Weiwei Wu
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Jiang Di
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Kechuan Tian
- The Key Laboratory for Genetics Breeding and Reproduction of Xinjiang Cashmere and Wool Sheep, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| |
Collapse
|
9
|
Bai L, Sun H, Jiang W, Yang L, Liu G, Zhao X, Hu H, Wang J, Gao S. DNA methylation and histone acetylation are involved in Wnt10b expression during the secondary hair follicle cycle in Angora rabbits. J Anim Physiol Anim Nutr (Berl) 2021; 105:599-609. [PMID: 33404138 DOI: 10.1111/jpn.13481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 09/03/2020] [Accepted: 11/02/2020] [Indexed: 12/25/2022]
Abstract
Secondary hair follicles (SHFs) in the Angora rabbit exhibit classic cyclic hair development, but the multiple molecular signals involved in hair cycling are yet to be explored in detail. In the present study, we investigated the expression pattern, methylation and histone H3 acetylation status of Wnt10b, as a molecular signal participating in hair cycling, during the SHF cycle in the Angora rabbit. Expression of Wnt10b at the anagen phase was significantly higher than that at both the telogen and catagen phases, suggesting that Wnt10b might serve as a critical activator during cyclic transition of SHFs. Methylation frequency of the fifth CpG site (CpG5-175 bp) in CpG islands at the anagen phase was lower than that at both the catagen and telogen phases. The methylation status of the CpG5 site was negatively correlated with Wnt10b expression. This indicated that the methylation of CpG5 might participate in Wnt10b transcriptional suppression in SHFs. Furthermore, histone H3 acetylation status in the regions-256~-11 bp and 98 ~ 361 bp were significantly lower at both the catagen and telogen phases than at the anagen phase. The histone H3 acetylation level was significantly positively correlated with Wnt10b expression. This confirmed that histone acetylation was likely involved in upregulating Wnt10b transcription in SHFs. Additionally, potential binding to the transcription factors ZF57 and HDBP was predicted within the CpG5 site. In conclusion, our findings reveal the epigenetic mechanism of Wnt10b transcription and provide a new insight into epigenetic regulation during the SHF cycle in the Angora rabbit.
Collapse
Affiliation(s)
- Liya Bai
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Haitao Sun
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Wenxue Jiang
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Liping Yang
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Gongyan Liu
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Xueyan Zhao
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Hongmei Hu
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Jianying Wang
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| | - Shuxia Gao
- Shandong Provincial Key Laboratory of Animal Disease Control & Breeding, Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China
| |
Collapse
|
10
|
Zhao C, Ji G, Carrillo JA, Li Y, Tian F, Baldwin RL, Zan L, Song J. The Profiling of DNA Methylation and Its Regulation on Divergent Tenderness in Angus Beef Cattle. Front Genet 2020; 11:939. [PMID: 33005170 PMCID: PMC7479246 DOI: 10.3389/fgene.2020.00939] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 07/28/2020] [Indexed: 01/18/2023] Open
Abstract
Beef is an essential food source in the world. Beef quality, especially tenderness, has a significant impact on consumer satisfaction and industry profit. Many types of research to date have focused on the exploration of physiological and developmental mechanisms of beef tenderness. Still, the role and impact of DNA methylation status on beef tenderness have yet to be elucidated. In this study, we exhaustively analyzed the DNA methylation status in divergent tenderness observed in Angus beef. We characterized the methylation profiles related to beef tenderness and explored methylation distributions on the whole genome. As a result, differentially methylated regions (DMRs) associated with tenderness and toughness of beef were identified. Importantly, we annotated these DMRs on the bovine genome and explored bio-pathways of underlying genes and methylation biomarkers in beef quality. Specifically, we observed that the ATP binding cassette subfamily and myosin-related genes were highly methylated gene sets, and generation of neurons, regulation of GTPase activity, ion transport and anion transport, etc., were the significant pathways related with beef tenderness. Moreover, we explored the relationship between DNA methylation and gene expression in DMRs. Some methylated genes were identified as candidate biomarkers for beef tenderness. These results provide not only novel epigenetic information associated with beef quality but offer more significant insights into meat science, which will further help us explore the mechanism of muscle biology.
Collapse
Affiliation(s)
- Chunping Zhao
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Guanyu Ji
- Shenzhen GenDo Health Sci&Tech Ltd., Shenzhen, China
| | - José A Carrillo
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Yaokun Li
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China.,Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Fei Tian
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, NEA, USDA, Beltsville, MD, United States
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, United States
| |
Collapse
|
11
|
Abstract
The sequencing and assembly of a reference genome for the horse has been revolutionary for investigation of horse health and performance. Next-generation sequencing (NGS) methods represent a second revolution in equine genomics. Researchers can align and compare DNA and RNA sequencing data to the reference genome to explore variation that may contribute or be attributed to disease. NGS has also facilitated the translation of research discovery to clinically relevant applications. This article discusses the history and development of NGS, details some of the available sequencing platforms, and describes currently available applications in the context of both discovery and clinical settings.
