Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver
Abstract
:1. Introduction
2. Results
2.1. The Slaughter Performance and Serum Biochemical Indices of Chickens with Fatty Liver
2.2. Transcriptome Profiling Analysis of Liver
2.3. Integration Analysis of Methylome and Transcriptome
2.4. Integration Analysis of the LncRNA and the mRNA Profiles
2.5. Integration Analysis of the Methylation, the LncRNA, and the mRNA Profiles
3. Discussion
4. Materials and Methods
4.1. Ethics Statement
4.2. Animal Model and Environment
4.3. Sample Collection
4.4. Serum Biochemical Analysis and Liver Histology
4.5. Evaluation of fatty liver
4.6. Sequencing and Identification of Differentially Expressed LncRNAs and mRNAs
4.7. Quantitative Real-Time PCR
4.8. Construction and Analysis of lncRNA-mRNA Network
4.9. Whole-Genome Bisulfite Sequencing and DMGs Identification
4.10. KEGG Pathways Analysis
4.11. Statistical Analysis
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
Abbreviations
DEG | Differentially Expressed Gene |
DMG | Differentially Methylated Gene |
DMR | Differentially Methylated Region |
FC | Fold Change |
FLS | Fatty Liver Syndrome |
HFD | High Fat Diet |
LncRNA | Long Noncoding RNA |
NAFLD | Non-Alcoholic Fatty Liver Disease |
PCC | Pearson Correlation Coefficient |
HDL | High-Density Lipoprotein |
LDL | Low-Density lipoprotein |
TC | Total Cholesterol |
TG | Triglyceride |
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ID | Pathway | Tendency of DEG | p-Value 1 | DMR | p-Value 2 |
---|---|---|---|---|---|
gga01200 | Carbon metabolism | up | 8.53 × 10−4 | promoter | 3.69 × 10−2 |
gga00020 | Citrate cycle (TCA cycle) | up | 1.70 × 10−2 | promoter | 4.82 ×10−2 |
gga04115 | p53 signaling pathway | up | 2.88 ×10−2 | gene body | 3.76 × 10−2 |
gga04020 | Calcium signaling pathway | down | 8.94 × 10−3 | gene body | 1.35 × 10−2 |
gga04933 | AGE-RAGE signaling pathway in diabetic complications | down | 4.41 × 10−2 | gene body | 3.09 × 10−2 |
lncRNA | Regulation | Gene | Log2FC | DMR | Methylation Difference |
---|---|---|---|---|---|
LNC_008609, LNC_008671 | trans | LIMD2 | −0.83 | gene body | −0.39 |
LNC_012679 | trans | BLMH1 | 0.67 | gene body | 0.35 |
LNC_008303 | trans | ASPA | 1.41 | promoter | −0.16 |
LNC_012355 | trans, cis | ABCD32 | 1.05 | gene body | −0.49 |
LNC_010111 | trans, cis | CCDC18 | −0.74 | gene body | 0.35 |
LNC_006756 | trans | HAO12 | 0.99 | gene body | 0.33 |
LNC_010111, LNC_010862 | trans | FLVCR2 | −1.16 | gene body | −0.4 |
LNC_010073, LNC_010240 | trans | FAM13A | 0.89 | gene body | −0.18 |
LNC_002556 | trans, cis | ENSGALG00000010639 | −0.73 | gene body | 0.52 |
LNC_009039 | trans, cis | ENSGALG00000011528 | −0.91 | gene body | 0.6 |
LNC_000820 | trans | SLC39A8 | 0.73 | gene body | −0.2 |
LNC_010111 | trans | MYO16 | 1.44 | gene body | −0.32 |
LNC_000333 | trans | COTL1 | −0.84 | gene body | −0.36 |
LNC_007320, LNC_007320 | trans | CELF2 | −0.72 | gene body | −0.24, −0.31 |
LNC_005357, LNC_007350, LNC_010111, LNC_010862 | trans | RAC21 | −0.78 | gene body | −0.17 |
