Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens
Long non-coding RNAs (lncRNAs) are implicated in mammalian adipogenesis and obesity. However, their genome-wide distribution, expression profiles, and regulatory mechanisms during chicken adipogenesis remain rarely understood. In the present study, lncRNAs associated with adipogenesis were identifie...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2022-04-01
|
| Series: | Animals |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2076-2615/12/9/1099 |
| _version_ | 1797505893829443584 |
|---|---|
| author | Weihua Tian Xin Hao Ruixue Nie Yao Ling Bo Zhang Hao Zhang Changxin Wu |
| author_facet | Weihua Tian Xin Hao Ruixue Nie Yao Ling Bo Zhang Hao Zhang Changxin Wu |
| author_sort | Weihua Tian |
| collection | DOAJ |
| description | Long non-coding RNAs (lncRNAs) are implicated in mammalian adipogenesis and obesity. However, their genome-wide distribution, expression profiles, and regulatory mechanisms during chicken adipogenesis remain rarely understood. In the present study, lncRNAs associated with adipogenesis were identified from chicken abdominal adipocytes at multiple differentiation stages using Ribo-Zero RNA-seq. A total of 15,179 lncRNAs were identified and characterized by stage-specific expression patterns. Of these, 840 differentially expressed lncRNAs were detected, and their <i>cis</i>- and <i>trans</i>-target genes were significantly enriched in multiple lipid-related pathways. Through weighted gene co-expression network analysis (WGCNA) and time-series expression profile clustering analysis, 14 key lncRNAs were identified as candidate regulatory lncRNAs in chicken adipogenic differentiation. The <i>cis</i>- and <i>trans</i>-regulatory interactions of key lncRNAs were constructed based on their differentially expressed <i>cis</i>- and <i>trans</i>-target genes, respectively. We also constructed a competing endogenous RNA (ceRNA) network based on the key lncRNAs, differentially expressed miRNAs, and differentially expressed mRNAs. MSTRG.25116.1 was identified as a potential regulator of chicken abdominal preadipocyte adipogenic differentiation by acting as a transcriptional <i>trans</i>-regulator of fatty acid amide hydrolase (<i>FAAH</i>) gene expression and/or a ceRNA that post-transcriptionally mediates <i>FAAH</i> gene expression by sponging gga-miR-1635. |
| first_indexed | 2024-03-10T04:24:50Z |
| format | Article |
| id | doaj.art-740327b21f284979989e1df1ecc016a7 |
| institution | Directory Open Access Journal |
| issn | 2076-2615 |
| language | English |
| last_indexed | 2024-03-10T04:24:50Z |
| publishDate | 2022-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Animals |
| spelling | doaj.art-740327b21f284979989e1df1ecc016a72023-11-23T07:42:22ZengMDPI AGAnimals2076-26152022-04-01129109910.3390/ani12091099Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in ChickensWeihua Tian0Xin Hao1Ruixue Nie2Yao Ling3Bo Zhang4Hao Zhang5Changxin Wu6National Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaNational Engineering Laboratory for Animal Breeding, Beijing Key Laboratory for Animal Genetic Improvement, College of Animal Science and Technology, China Agricultural University, Beijing 100193, ChinaLong non-coding RNAs (lncRNAs) are implicated in mammalian adipogenesis and obesity. However, their genome-wide distribution, expression profiles, and regulatory mechanisms during chicken adipogenesis remain rarely understood. In the present study, lncRNAs associated with adipogenesis were identified from chicken abdominal adipocytes at multiple differentiation stages using Ribo-Zero RNA-seq. A total of 15,179 lncRNAs were identified and characterized by stage-specific expression patterns. Of these, 840 differentially expressed lncRNAs were detected, and their <i>cis</i>- and <i>trans</i>-target genes were significantly enriched in multiple lipid-related pathways. Through weighted gene co-expression network analysis (WGCNA) and time-series expression profile clustering analysis, 14 key lncRNAs were identified as candidate regulatory lncRNAs in chicken adipogenic differentiation. The <i>cis</i>- and <i>trans</i>-regulatory interactions of key lncRNAs were constructed based on their differentially expressed <i>cis</i>- and <i>trans</i>-target genes, respectively. We also constructed a competing endogenous RNA (ceRNA) network based on the key lncRNAs, differentially expressed miRNAs, and differentially expressed mRNAs. MSTRG.25116.1 was identified as a potential regulator of chicken abdominal preadipocyte adipogenic differentiation by acting as a transcriptional <i>trans</i>-regulator of fatty acid amide hydrolase (<i>FAAH</i>) gene expression and/or a ceRNA that post-transcriptionally mediates <i>FAAH</i> gene expression by sponging gga-miR-1635.https://www.mdpi.com/2076-2615/12/9/1099adipogenic differentiationlncRNAscompeting endogenous RNAchicken |
| spellingShingle | Weihua Tian Xin Hao Ruixue Nie Yao Ling Bo Zhang Hao Zhang Changxin Wu Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens Animals adipogenic differentiation lncRNAs competing endogenous RNA chicken |
| title | Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens |
| title_full | Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens |
| title_fullStr | Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens |
| title_full_unstemmed | Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens |
| title_short | Comparative Transcriptome Analysis Reveals Regulatory Mechanism of Long Non-Coding RNAs during Abdominal Preadipocyte Adipogenic Differentiation in Chickens |
| title_sort | comparative transcriptome analysis reveals regulatory mechanism of long non coding rnas during abdominal preadipocyte adipogenic differentiation in chickens |
| topic | adipogenic differentiation lncRNAs competing endogenous RNA chicken |
| url | https://www.mdpi.com/2076-2615/12/9/1099 |
| work_keys_str_mv | AT weihuatian comparativetranscriptomeanalysisrevealsregulatorymechanismoflongnoncodingrnasduringabdominalpreadipocyteadipogenicdifferentiationinchickens AT xinhao comparativetranscriptomeanalysisrevealsregulatorymechanismoflongnoncodingrnasduringabdominalpreadipocyteadipogenicdifferentiationinchickens AT ruixuenie comparativetranscriptomeanalysisrevealsregulatorymechanismoflongnoncodingrnasduringabdominalpreadipocyteadipogenicdifferentiationinchickens AT yaoling comparativetranscriptomeanalysisrevealsregulatorymechanismoflongnoncodingrnasduringabdominalpreadipocyteadipogenicdifferentiationinchickens AT bozhang comparativetranscriptomeanalysisrevealsregulatorymechanismoflongnoncodingrnasduringabdominalpreadipocyteadipogenicdifferentiationinchickens AT haozhang comparativetranscriptomeanalysisrevealsregulatorymechanismoflongnoncodingrnasduringabdominalpreadipocyteadipogenicdifferentiationinchickens AT changxinwu comparativetranscriptomeanalysisrevealsregulatorymechanismoflongnoncodingrnasduringabdominalpreadipocyteadipogenicdifferentiationinchickens |