Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur quality
Abstract Background Tan and Hu sheep are well-known local breeds in China, producing lamb fur with unique ornamental and practical values highly appreciated by consumers worldwide. Fur quality is optimal at one month of age and gradually declines with time. Despite active research on its genetic mec...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-10-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09741-3 |
| _version_ | 1797453827359637504 |
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| author | Letian Zhang Jiankui Wang Ganxian Cai Lina Ma Zhengwei Zhao Qing Ma Xuemei Deng |
| author_facet | Letian Zhang Jiankui Wang Ganxian Cai Lina Ma Zhengwei Zhao Qing Ma Xuemei Deng |
| author_sort | Letian Zhang |
| collection | DOAJ |
| description | Abstract Background Tan and Hu sheep are well-known local breeds in China, producing lamb fur with unique ornamental and practical values highly appreciated by consumers worldwide. Fur quality is optimal at one month of age and gradually declines with time. Despite active research on its genetic mechanism using transcriptomic and whole genome bisulfite sequencing analysis, the main effective gene locus has not been found, and its regulatory mechanism is still unclear, which limits the breeding and improvement of fur traits. Results Scapular skin samples from newborn (1-month old) and adult (24-month old) Tan sheep were utilized for small ribonucleic acid (RNA) sequencing Principal Component Analysis (PCA) showed that the newborn and adult groups were completely separated. Differential expression analysis of micro-RNAs (miRNAs) identified 32 up-regulated miRNAs and 48 down-regulated miRNAs in the newborn groups. All up-regulated miRNAs were located in the imprinted. Dlk1-Gtl2 locus on chromosome 18, whereas all down-regulated miRNAs were distributed across the sheep chromosomes, without a clear pattern of positional consistency. Further, by systematically analyzing the target genes and signaling pathways of all 32 up-regulated miRNAs, we found that the PI3K-AKT signaling pathway has the potential to be targeted and regulated by most of the miRNAs in the Dlk1-Gtl2 region. In addition, we also re-analyzed miRNA sequencing data from public databases on Hu lambs (full sibling Hu lambs with high- and low-quality fur characteristics). Again, it was found that most of the up-regulated miRNAs in lambs with high-quality fur were also located in the Dlk1-Gtl2 region, whereas this patter was not present for down-regulated miRNAs. Conclusion Sequencing of miRNAs in conjunction with public databases was employed to identify miRNAs within the imprinted Dlk1-Gtl2 region on chromosome 18, suggesting their potential roles as epigenetic regulators of fur traits. Small RNAs located at the Dlk1-Gtl2 locus were identified as having the potential to systematically regulate the PI3K-AKT signaling pathway, thereby indicating the relevance of the Dlk1-Gtl2/PI3K-AKT axis in the context of fur traits. Selection of parental specific expressed imprinted genes in the process of conserving and exploiting lamb fur traits should be emphasized. |
| first_indexed | 2024-03-09T15:28:29Z |
| format | Article |
| id | doaj.art-ae3bb46240264ee5b5f285f638db73a6 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-09T15:28:29Z |
| publishDate | 2023-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-ae3bb46240264ee5b5f285f638db73a62023-11-26T12:25:10ZengBMCBMC Genomics1471-21642023-10-0124111210.1186/s12864-023-09741-3Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur qualityLetian Zhang0Jiankui Wang1Ganxian Cai2Lina Ma3Zhengwei Zhao4Qing Ma5Xuemei Deng6Beijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural UniversityBeijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural UniversityBeijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural UniversityInstitute of Animal Science, Ningxia Academy of Agriculture and Forestry SciencesInstitute of Animal Science, Ningxia Academy of Agriculture and Forestry SciencesInstitute of Animal Science, Ningxia Academy of Agriculture and Forestry SciencesBeijing Key Laboratory for Animal Genetic Improvement & Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & State Key Laboratory of Animal Biotech Breeding, China Agricultural UniversityAbstract Background Tan and Hu sheep are well-known local breeds in China, producing lamb fur with unique ornamental and practical values highly appreciated by consumers worldwide. Fur quality is optimal at one month of age and gradually declines with time. Despite active research on its genetic mechanism using transcriptomic and whole genome bisulfite sequencing analysis, the main effective gene locus has not been found, and its regulatory mechanism is still unclear, which limits the breeding and improvement of fur traits. Results Scapular skin samples from newborn (1-month old) and adult (24-month old) Tan sheep were utilized for small ribonucleic acid (RNA) sequencing Principal Component Analysis (PCA) showed that the newborn and adult groups were completely separated. Differential expression analysis of micro-RNAs (miRNAs) identified 32 up-regulated miRNAs and 48 down-regulated miRNAs in the newborn groups. All up-regulated miRNAs were located in the imprinted. Dlk1-Gtl2 locus on chromosome 18, whereas all down-regulated miRNAs were distributed across the sheep chromosomes, without a clear pattern of positional consistency. Further, by systematically analyzing the target genes and signaling pathways of all 32 up-regulated miRNAs, we found that the PI3K-AKT signaling pathway has the potential to be targeted and regulated by most of the miRNAs in the Dlk1-Gtl2 region. In addition, we also re-analyzed miRNA sequencing data from public databases on Hu lambs (full sibling Hu lambs with high- and low-quality fur characteristics). Again, it was found that most of the up-regulated miRNAs in lambs with high-quality fur were also located in the Dlk1-Gtl2 region, whereas this patter was not present for down-regulated miRNAs. Conclusion Sequencing of miRNAs in conjunction with public databases was employed to identify miRNAs within the imprinted Dlk1-Gtl2 region on chromosome 18, suggesting their potential roles as epigenetic regulators of fur traits. Small RNAs located at the Dlk1-Gtl2 locus were identified as having the potential to systematically regulate the PI3K-AKT signaling pathway, thereby indicating the relevance of the Dlk1-Gtl2/PI3K-AKT axis in the context of fur traits. Selection of parental specific expressed imprinted genes in the process of conserving and exploiting lamb fur traits should be emphasized.https://doi.org/10.1186/s12864-023-09741-3Dlk1-Gtl2Tan sheepHu sheepfurmiRNA-seqPI3K-AKT |
| spellingShingle | Letian Zhang Jiankui Wang Ganxian Cai Lina Ma Zhengwei Zhao Qing Ma Xuemei Deng Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur quality BMC Genomics Dlk1-Gtl2 Tan sheep Hu sheep fur miRNA-seq PI3K-AKT |
| title | Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur quality |
| title_full | Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur quality |
| title_fullStr | Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur quality |
| title_full_unstemmed | Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur quality |
| title_short | Imprinted Dlk1-Gtl2 cluster miRNAs are potential epigenetic regulators of lamb fur quality |
| title_sort | imprinted dlk1 gtl2 cluster mirnas are potential epigenetic regulators of lamb fur quality |
| topic | Dlk1-Gtl2 Tan sheep Hu sheep fur miRNA-seq PI3K-AKT |
| url | https://doi.org/10.1186/s12864-023-09741-3 |
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