Collapse
|
12
|
Zhou Y, Liu S, Hu Y, Fang L, Gao Y, Xia H, Schroeder SG, Rosen BD, Connor EE, Li CJ, Baldwin RL, Cole JB, Van Tassell CP, Yang L, Ma L, Liu GE. Comparative whole genome DNA methylation profiling across cattle tissues reveals global and tissue-specific methylation patterns. BMC Biol 2020; 18:85. [PMID: 32631327 PMCID: PMC7339546 DOI: 10.1186/s12915-020-00793-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 05/12/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Efforts to improve animal health, and understand genetic bases for production, may benefit from a comprehensive analysis of animal genomes and epigenomes. Although DNA methylation has been well studied in humans and other model species, its distribution patterns and regulatory impacts in cattle are still largely unknown. Here, we present the largest collection of cattle DNA methylation epigenomic data to date. RESULTS Using Holstein cattle, we generated 29 whole genome bisulfite sequencing (WGBS) datasets for 16 tissues, 47 corresponding RNA-seq datasets, and 2 whole genome sequencing datasets. We did read mapping and DNA methylation calling based on two different cattle assemblies, demonstrating the high quality of the long-read-based assembly markedly improved DNA methylation results. We observed large differences across cattle tissues in the methylation patterns of global CpG sites, partially methylated domains (PMDs), hypomethylated regions (HMRs), CG islands (CGIs), and common repeats. We detected that each tissue had a distinct set of PMDs, which showed tissue-specific patterns. Similar to human PMD, cattle PMDs were often linked to a general decrease of gene expression and a decrease in active histone marks and related to long-range chromatin organizations, like topologically associated domains (TADs). We tested a classification of the HMRs based on their distributions relative to transcription start sites (TSSs) and detected tissue-specific TSS-HMRs and genes that showed strong tissue effects. When performing cross-species comparisons of paired genes (two opposite strand genes with their TSS located in the same HMR), we found out they were more consistently co-expressed among human, mouse, sheep, goat, yak, pig, and chicken, but showed lower consistent ratios in more divergent species. We further used these WGBS data to detect 50,023 experimentally supported CGIs across bovine tissues and found that they might function as a guard against C-to-T mutations for TSS-HMRs. Although common repeats were often heavily methylated, some young Bov-A2 repeats were hypomethylated in sperm and could affect the promoter structures by exposing potential transcription factor binding sites. CONCLUSIONS This study provides a comprehensive resource for bovine epigenomic research and enables new discoveries about DNA methylation and its role in complex traits.
Collapse
Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Shuli Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yan Hu
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Lingzhao Fang
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Yahui Gao
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Han Xia
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Steven G. Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Benjamin D. Rosen
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Erin E. Connor
- Department of Animal and Food Sciences, University of Delaware, Newark, DE 19716 USA
| | - Cong-jun Li
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Ransom L. Baldwin
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - John B. Cole
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Curtis P. Van Tassell
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 China
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742 USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705 USA
| |
Collapse
|
13
|
Hu Q, Ao Q, Tan Y, Gan X, Luo Y, Zhu J. Genome-Wide DNA Methylation and RNA Analysis Reveal Potential Mechanism of Resistance to Streptococcus agalactiae in GIFT Strain of Nile Tilapia ( Oreochromis niloticus ). THE JOURNAL OF IMMUNOLOGY 2020; 204:3182-3190. [PMID: 32332111 DOI: 10.4049/jimmunol.1901496] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/07/2020] [Indexed: 11/19/2022]
Abstract
Streptococcus agalactiae is an important pathogenic bacterium causing great economic loss in Nile tilapia (Oreochromis niloticus) culture. Resistant and susceptible groups sharing the same genome showed significantly different resistance to S. agalactiae in the genetically improved farmed tilapia strain of Nile tilapia. The resistance mechanism is unclear. We determined genome-wide DNA methylation profiles in spleen of resistant and susceptible O. niloticus at 5 h postinfection with S. agalactiae using whole-genome bisulfite sequencing. The methylation status was higher in the spleen samples from resistant fish than in the susceptible group. A total of 10,177 differentially methylated regions were identified in the two groups, including 3725 differentially methylated genes (DMGs) (3129 hyper-DMGs and 596 hypo-DMGs). The RNA sequencing showed 2374 differentially expressed genes (DEGs), including 1483 upregulated and 891 downregulated. Integrated analysis showed 337 overlapping DEGs and DMGs and 82 overlapping DEGs and differentially methylated region promoters. By integrating promoter DNA methylation with gene expression, we revealed four immune-related genes (Arnt2, Nhr38, Pcdh10, and Ccdc158) as key factors in epigenetic mechanisms contributing to pathogen resistance. Our study provided systematic methylome maps to explore the epigenetic mechanism and reveal the methylation loci of pathogen resistance and identified methylation-regulated genes that are potentially involved in defense against pathogens.
Collapse
Affiliation(s)
- Qiaomu Hu
- Yangtze River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Wuhan, Hubei 430223, China; and
| | - Qiuwei Ao
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, Guangxi 530021, China
| | - Yun Tan
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, Guangxi 530021, China
| | - Xi Gan
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, Guangxi 530021, China
| | - Yongju Luo
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, Guangxi 530021, China
| | - Jiajie Zhu
- Guangxi Academy of Fishery Sciences, Guangxi Key Laboratory of Aquatic Genetic Breeding and Healthy Aquaculture, Nanning, Guangxi 530021, China
| |
Collapse
|
14
|
Ma C, Zhang L, Wang X, He S, Bai J, Li Q, Zhang M, Zhang C, Yu X, Zhang J, Xin W, Li Y, Zhu D. piRNA-63076 contributes to pulmonary arterial smooth muscle cell proliferation through acyl-CoA dehydrogenase. J Cell Mol Med 2020; 24:5260-5273. [PMID: 32227582 PMCID: PMC7205801 DOI: 10.1111/jcmm.15179] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 02/09/2020] [Accepted: 03/06/2020] [Indexed: 12/18/2022] Open
Abstract
Piwi-interacting RNAs (piRNAs) are thought to be germline-specific and to be involved in maintaining genome stability during development. Recently, piRNA expression has been identified in somatic cells in diverse organisms. However, the roles of piRNAs in pulmonary arterial smooth muscle cell (PASMC) proliferation and the molecular mechanism underlying the hypoxia-regulated pathological process of pulmonary hypertension are not well understood. Using hypoxic animal models, cell and molecular biology, we obtained the first evidence that the expression of piRNA-63076 was up-regulated in hypoxia and was positively correlated with cell proliferation. Subsequently, we showed that acyl-CoA dehydrogenase (Acadm), which is negatively regulated by piRNA-63076 and interacts with Piwi proteins, was involved in hypoxic PASMC proliferation. Finally, Acadm inhibition under hypoxia was partly attributed to DNA methylation of the Acadm promoter region mediated by piRNA-63076. Overall, these findings represent invaluable resources for better understanding the role of epigenetics in pulmonary hypertension associated with piRNAs.
