Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-Lactation
In this study, circular RNAs (circRNAs) from Holstein cow mammary tissues were identified and compared between early lactation and non-lactation. After analysis, 10,684 circRNAs were identified, ranging from 48 to 99,406 bp, and the average size was 882 bp. The circRNAs were mainly distributed on ch...
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MDPI AG
2022-03-01
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| Online Access: | https://www.mdpi.com/2218-273X/12/3/478 |
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| author | Yan Liang Qisong Gao Haiyang Wang Mengling Guo Abdelaziz Adam Idriss Arbab Mudasir Nazar Mingxun Li Zhangping Yang Niel A. Karrow Yongjiang Mao |
| author_facet | Yan Liang Qisong Gao Haiyang Wang Mengling Guo Abdelaziz Adam Idriss Arbab Mudasir Nazar Mingxun Li Zhangping Yang Niel A. Karrow Yongjiang Mao |
| author_sort | Yan Liang |
| collection | DOAJ |
| description | In this study, circular RNAs (circRNAs) from Holstein cow mammary tissues were identified and compared between early lactation and non-lactation. After analysis, 10,684 circRNAs were identified, ranging from 48 to 99,406 bp, and the average size was 882 bp. The circRNAs were mainly distributed on chromosomes 1 to 11, and 89.89% of the circRNAs belonged to sense-overlapping circRNA. The exons contained with circRNAs ranged from 1 to 47 and were concentrated from 1 to 5. Compared with the non-lactating cows, 87 circRNAs were significantly differentially expressed in the peak lactation cows. There were 68 upregulated circRNAs and 19 downregulated circRNAs. Enrichment analysis of circRNAs showed that GO analysis mainly focused on immune response, triglyceride transport, T cell receptor signaling pathway, etc. Pathway analysis mainly focused on cytokine-cytokine receptor interaction, T helper 17 cell differentiation, fatty acid biosynthesis, the JAK-STAT signaling pathway, etc. Specific primers were designed for two proximal ends of the circRNA junction sites to allow for PCR validation of four randomly selected circRNAs and carry out circRNA-miRNA interaction research. This study revealed the expression profile and characteristics of circRNAs in mammary tissue from Holstein cows at early lactation and non-lactation, thus providing rich information for the study of circRNA functions and mechanisms, as well as potential candidate miRNA genes for studying lactation in Holstein cows. |
| first_indexed | 2024-03-09T13:49:06Z |
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| id | doaj.art-6c45583b5dbb4dadaed41fa6d925e435 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-09T13:49:06Z |
| publishDate | 2022-03-01 |
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| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-6c45583b5dbb4dadaed41fa6d925e4352023-11-30T20:53:22ZengMDPI AGBiomolecules2218-273X2022-03-0112347810.3390/biom12030478Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-LactationYan Liang0Qisong Gao1Haiyang Wang2Mengling Guo3Abdelaziz Adam Idriss Arbab4Mudasir Nazar5Mingxun Li6Zhangping Yang7Niel A. Karrow8Yongjiang Mao9Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaCenter for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, CanadaKey Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Department of Animal Breeding and Production, College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, ChinaIn this study, circular RNAs (circRNAs) from Holstein cow mammary tissues were identified and compared between early lactation and non-lactation. After analysis, 10,684 circRNAs were identified, ranging from 48 to 99,406 bp, and the average size was 882 bp. The circRNAs were mainly distributed on chromosomes 1 to 11, and 89.89% of the circRNAs belonged to sense-overlapping circRNA. The exons contained with circRNAs ranged from 1 to 47 and were concentrated from 1 to 5. Compared with the non-lactating cows, 87 circRNAs were significantly differentially expressed in the peak lactation cows. There were 68 upregulated circRNAs and 19 downregulated circRNAs. Enrichment analysis of circRNAs showed that GO analysis mainly focused on immune response, triglyceride transport, T cell receptor signaling pathway, etc. Pathway analysis mainly focused on cytokine-cytokine receptor interaction, T helper 17 cell differentiation, fatty acid biosynthesis, the JAK-STAT signaling pathway, etc. Specific primers were designed for two proximal ends of the circRNA junction sites to allow for PCR validation of four randomly selected circRNAs and carry out circRNA-miRNA interaction research. This study revealed the expression profile and characteristics of circRNAs in mammary tissue from Holstein cows at early lactation and non-lactation, thus providing rich information for the study of circRNA functions and mechanisms, as well as potential candidate miRNA genes for studying lactation in Holstein cows.https://www.mdpi.com/2218-273X/12/3/478circular RNAmammary tissueHolstein cowsRNA sequencing |
| spellingShingle | Yan Liang Qisong Gao Haiyang Wang Mengling Guo Abdelaziz Adam Idriss Arbab Mudasir Nazar Mingxun Li Zhangping Yang Niel A. Karrow Yongjiang Mao Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-Lactation Biomolecules circular RNA mammary tissue Holstein cows RNA sequencing |
| title | Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-Lactation |
| title_full | Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-Lactation |
| title_fullStr | Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-Lactation |
| title_full_unstemmed | Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-Lactation |
| title_short | Identification and Characterization of Circular RNAs in Mammary Tissue from Holstein Cows at Early Lactation and Non-Lactation |
| title_sort | identification and characterization of circular rnas in mammary tissue from holstein cows at early lactation and non lactation |
| topic | circular RNA mammary tissue Holstein cows RNA sequencing |
| url | https://www.mdpi.com/2218-273X/12/3/478 |
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