RNAseq Analysis of Brown Adipose Tissue and Thyroid of Newborn Lambs Subjected to Short-Term Cold Exposure Reveals Signs of Early Whitening of Adipose Tissue
Abstract
:1. Introduction
2. Materials and Methods
2.1. Animals and Sampling
2.2. RNA Isolation and Transcriptome Sequencing
2.3. Quality Control, Mapping and Reads Quantification
2.4. Differential Expression Analysis
2.5. Functional Analysis of DEGs
2.6. Validation by Reverse Transcription-Quantitative Polymerase Chain Reaction (RT-qPCR)
3. Results
3.1. Summary of Sequencing Reads
3.2. Summary of DEGs
3.3. Differential Gene Expression and Enrichment in BAT under Cold Conditions
3.4. Differential Gene Expression and Enrichment in BAT under Ambient-Temperature Conditions
3.5. Differential Gene Expression and Enrichment in Thyroid Tissue under Cold Conditions
3.6. Differential Gene Expression and Enrichment in Thyroid Tissue under Ambient-Temperature Conditions
3.7. RT-qPCR Validation of RNAseq Results, and Expression of Selected Genes Involved in Thermogenesis and BAT Whitening
4. Discussion
4.1. Analysis on the Main Factors That Regulate Thermogenesis
4.2. BAT and Thyroid Thermogenesis Association
4.3. Transition from BAT to WAT
4.4. Downregulation of Protein Synthesis
4.5. Highly Expressed Immune Defence and Cell Cycle Processes
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
References
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Gene | Tissue | Cold/Ctrl log2FoldChange | Cold/Ctrl p-adj | AT/Ctrl log2FoldChange | AT/Ctrl p-adj | Cold/AT log2FoldChange | Cold/AT p-adj |
---|---|---|---|---|---|---|---|
PPARGC1A | BAT | −0.52 | 0.64 | −1.3 | 0.08 | 0.78 | 0.32 |
Thyroid | −1.23 | <0.05 | −1.2 | <0.05 | −0.03 | 1.00 | |
BMP4 | BAT | 0.97 | 0.13 | 1.08 | <0.05 | −0.11 | 0.89 |
Thyroid | 0.43 | 0.59 | 1.23 | 0.06 | −0.80 | 0.96 | |
PDK4 | BAT | 0.76 | 0.48 | −0.29 | 0.79 | 1.04 | 0.17 |
Thyroid | −2.40 | <0.05 | −1.83 | 0.09 | −0.57 | 1.00 | |
TGM2 | BAT | 0.14 | 0.85 | −0.05 | 0.94 | 0.19 | 0.72 |
Thyroid | −1.36 | <0.05 | −1.31 | <0.05 | −0.05 | 1.00 | |
FNDC5 | BAT | 1.27 | 0.06 | 1.95 | <0.05 | −0.69 | 0.27 |
Thyroid | 0.33 | 0.65 | 0.97 | 0.11 | −0.64 | 1.00 | |
ACSL5 | BAT | 0.28 | 0.73 | 0.28 | 0.65 | −0.01 | 0.99 |
Thyroid | −0.88 | <0.05 | −0.81 | <0.05 | −0.07 | 1.00 | |
CPT1A | BAT | −0.95 | 0.06 | −1.59 | <0.05 | 0.63 | 0.17 |
Thyroid | −0.94 | <0.05 | −0.93 | <0.05 | 0.00 | 1.00 | |
FABP3 | BAT | −1.74 | <0.05 | −2.01 | <0.05 | 0.27 | 0.78 |
Thyroid | −2.20 | <0.05 | −2.29 | <0.05 | 0.09 | 1.00 | |
NOS3 | BAT | −1.40 | <0.05 | −1.87 | <0.05 | 0.47 | 0.35 |
Thyroid | −1.53 | <0.05 | −1.46 | <0.05 | −0.07 | 1.00 | |
VASP | BAT | −0.38 | 0.33 | −0.75 | <0.05 | 0.37 | 0.23 |
Thyroid | −0.94 | <0.05 | −0.92 | <0.05 | −0.02 | 1.00 | |
PRDM16 | BAT | 0.98 | 0.15 | 1.16 | <0.05 | −0.18 | 0.81 |
Thyroid | −0.12 | 0.87 | 0.72 | 0.21 | −0.85 | 0.66 | |
VEGFA | BAT | −1.79 | <0.05 | −1.53 | <0.05 | −0.26 | 0.73 |
Thyroid | −1.32 | <0.05 | −1.16 | <0.05 | −0.16 | 1.00 | |
CYP1A1 | BAT | 12.80 | <0.05 | 7.33 | <0.05 | 5.47 | <0.05 |
Thyroid | 8.98 | <0.05 | 6.44 | <0.05 | 2.54 | 0.22 | |
MKI67 | BAT | 2.39 | <0.05 | 1.45 | 0.07 | 0.94 | 0.25 |
Thyroid | 3.01 | <0.05 | 3.33 | <0.05 | −0.33 | 1.00 |
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Graña-Baumgartner, A.; Dukkipati, V.S.R.; Kenyon, P.R.; Blair, H.T.; López-Villalobos, N.; Gedye, K.; Biggs, P.J. RNAseq Analysis of Brown Adipose Tissue and Thyroid of Newborn Lambs Subjected to Short-Term Cold Exposure Reveals Signs of Early Whitening of Adipose Tissue. Metabolites 2022, 12, 996. https://doi.org/10.3390/metabo12100996
Graña-Baumgartner A, Dukkipati VSR, Kenyon PR, Blair HT, López-Villalobos N, Gedye K, Biggs PJ. RNAseq Analysis of Brown Adipose Tissue and Thyroid of Newborn Lambs Subjected to Short-Term Cold Exposure Reveals Signs of Early Whitening of Adipose Tissue. Metabolites. 2022; 12(10):996. https://doi.org/10.3390/metabo12100996
Chicago/Turabian StyleGraña-Baumgartner, Andrea, Venkata S. R. Dukkipati, Paul R. Kenyon, Hugh T. Blair, Nicolás López-Villalobos, Kristene Gedye, and Patrick J. Biggs. 2022. "RNAseq Analysis of Brown Adipose Tissue and Thyroid of Newborn Lambs Subjected to Short-Term Cold Exposure Reveals Signs of Early Whitening of Adipose Tissue" Metabolites 12, no. 10: 996. https://doi.org/10.3390/metabo12100996
APA StyleGraña-Baumgartner, A., Dukkipati, V. S. R., Kenyon, P. R., Blair, H. T., López-Villalobos, N., Gedye, K., & Biggs, P. J. (2022). RNAseq Analysis of Brown Adipose Tissue and Thyroid of Newborn Lambs Subjected to Short-Term Cold Exposure Reveals Signs of Early Whitening of Adipose Tissue. Metabolites, 12(10), 996. https://doi.org/10.3390/metabo12100996