Collapse
Affiliation(s)
- Cui Ma
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of Medical Laboratory Science and TechnologyHarbin Medical University (Daqing)DaqingChina
| | - Lixin Zhang
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of Medical Laboratory Science and TechnologyHarbin Medical University (Daqing)DaqingChina
| | - Xiaoying Wang
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of PharmacyHarbin Medical UniversityHarbinChina
| | - Siyu He
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of PharmacyHarbin Medical UniversityHarbinChina
| | - June Bai
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of PharmacyHarbin Medical UniversityHarbinChina
| | - Qian Li
- College of PharmacyHarbin Medical UniversityHarbinChina
| | - Min Zhang
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of PharmacyHarbin Medical UniversityHarbinChina
| | - Chen Zhang
- College of PharmacyHarbin University of CommerceHarbinChina
| | - Xiufeng Yu
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of Medical Laboratory Science and TechnologyHarbin Medical University (Daqing)DaqingChina
| | - Junting Zhang
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of PharmacyHarbin Medical UniversityHarbinChina
| | - Wei Xin
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of PharmacyHarbin Medical UniversityHarbinChina
| | - Yiying Li
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of PharmacyHarbin Medical UniversityHarbinChina
| | - Daling Zhu
- Central Laboratory of Harbin Medical University (Daqing)DaqingChina
- College of PharmacyHarbin Medical UniversityHarbinChina
- State Province Key Laboratories of BiomedicinePharmaceutics of ChinaDaqingChina
- Key Laboratory of Cardiovascular Medicine ResearchMinistry of EducationHarbin Medical UniversityHarbinChina
| |
Collapse
|
15
|
Srikanth K, Kim NY, Park W, Kim JM, Kim KD, Lee KT, Son JH, Chai HH, Choi JW, Jang GW, Kim H, Ryu YC, Nam JW, Park JE, Kim JM, Lim D. Comprehensive genome and transcriptome analyses reveal genetic relationship, selection signature, and transcriptome landscape of small-sized Korean native Jeju horse. Sci Rep 2019; 9:16672. [PMID: 31723199 PMCID: PMC6853925 DOI: 10.1038/s41598-019-53102-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 10/18/2019] [Indexed: 12/16/2022] Open
Abstract
The Jeju horse, indigenous to the Jeju Island in Korea may have originated from Mongolian horses. Adaptations to the local harsh environment have conferred Jeju horse with unique traits such as small-sized body, stocky head, and shorter limbs. These characteristics have not been studied previously at the genomic level. Therefore, we sequenced and compared the genome of 41 horses belonging to 6 breeds. We identified numerous breed-specific non-synonymous SNPs and loss-of-function mutants. Demographic and admixture analyses showed that, though Jeju horse is genetically the closest to the Mongolian breeds, its genetic ancestry is independent of that of the Mongolian breeds. Genome wide selection signature analysis revealed that genes such as LCORL, MSTN, HMGA2, ZFAT, LASP1, PDK4, and ACTN2, were positively selected in the Jeju horse. RNAseq analysis showed that several of these genes were also differentially expressed in Jeju horse compared to Thoroughbred horse. Comparative muscle fiber analysis showed that, the type I muscle fibre content was substantially higher in Jeju horse compared to Thoroughbred horse. Our results provide insights about the selection of complex phenotypic traits in the small-sized Jeju horse and the novel SNPs identified will aid in designing high-density SNP chip for studying other native horse breeds.
Collapse
Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Nam-Young Kim
- Subtropical Livestock Research Institute, National Institute of Animal Science, Rural Development Administration, Jeju-do, 63242, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jae-Min Kim
- Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | | | - Kyung-Tai Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Ju-Hwan Son
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Han-Ha Chai
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jung-Woo Choi
- College of Animal Life Science, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Gul-Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | | | - Youn-Chul Ryu
- Division of Biotechnology, Jeju National University, Jeju, 63243, Republic of Korea
| | - Jin-Wu Nam
- Department of Life Science, Hanyang University, Seoul, 133-791, Republic of Korea
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Ansung-si, 17546, Republic of Korea.
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, Rural Development Administration, Wanju, 55365, Republic of Korea.
