Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats
Abstract Background The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and inte...
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| Format: | Article |
| Language: | English |
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BMC
2020-03-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-020-6656-3 |
| _version_ | 1818295302415712256 |
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| author | Zhibin Ji Tianle Chao Zhaohua Liu Lei Hou Jin Wang Aili Wang Jie Zhou Rong Xuan Guizhi Wang Jianmin Wang |
| author_facet | Zhibin Ji Tianle Chao Zhaohua Liu Lei Hou Jin Wang Aili Wang Jie Zhou Rong Xuan Guizhi Wang Jianmin Wang |
| author_sort | Zhibin Ji |
| collection | DOAJ |
| description | Abstract Background The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation. |
| first_indexed | 2024-12-13T03:45:29Z |
| format | Article |
| id | doaj.art-9701ca1052c64df299e5d3dcbfcbdfda |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T03:45:29Z |
| publishDate | 2020-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-9701ca1052c64df299e5d3dcbfcbdfda2022-12-22T00:00:50ZengBMCBMC Genomics1471-21642020-03-0121111110.1186/s12864-020-6656-3Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goatsZhibin Ji0Tianle Chao1Zhaohua Liu2Lei Hou3Jin Wang4Aili Wang5Jie Zhou6Rong Xuan7Guizhi Wang8Jianmin Wang9Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityShandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural UniversityAbstract Background The mammary gland is a unique organ for milk synthesis, secretion and storage, and it undergoes cyclical processes of development, differentiation, lactation and degeneration. At different developmental periods, the biological processes governing mammary gland physiology and internal environmental homeostasis depend on a complex network of genes and regulatory factors. Emerging evidence indicates that lncRNAs have arbitrarily critical functions in regulating gene expression in many organisms; however, the systematic characteristics, expression, and regulatory roles of lncRNAs in the mammary gland tissues of dairy goats have not been determined. Result In the present study, we profiled long noncoding RNA (lncRNA) expression in the mammary gland tissues of Laoshan dairy goats (Capra hircus) from different lactation periods at the whole-genome level, to identify, characterize and explore the regulatory functions of lncRNAs. A total of 37,249 transcripts were obtained, of which 2381 lncRNAs and 37,249 mRNAs were identified, 22,488 transcripts, including 800 noncoding transcripts and 21,688 coding transcripts, differed significantly (p ≤ 0.01) among the different lactation stages. The results of lncRNA-RNA interaction analysis showed that six known lncRNAs belonging to four families were identified as the precursors of 67 known microRNAs; 1478 and 573 mRNAs were predicted as hypothetical cis-regulation elements and antisense mRNAs, respectively. GO annotation and KEGG analysis indicated that the coexpressed mRNAs were largely enriched in biological processes related to such activities as metabolism, immune activation, and stress,., and most genes were involved in pathways related to such phenomena as inflammation, cancer, signal transduction, and metabolism. Conclusions Our results clearly indicated that lncRNAs involved in responses to stimuli, multiorganism processes, development, reproductive processes and growth, are closely related to mammary gland development and lactation.http://link.springer.com/article/10.1186/s12864-020-6656-3RNA-SeqlncRNAmRNAMammary glandGoat |
| spellingShingle | Zhibin Ji Tianle Chao Zhaohua Liu Lei Hou Jin Wang Aili Wang Jie Zhou Rong Xuan Guizhi Wang Jianmin Wang Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats BMC Genomics RNA-Seq lncRNA mRNA Mammary gland Goat |
| title | Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats |
| title_full | Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats |
| title_fullStr | Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats |
| title_full_unstemmed | Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats |
| title_short | Genome‑wide integrated analysis demonstrates widespread functions of lncRNAs in mammary gland development and lactation in dairy goats |
| title_sort | genome wide integrated analysis demonstrates widespread functions of lncrnas in mammary gland development and lactation in dairy goats |
| topic | RNA-Seq lncRNA mRNA Mammary gland Goat |
| url | http://link.springer.com/article/10.1186/s12864-020-6656-3 |
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