LNC_001439, LNC_001531, LNC_007015, LNC_010098 | trans | JAM2 | 0.59 | gene body | 0.38 |
LNC_001714, LNC_001742, LNC_006829, LNC_012722 | trans | WDPCP | 1.92 | gene body | −0.24 |
LNC_001439, LNC_001531, LNC_005357, LNC_007015, LNC_010098, LNC_010111 | trans | ENSGALG00000033919 | 0.84 | gene body | 0.11 |
LNC_001272, LNC_002705, LNC_003079, LNC_007151, LNC_010862, LNC_011070 | trans | DOCK21 | −0.62 | gene body | 0.19 |
LNC_002705, LNC_003079, LNC_008608, LNC_012083, LNC_012722 | trans | DIP2C | 0.92 | gene body | −0.22 |
LNC_001272, LNC_002705, LNC_003079, LNC_007151, LNC_008608, LNC_010862, LNC_011070 | trans | GALNT17 | −1.32 | gene body | −0.18 |
ENSGALT00000085791, LNC_001272, LNC_007151, LNC_007350, LNC_010862, LNC_011070 | trans | MARCH11 | −0.78 | gene body | −0.27, −0.33 |
LNC_001272, LNC_001439, LNC_002556, LNC_005357, LNC_007151, LNC_007350, LNC_008609, LNC_010111, LNC_010494 | trans | MEGF11 | 3.15 | gene body | −0.17 |
Gene ID | Gene | Primer Sequence | Product Size (bp) |
---|---|---|---|
ENSGALG00000002549 | RGS1 | F:5′-AGGATTTACGAGGAGTTTGT-3′ | 105 |
R:5′-TGTGTGAGTTGGGTCTTG-3′ | |||
ENSGALG00000033511 | CYP8B1 | F:5′-GGATAAGTGAACAAGACCAGTA-3′ | 132 |
R:5′-GATACAAGAGGAGCCAGAAG-3′ | |||
ENSGALG00000007904 | DLAT | F:5′-TTGCTCTCCCTGCTCTGT-3′ | 127 |
R:5′-CCTATTGTGGCTTTATCTGTCT-3′ | |||
ENSGALG00000013594 | PARD6G | F:5′-GCCAACAGCCATAACCTT-3′ | 184 |
R:5′-CCTCTTCGTCACTCTCCA-3′ | |||
ENSGALG00000005739 | SCD | F:5′-GGCTGACAAAGTGGTGATG-3′ | 137 |
R:5′-GGATGGCTGGAATGAAGA-3′ | |||
ENSGALG00000007178 | FADS2 | F:5′-CTGAGGAAGACAGCAGAGGACAT-3′ | 153 |
R:5′-GCAGGCAAGGATTAGAGTTGTG-3′ | |||
ENSGALG00000025796 | ADI1 | F:5′-ACATGGACGAGTCCCAGGAG-3′ | 113 |
R:5′-AGCATCCAATCTGCGGTAGG-3′ | |||
ENSGALG00000011016 | PGM1 | F:5′-ACGGTGAAAACCAAGGCGT-3′ | 103 |
R:5′-TGAAGTTCTCGGCGTAGTGG-3′ | |||
ENSGALG00000023395 | PLIN1 | F:5′-GCAATCCAGGGCTTACAG-3′ | 171 |
R:5′-ATCCAGACGACCAGTTCC-3′ | |||
ENSGALG00000008845 | HAO1 | F:5′-CGGTTTGTGTTGCTGATTT-3′ | 116 |
R:5′-TGCTGCTACATTATCTGCTA-3′ | |||
ENSGALG00000015082 | RPS6 | F:5′-GAGCGCAACGTGAGAACATT-3′ | 92 |
R:5′-CGGACAACATAGCCCTTCCA-3′ | |||
ENSGALG00000009621 | ACTB | F:5′-GAGAAATTGTGCGTGACATCA-3′ | 152 |
R:5′-CCTGAACCTCTCATTGCCA-3′ |
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Tan, X.; Liu, R.; Xing, S.; Zhang, Y.; Li, Q.; Zheng, M.; Zhao, G.; Wen, J. Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver. Int. J. Mol. Sci. 2020, 21, 1800. https://doi.org/10.3390/ijms21051800
Tan X, Liu R, Xing S, Zhang Y, Li Q, Zheng M, Zhao G, Wen J. Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver. International Journal of Molecular Sciences. 2020; 21(5):1800. https://doi.org/10.3390/ijms21051800
Chicago/Turabian StyleTan, Xiaodong, Ranran Liu, Siyuan Xing, Yonghong Zhang, Qinghe Li, Maiqing Zheng, Guiping Zhao, and Jie Wen. 2020. "Genome-Wide Detection of Key Genes and Epigenetic Markers for Chicken Fatty Liver" International Journal of Molecular Sciences 21, no. 5: 1800. https://doi.org/10.3390/ijms21051800