| |
Collapse
|
16
|
Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
Collapse
Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
| |
Collapse
|
17
|
An X, Ma H, Han P, Zhu C, Cao B, Bai Y. Genome-wide differences in DNA methylation changes in caprine ovaries between oestrous and dioestrous phases. J Anim Sci Biotechnol 2018; 9:85. [PMID: 30524725 PMCID: PMC6277999 DOI: 10.1186/s40104-018-0301-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 10/22/2018] [Indexed: 12/22/2022] Open
Abstract
Background DNA methylation plays a vital role in reproduction. Entire genome DNA methylation changes during the oestrous phase (ES) and dioestrous phase (DS) in the ovaries of Guanzhong dairy goats were investigated using bisulphite sequencing to understand the molecular biological mechanisms of these goats’ oestrous cycle. Results We discovered distinct genome-wide DNA methylation patterns in ES and DS ovaries. A total of 26,910 differentially methylated regions were upregulated and 21,453 differentially methylated regions were downregulated in the ES samples compared with the DS samples (P-values ≤0.05 and fold change of methylation ratios ≥2). Differentially methylated region analysis showed hypomethylation in the gene body regions and hypermethylation in the joining region between upstream regions and gene bodies. The methylation ratios of the STAR, FGF2, FGF12, BMP5 and SMAD6 genes in the ES samples were lower than those of the DS samples (P-values ≤0.05 and fold change of methylation ratios ≥2). Conversely, the methylation ratios of the EGFR, TGFBR2, IGF2BP1 and MMD2 genes increased in the ES samples compared with the DS samples. In addition, 223 differentially methylated genes were found in the GnRH signalling pathway (KO04912), ovarian steroidogenesis pathway (KO04913), oestrogen signalling pathway (KO04915), oxytocin signalling pathway (KO04921), insulin secretion pathway (KO04911) and MAPK signalling pathway (KO04010). Conclusions This study is the first large-scale comparison of the high-resolution DNA methylation landscapes of oestrous and dioestrous ovaries from dairy goats. Previous studies and our investigations have shown that the NR5A2, STAR, FGF2 and BMP5 genes might have potential application value in regulating caprine oestrus. Electronic supplementary material The online version of this article (10.1186/s40104-018-0301-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Xiaopeng An
- 1College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100 People's Republic of China
| | - Haidong Ma
- 1College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100 People's Republic of China
| | - Peng Han
- 1College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100 People's Republic of China
| | - Chao Zhu
- 1College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100 People's Republic of China
| | - Binyun Cao
- 1College of Animal Science and Technology, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100 People's Republic of China
| | - Yueyu Bai
- Animal Health Supervision Institute of Henan Province, No. 91 Jingsan Road, Zhengzhou, Henan 450008 People's Republic of China
| |
Collapse
|
18
|
Zhou Y, Connor EE, Bickhart DM, Li C, Baldwin RL, Schroeder SG, Rosen BD, Yang L, Van Tassell CP, Liu GE. Comparative whole genome DNA methylation profiling of cattle sperm and somatic tissues reveals striking hypomethylated patterns in sperm. Gigascience 2018; 7:4965117. [PMID: 29635292 PMCID: PMC5928411 DOI: 10.1093/gigascience/giy039] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2017] [Accepted: 03/28/2018] [Indexed: 12/21/2022] Open
Abstract
Background Although sperm DNA methylation has been studied in humans and other species, its status in cattle is largely unknown. Results Using whole-genome bisulfite sequencing (WGBS), we profiled the DNA methylome of cattle sperm through comparison with three somatic tissues (mammary gland, brain, and blood). Large differences between cattle sperm and somatic cells were observed in the methylation patterns of global CpGs, pericentromeric satellites, partially methylated domains (PMDs), hypomethylated regions (HMRs), and common repeats. As expected, we observed low methylation in the promoter regions and high methylation in the bodies of active genes. We detected selective hypomethylation of megabase domains of centromeric satellite clusters, which may be related to chromosome segregation during meiosis and their rapid transcriptional activation upon fertilization. We found more PMDs in sperm cells than in somatic cells and identified meiosis-related genes such asKIF2B and REPIN1, which are hypomethylated in sperm but hypermethylated in somatic cells. In addition to the common HMRs around gene promoters, which showed substantial differences between sperm and somatic cells, the sperm-specific HMRs also targeted to distinct spermatogenesis-related genes, including BOLL, MAEL, ASZ1, SYCP3, CTCFL, MND1, SPATA22, PLD6, DDX4, RBBP8, FKBP6, and SYCE1. Although common repeats were heavily methylated in both sperm and somatic cells, some young Bov-A2 repeats, which belong to the SINE family, were hypomethylated in sperm and could affect the promoter structures by introducing new regulatory elements. Conclusions Our study provides a comprehensive resource for bovine sperm epigenomic research and enables new discoveries about DNA methylation and its role in male fertility.
Collapse
Affiliation(s)
- Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China.,Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Erin E Connor
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Derek M Bickhart
- The Cell Wall Utilization and Biology Laboratory, US Department of Agriculture, Agriculture Research Service, Madison, WI, 53706, USA
| | - Congjun Li
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Ransom L Baldwin
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - Liguo Yang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, US Department of Agriculture, Agriculture Research Service, Beltsville, MD 20705, USA
| |
Collapse
|
19
|
Giuffra E, Tuggle CK. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Annu Rev Anim Biosci 2018; 7:65-88. [PMID: 30427726 DOI: 10.1146/annurev-animal-020518-114913] [Citation(s) in RCA: 94] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community-driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.
Collapse
Affiliation(s)
- Elisabetta Giuffra
- Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France;
| | | | | |
Collapse
|
20
|
Li C, Li Y, Zhou G, Gao Y, Ma S, Chen Y, Song J, Wang X. Whole-genome bisulfite sequencing of goat skins identifies signatures associated with hair cycling. BMC Genomics 2018; 19:638. [PMID: 30153818 PMCID: PMC6114738 DOI: 10.1186/s12864-018-5002-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 08/08/2018] [Indexed: 01/07/2023] Open
Abstract
Background Hair follicles (HFs), upon development, undergo repetitive cycles of growth (anagen), regression (catagen), and rest (telogen). The transition between the stages is determined by multiple molecular signals, including DNA methylation, which plays important roles in mammalian cellular identity and is essential for the development of HFs. Secondary hair follicles (SHFs) in cashmere goat exhibit classic cyclic hair development, and little has been done on a genome-wide scale to examine potentially methylated genes involved in the hair cyclic transition. Results Genome-wide DNA methylation profiles between skin tissues sampled during the anagen and telogen stages in cashmere goats were investigated using whole-genome bisulfite sequencing (WGBS). The methylation status was observed to be higher in the skin samples with HFs in the telogen than those in the anagen stage. A total of 1311 differentially methylated regions (DMRs) were identified between the two groups, which contained 493 fully annotated DMR-related genes (DMGs) (269 Hyper- DMGs and 224 Hypo-DMGs). Furthermore, a significant over-representation of the functional categories for DMGs related to immune response and intercellular crosstalk during hair cycling was observed. By integrating DNA methylation and mRNA expression data, we revealed that four genes (FMN1, PCOLCE, SPTLC3, and COL5A1) are crucial factors for elucidating epigenetic mechanisms contributing to the telogen-to-anagen transition. Conclusion Our study provided systematic methylome maps pertaining to the hair cycling stages (anagen vs telogen) at a single-base resolution, and revealed stage-specific methylation loci during cashmere growth or quiescence. Furthermore, we identified epigenetically regulated genes that are potentially involved in HF development and growth in cashmere goats, and likely in other mammal species. Electronic supplementary material The online version of this article (10.1186/s12864-018-5002-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Chao Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yan Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Guangxian Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Ye Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Sen Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Yulin Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China
| | - Jiuzhou Song
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
| | - Xiaolong Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, 712100, China.
