Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle
Abstract Chinese red steppe cattle, a highly developed breed for their meat and milk, are not well known about the formation mechanisms for high-quality beef. Furthermore, many fundamental investigations of cattle are hampered by deficient full-length cDNAs. Here, we utilized ONT full-length transcr...
Saved in:
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2025-08-01
|
| Series: | Scientific Reports |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s41598-025-15106-5 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1849333130355277824 |
|---|---|
| author | Wenwen Fang Shaoying Yang Xuanyu Li Asadollahpour Nanaei Yu Liu Yang Cao Cheng Xiao Xin Li Haiguo Jin Yumin Zhao Yang Cao |
| author_facet | Wenwen Fang Shaoying Yang Xuanyu Li Asadollahpour Nanaei Yu Liu Yang Cao Cheng Xiao Xin Li Haiguo Jin Yumin Zhao Yang Cao |
| author_sort | Wenwen Fang |
| collection | DOAJ |
| description | Abstract Chinese red steppe cattle, a highly developed breed for their meat and milk, are not well known about the formation mechanisms for high-quality beef. Furthermore, many fundamental investigations of cattle are hampered by deficient full-length cDNAs. Here, we utilized ONT full-length transcript sequencing from 9 bovine preadipocytes during 3 periods to find 2502 novel genes and 3253 novel transcriptomes, further improving the quality of reference genome annotation. At the same time, based on diverse expression patterns in 3 periods (early, middle and late), we identified 754 significantly differentially expressed genes (DEGs) and 932 significantly differentially expressed transcripts (DETs) in the first contrast group (0d_vs_4d), 197 significantly DEGs and 297 significantly DETs in the second contrast group (0d_vs_8d), 465 and 555 significantly DEGs and DETs in the third contrast group (4d_vs_8d). These DEGs mainly enriched the pathways related to cell differentiation such as Wnt signaling pathway and positive regulation of fat cell differentiation. A total of 35,616 alternative splicing (AS) events were detected, in which 111, 109 and 101 significantly different AS events were found in the group 0d_vs_4d, 0d_vs_8d and 4d_vs_8d respectively. In particular, two essential DEGs, N4BP2L1 and PRKAA1 related to cell differentiation were shown to take part in distinct AS events and were therefore considered as key candidate genes for improving fat deposition and meat quality in Chinese red steppe cattle. These findings provide novel insights into the adipocyte differentiation in cattle and metabolic processes that regulate fat storage, which is essential for optimizing growth and production. |
| format | Article |
| id | doaj-art-a4a8df0c8fd94400b22853e18e217c8e |
| institution | Kabale University |
| issn | 2045-2322 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj-art-a4a8df0c8fd94400b22853e18e217c8e2025-08-20T03:45:59ZengNature PortfolioScientific Reports2045-23222025-08-0115111310.1038/s41598-025-15106-5Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattleWenwen Fang0Shaoying Yang1Xuanyu Li2Asadollahpour Nanaei3Yu Liu4Yang Cao5Cheng Xiao6Xin Li7Haiguo Jin8Yumin Zhao9Yang Cao10Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Institute of Special Animal and Plant Sciences CAASInstitute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Inner Mongolia Academy of Agricultural & Animal Husbandry SciencesInstitute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Institute of Animal Husbandry and Veterinary Medicine, Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China)Abstract Chinese red steppe cattle, a highly developed breed for their meat and milk, are not well known about the formation mechanisms for high-quality beef. Furthermore, many fundamental investigations of cattle are hampered by deficient full-length cDNAs. Here, we utilized ONT full-length transcript sequencing from 9 bovine preadipocytes during 3 periods to find 2502 novel genes and 3253 novel transcriptomes, further improving the quality of reference genome annotation. At the same time, based on diverse expression patterns in 3 periods (early, middle and late), we identified 754 significantly differentially expressed genes (DEGs) and 932 significantly differentially expressed transcripts (DETs) in the first contrast group (0d_vs_4d), 197 significantly DEGs and 297 significantly DETs in the second contrast group (0d_vs_8d), 465 and 555 significantly DEGs and DETs in the third contrast group (4d_vs_8d). These DEGs mainly enriched the pathways related to cell differentiation such as Wnt signaling pathway and positive regulation of fat cell differentiation. A total of 35,616 alternative splicing (AS) events were detected, in which 111, 109 and 101 significantly different AS events were found in the group 0d_vs_4d, 0d_vs_8d and 4d_vs_8d respectively. In particular, two essential DEGs, N4BP2L1 and PRKAA1 related to cell differentiation were shown to take part in distinct AS events and were therefore considered as key candidate genes for improving fat deposition and meat quality in Chinese red steppe cattle. These findings provide novel insights into the adipocyte differentiation in cattle and metabolic processes that regulate fat storage, which is essential for optimizing growth and production.https://doi.org/10.1038/s41598-025-15106-5ONTPreadipocyte differentiationGenesASChinese red steppe cattle |
| spellingShingle | Wenwen Fang Shaoying Yang Xuanyu Li Asadollahpour Nanaei Yu Liu Yang Cao Cheng Xiao Xin Li Haiguo Jin Yumin Zhao Yang Cao Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle Scientific Reports ONT Preadipocyte differentiation Genes AS Chinese red steppe cattle |
| title | Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle |
| title_full | Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle |
| title_fullStr | Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle |
| title_full_unstemmed | Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle |
| title_short | Long-read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of Chinese red steppe cattle |
| title_sort | long read sequencing uncovers key regulatory genes involved in the differentiation of preadipocytes of chinese red steppe cattle |
| topic | ONT Preadipocyte differentiation Genes AS Chinese red steppe cattle |
| url | https://doi.org/10.1038/s41598-025-15106-5 |
| work_keys_str_mv | AT wenwenfang longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT shaoyingyang longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT xuanyuli longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT asadollahpournanaei longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT yuliu longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT yangcao longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT chengxiao longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT xinli longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT haiguojin longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT yuminzhao longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle AT yangcao longreadsequencinguncoverskeyregulatorygenesinvolvedinthedifferentiationofpreadipocytesofchineseredsteppecattle |