| |
Collapse
|
21
|
Transcriptome analysis reveals long intergenic non-coding RNAs involved in skeletal muscle growth and development in pig. Sci Rep 2017; 7:8704. [PMID: 28821716 PMCID: PMC5562803 DOI: 10.1038/s41598-017-07998-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 07/06/2017] [Indexed: 02/06/2023] Open
Abstract
Long intergenic non-coding RNAs (lincRNAs) play essential roles in numerous biological processes and are widely studied. The skeletal muscle is an important tissue that plays an essential role in individual movement ability. However, lincRNAs in pig skeletal muscles are largely undiscovered and their biological functions remain elusive. In this study, we assembled transcriptomes using RNA-seq data published in previous studies of our laboratory group and identified 323 lincRNAs in porcine leg muscle. We found that these lincRNAs have shorter transcript length, fewer exons and lower expression level than protein-coding genes. Gene ontology and pathway analyses indicated that many potential target genes (PTGs) of lincRNAs were involved in skeletal-muscle-related processes, such as muscle contraction and muscle system process. Combined our previous studies, we found a potential regulatory mechanism in which the promoter methylation of lincRNAs can negatively regulate lincRNA expression and then positively regulate PTG expression, which can finally result in abnormal phenotypes of cloned piglets through a certain unknown pathway. This work detailed a number of lincRNAs and their target genes involved in skeletal muscle growth and development and can facilitate future studies on their roles in skeletal muscle growth and development.
Collapse
|
22
|
Frattini S, Capra E, Lazzari B, McKay SD, Coizet B, Talenti A, Groppetti D, Riccaboni P, Pecile A, Chessa S, Castiglioni B, Williams JL, Pagnacco G, Stella A, Crepaldi P. Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus. BMC Genomics 2017. [PMID: 28645321 PMCID: PMC5481934 DOI: 10.1186/s12864-017-3866-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND DNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and hence in biological processes and in determining phenotypic plasticity in organisms. Rudimentary DNA methylation patterns for some livestock species are publically available: among these, goat methylome deserves to be further explored. RESULTS Genome-wide DNA methylation maps of the hypothalamus and ovary from Saanen goats were generated using Methyl-CpG binding domain protein sequencing (MBD-seq). Analysis of DNA methylation patterns indicate that the majority of methylation peaks found within genes are located gene body regions, for both organs. Analysis of the distribution of methylated sites per chromosome showed that chromosome X had the lowest number of methylation peaks. The X chromosome has one of the highest percentages of methylated CpG islands in both organs, and approximately 50% of the CpG islands in the goat epigenome are methylated in hypothalamus and ovary. Organ-specific Differentially Methylated Genes (DMGs) were correlated with the expression levels. CONCLUSIONS The comparison between transcriptome and methylome in hypothalamus and ovary showed that a higher level of methylation is not accompanied by a higher gene suppression. The genome-wide DNA methylation map for two goat organs produced here is a valuable starting point for studying the involvement of epigenetic modifications in regulating goat reproduction performance.
Collapse
Affiliation(s)
- Stefano Frattini
- Department of Veterinary Science, University of Milan, Milan, Italy
| | - Emanuele Capra
- Institute of Agricultural Biology and Biotechnology, National Research Council UOS of Lodi, Lodi, Italy
| | - Barbara Lazzari
- Institute of Agricultural Biology and Biotechnology, National Research Council UOS of Lodi, Lodi, Italy.,PTP Science Park, Lodi, Italy
| | - Stephanie D McKay
- Department of Animal & Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Beatrice Coizet
- Department of Veterinary Science, University of Milan, Milan, Italy
| | - Andrea Talenti
- Department of Veterinary Science, University of Milan, Milan, Italy
| | - Debora Groppetti
- Department of Veterinary Science, University of Milan, Milan, Italy
| | - Pietro Riccaboni
- Department of Veterinary Science, University of Milan, Milan, Italy
| | | | - Stefania Chessa
- Institute of Agricultural Biology and Biotechnology, National Research Council UOS of Lodi, Lodi, Italy
| | - Bianca Castiglioni
- Institute of Agricultural Biology and Biotechnology, National Research Council UOS of Lodi, Lodi, Italy
| | - John L Williams
- The Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, 5371, Australia
| | - Giulio Pagnacco
- Department of Veterinary Science, University of Milan, Milan, Italy
| | - Alessandra Stella
- Institute of Agricultural Biology and Biotechnology, National Research Council UOS of Lodi, Lodi, Italy.,PTP Science Park, Lodi, Italy
| | - Paola Crepaldi
- Department of Veterinary Science, University of Milan, Milan, Italy.
| |
Collapse
|
23
|
Comparative analysis of DNA methylome and transcriptome of skeletal muscle in lean-, obese-, and mini-type pigs. Sci Rep 2017; 7:39883. [PMID: 28045116 PMCID: PMC5206674 DOI: 10.1038/srep39883] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 11/29/2016] [Indexed: 02/07/2023] Open
Abstract
DNA methylation plays a pivotal role in biological processes by affecting gene expression. However, how DNA methylation mediates phenotype difference of skeletal muscle between lean-, obese-, and mini-type pigs remains unclear. We systematically carried out comparative analysis of skeletal muscle by integrating analysis of genome-wide DNA methylation, mRNA, lncRNA and miRNA profiles in three different pig breeds (obese-type Tongcheng, lean-type Landrace, and mini-type Wuzhishan pigs). We found that the differentially methylated genes (DMGs) were significantly associated with lipid metabolism, oxidative stress and muscle development. Among the identified DMGs, 253 genes were related to body-size and obesity. A set of lncRNAs and mRNAs including UCP3, FHL1, ANK1, HDAC4, and HDAC5 exhibited inversely changed DNA methylation and expression level; these genes were associated with oxidation reduction, fatty acid metabolism and cell proliferation. Gene regulatory networks involved in phenotypic variation of skeletal muscle were related to lipid metabolism, cellular movement, skeletal muscle development, and the p38 MAPK signaling pathway. DNA methylation potentially influences the propensity for obesity and body size by affecting gene expression in skeletal muscle. Our findings provide an abundant information of epigenome and transcriptome that will be useful for animal breeding and biomedical research.
Collapse
|
24
|
Zhou Y, Xu L, Bickhart DM, Abdel Hay EH, Schroeder SG, Connor EE, Alexander LJ, Sonstegard TS, Van Tassell CP, Chen H, Liu GE. Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression. BMC Genomics 2016; 17:779. [PMID: 27716143 PMCID: PMC5053184 DOI: 10.1186/s12864-016-3116-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 09/23/2016] [Indexed: 01/16/2023] Open
Abstract
Background As a major epigenetic component, DNA methylation plays important functions in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in economically important animals like cattle. Results Using reduced representation bisulphite sequencing (RRBS), we obtained single-base-resolution maps of bovine DNA methylation from ten somatic tissues. In total, we evaluated 1,868,049 cytosines in CG-enriched regions. While we found slightly low methylation levels (29.87 to 38.06 %) in cattle, the methylation contexts (CGs and non-CGs) of cattle showed similar methylation patterns to other species. Non-CG methylation was detected but methylation levels in somatic tissues were significantly lower than in pluripotent cells. To study the potential function of the methylation, we detected 10,794 differentially methylated cytosines (DMCs) and 836 differentially methylated CG islands (DMIs). Further analyses in the same tissues revealed many DMCs (including non-CGs) and DMIs, which were highly correlated with the expression of genes involved in tissue development. Conclusions In summary, our study provides a baseline dataset and essential information for DNA methylation profiles of cattle. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3116-1) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yang Zhou
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.,Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Science, Beijing, 100193, People's Republic of China
| | - Derek M Bickhart
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - El Hamidi Abdel Hay
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - Erin E Connor
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - Leeson J Alexander
- USDA Agricultural Research Service, Fort Keogh Livestock and Range Research Laboratory, Miles City, MT, 59301, USA
| | | | - Curtis P Van Tassell
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA
| | - Hong Chen
- Shaanxi Key Laboratory of Agricultural Molecular Biology, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, People's Republic of China.
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, Beltsville, MD, 20705, USA.
| |
Collapse
|
25
|
Yang Y, Zhou R, Mu Y, Hou X, Tang Z, Li K. Genome-wide analysis of DNA methylation in obese, lean, and miniature pig breeds. Sci Rep 2016; 6:30160. [PMID: 27444743 PMCID: PMC4957084 DOI: 10.1038/srep30160] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2015] [Accepted: 06/28/2016] [Indexed: 12/20/2022] Open
Abstract
DNA methylation is a crucial epigenetic modification involved in diverse biological processes. There is significant phenotypic variance between Chinese indigenous and western pig breeds. Here, we surveyed the genome-wide DNA methylation profiles of blood leukocytes from three pig breeds (Tongcheng, Landrace, and Wuzhishan) by methylated DNA immunoprecipitation sequencing. The results showed that DNA methylation was enriched in gene body regions and repetitive sequences. LINE/L1 and SINE/tRNA-Glu were the predominant methylated repeats in pigs. The methylation level in the gene body regions was higher than in the 5' and 3' flanking regions of genes. About 15% of CpG islands were methylated in the pig genomes. Additionally, 2,807, 2,969, and 5,547 differentially methylated genes (DMGs) were identified in the Tongcheng vs. Landrace, Tongcheng vs. Wuzhishan, and Landrace vs. Wuzhishan comparisons, respectively. A total of 868 DMGs were shared by the three contrasts. The DMGs were significantly enriched in development- and metabolism-related biological processes and pathways. Finally, we identified 32 candidate DMGs associated with phenotype variance in pigs. Our research provides a DNA methylome resource for pigs and furthers understanding of epigenetically regulated phenotype variance in mammals.
Collapse
Affiliation(s)
- Yalan Yang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Rong Zhou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Yulian Mu
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xinhua Hou
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhonglin Tang
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| | - Kui Li
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518124, China
| |
Collapse
|
26
|
Profiling the genome-wide DNA methylation pattern of porcine ovaries using reduced representation bisulfite sequencing. Sci Rep 2016; 6:22138. [PMID: 26912189 PMCID: PMC4766444 DOI: 10.1038/srep22138] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 02/08/2016] [Indexed: 12/16/2022] Open
Abstract
Substantial evidence has shown that DNA methylation regulates the initiation of ovarian and sexual maturation. Here, we investigated the genome-wide profile of DNA methylation in porcine ovaries at single-base resolution using reduced representation bisulfite sequencing. The biological variation was minimal among the three ovarian replicates. We found hypermethylation frequently occurred in regions with low gene abundance, while hypomethylation in regions with high gene abundance. The DNA methylation around transcriptional start sites was negatively correlated with their own CpG content. Additionally, the methylation level in the bodies of genes was higher than that in their 5′ and 3′ flanking regions. The DNA methylation pattern of the low CpG content promoter genes differed obviously from that of the high CpG content promoter genes. The DNA methylation level of the porcine ovary was higher than that of the porcine intestine. Analyses of the genome-wide DNA methylation in porcine ovaries would advance the knowledge and understanding of the porcine ovarian methylome.
Collapse
|
27
|
Su Y, Fan Z, Wu X, Li Y, Wang F, Zhang C, Wang J, Du J, Wang S. Genome-wide DNA methylation profile of developing deciduous tooth germ in miniature pigs. BMC Genomics 2016; 17:134. [PMID: 26911717 PMCID: PMC4766650 DOI: 10.1186/s12864-016-2485-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 02/17/2016] [Indexed: 12/28/2022] Open
Abstract
Background DNA methylation is an important epigenetic modification critical to the regulation of gene expression during development. To date, little is known about the role of DNA methylation in tooth development in large animal models. Thus, we carried out a comparative genomic analysis of genome-wide DNA methylation profiles in E50 and E60 tooth germ from miniature pigs using methylated DNA immunoprecipitation-sequencing (MeDIP-seq). Results We observed different DNA methylation patterns during the different developmental stages of pig tooth germ. A total of 2469 differentially methylated genes were identified. Functional analysis identified several signaling pathways and 104 genes that may be potential key regulators of pig tooth development from E50 to E60. Conclusions The present study provided a comprehensive analysis of the global DNA methylation pattern of tooth germ in miniature pigs and identified candidate genes that potentially regulate tooth development from E50 to E60. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2485-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yingying Su
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Zhipeng Fan
- Laboratory of Molecular Signaling and Stem Cells Therapy, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Xiaoshan Wu
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Yang Li
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Fu Wang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Chunmei Zhang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China.
| | - Jinsong Wang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China. .,Department of Biochemistry and Molecular Biology, Capital Medical University School of Basic Medical Sciences, You An Men Wai Xi Tou Tiao No.10, Beijing, 100069, China.
| | - Jie Du
- Department of Physiology and Pathophysiology, Beijing An Zhen Hospital the Key Laboratory of Remodeling-Related Cardiovascular Diseases, School of Basic Medical Sciences, Capital Medical University, You An Men Wai Xi Tou Tiao No.10, Beijing, 100069, China.
| | - Songlin Wang
- Molecular Laboratory for Gene Therapy and Tooth Regeneration, Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction, Capital Medical University School of Stomatology, Tian Tan Xi Li No.4, Beijing, 100050, China. .,Department of Biochemistry and Molecular Biology, Capital Medical University School of Basic Medical Sciences, You An Men Wai Xi Tou Tiao No.10, Beijing, 100069, China.
| |
Collapse
|
28
|
Wang Y, Wu J, Ma X, Liu B, Su R, Jiang Y, Wang W, Dong Y. Single Base-Resolution Methylome of the Dizygotic Sheep. PLoS One 2015; 10:e0142034. [PMID: 26536671 PMCID: PMC4633158 DOI: 10.1371/journal.pone.0142034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 10/17/2015] [Indexed: 12/12/2022] Open
Abstract
Sheep is an important livestock in the world for meat, dairy and wool production. The third version of sheep reference genome has been recently assembled, but sheep DNA methylome has not been profiled yet. In this study, we report the comprehensive sheep methylome with 94.38% cytosine coverage at single base resolution by sequencing DNA samples from Longissimus dorsi of dizygotic Sunit sheep, which were bred in different habitats. We also compared methylomes between the twin sheep. DNA methylation status at genome-scale differentially methylated regions (DMRs), functional genomic regions and 248 DMR-containing genes were identified between the twin sheep. Gene ontology (GO) and KEGG annotations of these genes were performed to discover computationally predicted function. Lipid metabolism, sexual maturity and tumor-associated categories were observed to significantly enrich DMR-containing genes. These findings could be used to illustrate the relationship between phenotypic variations and gene methylation patterns.
Collapse
Affiliation(s)
- Yangzi Wang
- Kunming University of Science and Technology, Chenggong District, Kunming, China
| | - Jianghong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Animal Husbandry Institute, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
- Inner Mongolia Prataculture Research Center, Chinese Academy of Science, Hohhot, China
| | - Xiao Ma
- Yunnan Agricultural University, Kunming, China
| | - Bin Liu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- Animal Husbandry Institute, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot, China
| | - Rui Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu Jiang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail: (WW); (YD)
| | - Yang Dong
- Kunming University of Science and Technology, Chenggong District, Kunming, China
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
- * E-mail: (WW); (YD)
| |
Collapse
|
29
|
Choi M, Lee J, Le MT, Nguyen DT, Park S, Soundrarajan N, Schachtschneider KM, Kim J, Park JK, Kim JH, Park C. Genome-wide analysis of DNA methylation in pigs using reduced representation bisulfite sequencing. DNA Res 2015; 22:343-55. [PMID: 26358297 PMCID: PMC4596400 DOI: 10.1093/dnares/dsv017] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 07/31/2015] [Indexed: 01/15/2023] Open
Abstract
DNA methylation plays a major role in the epigenetic regulation of gene expression. Although a few DNA methylation profiling studies of porcine genome which is one of the important biomedical models for human diseases have been reported, the available data are still limited. We tried to study methylation patterns of diverse pig tissues as a study of the International Swine Methylome Consortium to generate the swine reference methylome map to extensively evaluate the methylation profile of the pig genome at a single base resolution. We generated and analysed the DNA methylome profiles of five different tissues and a cell line originated from pig. On average, 39.85 and 62.1% of cytosine and guanine dinucleotides (CpGs) of CpG islands and 2 kb upstream of transcription start sites were covered, respectively. We detected a low rate (an average of 1.67%) of non-CpG methylation in the six samples except for the neocortex (2.3%). The observed global CpG methylation patterns of pigs indicated high similarity to other mammals including humans. The percentage of CpG methylation associated with gene features was similar among the tissues but not for a 3D4/2 cell line. Our results provide essential information for future studies of the porcine epigenome.
Collapse
Affiliation(s)
- Minkyeung Choi
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Jongin Lee
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Min Thong Le
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Dinh Truong Nguyen
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Suhyun Park
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | | | - Kyle M Schachtschneider
- Department of Animal Sciences, University of Illinois, Urbana, IL, USA Animal Breeding and Genomics Center, Wageningen University, Wageningen, The Netherlands
| | - Jaebum Kim
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Jin-Ki Park
- Animal Biotechnology Division, National Institute of Animal Science, Suwon, Korea
| | - Jin-Hoi Kim
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| | - Chankyu Park
- Department of Animal Biotechnology, Konkuk University, Kwangjin-gu, Seoul 143-701, Korea
| |
Collapse
|
30
|
Jellyman JK, Valenzuela OA, Fowden AL. HORSE SPECIES SYMPOSIUM: Glucocorticoid programming of hypothalamic-pituitary-adrenal axis and metabolic function: Animal studies from mouse to horse1,2. J Anim Sci 2015; 93:3245-60. [DOI: 10.2527/jas.2014-8612] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- J. K. Jellyman
- Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502
| | - O. A. Valenzuela
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| | - A. L. Fowden
- Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge CB2 3EG, UK
| |
Collapse
|
31
|
Gim JA, Lee S, Kim DS, Jeong KS, Hong CP, Bae JH, Moon JW, Choi YS, Cho BW, Cho HG, Bhak J, Kim HS. HEpD: a database describing epigenetic differences between Thoroughbred and Jeju horses. Gene 2015; 560:83-8. [PMID: 25637569 DOI: 10.1016/j.gene.2015.01.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2014] [Revised: 12/19/2014] [Accepted: 01/23/2015] [Indexed: 11/19/2022]
Abstract
With the advent of next-generation sequencing technology, genome-wide maps of DNA methylation are now available. The Thoroughbred horse is bred for racing, while the Jeju horse is a traditional Korean horse bred for racing or food. The methylation profiles of equine organs may provide genomic clues underlying their athletic traits. We have developed a database to elucidate genome-wide DNA methylation patterns of the cerebrum, lung, heart, and skeletal muscle from Thoroughbred and Jeju horses. Using MeDIP-Seq, our database provides information regarding significantly enriched methylated regions beyond a threshold, methylation density of a specific region, and differentially methylated regions (DMRs) for tissues from two equine breeds. It provided methylation patterns at 784 gene regions in the equine genome. This database can potentially help researchers identify DMRs in the tissues of these horse species and investigate the differences between the Thoroughbred and Jeju horse breeds.
Collapse
Affiliation(s)
- Jeong-An Gim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 609-735, Republic of Korea
| | - Sugi Lee
- Department of Statistics, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Dae-Soo Kim
- Genome Resource Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), 111 Gwahangno, Yuseong-gu, Daejeon 305-806, Republic of Korea
| | - Kwang-Seuk Jeong
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Institute of Environmental Technology & Industry, Pusan National University, Busan 609-735, Republic of Korea
| | - Chang Pyo Hong
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Jin-Han Bae
- Research Center, Dongnam Institute of Radiological and Medical Sciences (DIRAMS), Busan, Republic of Korea
| | - Jae-Woo Moon
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea
| | - Yong-Seok Choi
- Genetic Engineering Institute, Pusan National University, Busan 609-735, Republic of Korea; Department of Statistics, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea
| | - Byung-Wook Cho
- Department of Animal Science, College of Life Sciences, Pusan National University, Miryang 627-702, Republic of Korea
| | - Hwan-Gue Cho
- School of Computer Science and Engineering, College of Engineering, Pusan National University, Busan 609-735, Republic of Korea
| | - Jong Bhak
- TBI, Theragen BiO Institute, TheragenEtex, Suwon 443-270, Republic of Korea; BioMedical Engineering, UNIST, Ulsan, Republic of Korea
| | - Heui-Soo Kim
- Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea; Genetic Engineering Institute, Pusan National University, Busan 609-735, Republic of Korea.
| |
Collapse
|
32
|
Kantanen J, Løvendahl P, Strandberg E, Eythorsdottir E, Li MH, Kettunen-Præbel A, Berg P, Meuwissen T. Utilization of farm animal genetic resources in a changing agro-ecological environment in the Nordic countries. Front Genet 2015; 6:52. [PMID: 25767477 PMCID: PMC4341116 DOI: 10.3389/fgene.2015.00052] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Accepted: 02/05/2015] [Indexed: 12/16/2022] Open
Abstract
Livestock production is the most important component of northern European agriculture and contributes to and will be affected by climate change. Nevertheless, the role of farm animal genetic resources in the adaptation to new agro-ecological conditions and mitigation of animal production’s effects on climate change has been inadequately discussed despite there being several important associations between animal genetic resources and climate change issues. The sustainability of animal production systems and future food security require access to a wide diversity of animal genetic resources. There are several genetic questions that should be considered in strategies promoting adaptation to climate change and mitigation of environmental effects of livestock production. For example, it may become important to choose among breeds and even among farm animal species according to their suitability to a future with altered production systems. Some animals with useful phenotypes and genotypes may be more useful than others in the changing environment. Robust animal breeds with the potential to adapt to new agro-ecological conditions and tolerate new diseases will be needed. The key issue in mitigation of harmful greenhouse gas effects induced by livestock production is the reduction of methane (CH4) emissions from ruminants. There are differences in CH4 emissions among breeds and among individual animals within breeds that suggest a potential for improvement in the trait through genetic selection. Characterization of breeds and individuals with modern genomic tools should be applied to identify breeds that have genetically adapted to marginal conditions and to get critical information for breeding and conservation programs for farm animal genetic resources. We conclude that phenotyping and genomic technologies and adoption of new breeding approaches, such as genomic selection introgression, will promote breeding for useful characters in livestock species.
Collapse
Affiliation(s)
- Juha Kantanen
- Green Technology, Natural Resources Institute Finland , Jokioinen, Finland ; Department of Biology, University of Eastern Finland , Kuopio, Finland
| | - Peter Løvendahl
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University , Tjele, Denmark
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences , Uppsala, Sweden
| | - Emma Eythorsdottir
- Faculty of Land and Animal Resources, Agricultural University of Iceland , Reykjavik, Iceland
| | - Meng-Hua Li
- Green Technology, Natural Resources Institute Finland , Jokioinen, Finland ; Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences , Beijing, China
| | | | - Peer Berg
- NordGen - Nordic Genetic Resource Center , Aas, Norway
| | - Theo Meuwissen
- Department of Animal and Aquacultural Sciences, Norwegian University of Life Sciences , Aas, Norway
| |
Collapse
|