Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Ethics Approval
2.2. Selection of Experimental Animals and Sample Collection
2.3. RNA Extraction and Library Construction
2.4. Sequence Mapping and CircRNA Prediction
2.5. Differential Expression Analysis of CircRNAs
2.6. STEM Cluster and Weighted Gene Co-Expression Network Analysis (WGCNA) Analysis of CircRNAs
2.7. Functional Analysis of CircRNAs in Follicular and Luteal Period
2.8. Analysis of MiRNA Target Sites
2.9. Validation of CircRNA Expression
3. Results
3.1. Genomic Characteristics of CircRNA in Sheep Ovaries
3.2. Diversity of CircRNA Isoforms and Circularization Forms
3.3. Identification of DE-CircRNAs
3.4. Functional Analysis of CircRNAs in Sheep of Varying Fecundity in the Follicular and Luteal Phases
3.5. STEM Cluster Analysis of DE-CircRNAs
3.6. Construction of WGCNA Network
3.7. MiRNA Targets of DE-CircRNAs
3.8. qRT-PCR Validation of DE-CircRNAs in the Regulatory Network
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Group | Without Pregnancy Sheep (Earmark) | Litter Size | |||
---|---|---|---|---|---|
First Parity | Second Parity | Third Parity | Four Parity | ||
Polytocous group | 3E202 | 3 | 3 | 5 | |
6T01 | 3 | 4 | 2 | ||
6T06 | 3 | 3 | 4 | 3 | |
CE104 | 3 | 3 | 3 | ||
3E161 | 3 | 3 | 4 | ||
CE103 | 3 | 4 | 3 | 4 | |
Monotocous group | 9M06 | 1 | |||
MY91 | |||||
MY86 | |||||
3E146 | |||||
3E79 | |||||
MY66 |
Type | Gene Name | Primer Sequences (5′-3′) | Amplicon Size (bp) |
---|---|---|---|
CircRNA | novel_circ_0006554 | F: ACGACAATGAGGAGTGTGGG | 198 |
R: GTCCTTCAATGACCGAGCAGT | |||
novel_circ_0005901 | F: ACACTAAGTGATGACGAATCTTTTC | 190 | |
R: CCACCCACAAAGCAGAGGAT | |||
novel_circ_0008937 | F: TGACGTGAATGTCTATGCTCAGT | 153 | |
R: GGAGAGGGTGAAGGATCCCA | |||
novel_circ_0016082 | F: CTGAGAACCAACAGCAGTGGA | 187 | |
R: AGCTCTTCCAGGCGGTTTC | |||
novel_circ_0002314 | F: GCTGCTGATGCAACAGGGTT | 198 | |
R: CAGGCAGAGGGCAGGTTTTA | |||
novel_circ_0005615 | F: GAGGCTGTAACGGAAGAGGA | 199 | |
R: AGCACGTTAGGTTTGTTGGT | |||
novel_circ_0005617 | F: GGGCTTTTCTTTGCCTCCTG | 199 | |
R: TTGTGGGACAAAATATTCGGGA | |||
novel_circ_0010148 | F: GGAGCCAAAACCCAGAGTCAA | 187 | |
R: ACCTGAAGCTGGAGTCACAAG | |||
novel_circ_0014289 | F: TTGGAGGATGTCAAGGCCAA | 180 | |
R: TACTGGTGATAGGCCAGCCA | |||
Control | GADPH | F: ACAGTCAAGGCAGAGAACGG | 107 |
R: CCAGCATCACCCCACTTGAT | |||
miRNA | oar-miR-16b | GCGCGTAGCAGCACGTAAA | |
oar-miR-200a | CGCGCGAACACTGTCTGGT | ||
oar-miR-432 | CGCGTCTTGGAGTAGGTCATT | ||
Control | U6 | AGTGCAGGGTCCGAGGTATT |
ID | Host_Gene_Name | MF. TPM | PF. TPM | ML. TPM | PL. TPM |
---|---|---|---|---|---|
novel_circ_0005901 | SNX13 | 527 | 151 | 377 | 663 |
novel_circ_0006554 | INSR | 533 | 122 | 343 | 774 |
novel_circ_0014057 | ARHGAP10 | 457 | 129 | 330 | 615 |
novel_circ_0008317 | SLTM | 444 | 150 | 220 | 504 |
novel_circ_0012048 | ZEB1 | 410 | 221 | 165 | 264 |
novel_circ_0014135 | UBE3A | 334 | 164 | 135 | 335 |
novel_circ_0008261 | USP3 | 426 | 207 | 291 | 450 |
novel_circ_0009916 | ANKRD46 | 273 | 94 | 212 | 335 |
novel_circ_0010401 | PDS5B | 271 | 69 | 199 | 292 |
novel_circ_0001969 | SLC30A7 | 189 | 103 | 118 | 175 |
novel_circ_0001127 | CEP70 | 254 | 82 | 288 | 397 |
novel_circ_0016729 | HERC4 | 198 | 89 | 159 | 249 |
novel_circ_0003675 | KDM4C | 190 | 107 | 109 | 223 |
novel_circ_0013646 | ELF2 | 221 | 78 | 158 | 264 |
novel_circ_0006681 | CEP120 | 168 | 88 | 169 | 238 |
novel_circ_0009038 | REV3L | 133 | 29 | 70 | 156 |
novel_circ_0004301 | RAP1B | 191 | 50 | 109 | 233 |
Pathway Name | p-Value | Genes |
---|---|---|
Cell adhesion molecules (CAMs) | 0.01 | ITGAV, JAM2 |
Glycosaminoglycan degradation | 0.02 | ARSB |
Dorso-ventral axis formation | 0.02 | SPIRE1 |
Arrhythmogenic right ventricular cardiomyopathy (ARVC) | 0.06 | ITGAV |
Hypertrophic cardiomyopathy (HCM) | 0.06 | ITGAV |
Dilated cardiomyopathy | 0.07 | ITGAV |
ECM-receptor interaction | 0.07 | ITGAV |
Small cell lung cancer | 0.08 | ITGAV |
Protein digestion and absorption | 0.09 | COL14A1 |
Thyroid hormone signaling pathway | 0.10 | ITGAV |
Lysosome | 0.10 | ARSB |
Leukocyte transendothelial migration | 0.10 | JAM2 |
Tight junction | 0.11 | JAM2 |
Phagosome | 0.13 | ITGAV |
Focal adhesion | 0.16 | ITGAV |
Proteoglycans in cancer | 0.17 | ITGAV |
Regulation of actin cytoskeleton | 0.17 | ITGAV |
Pathways in cancer | 0.25 | ITGAV |
PI3K-Akt signaling pathway | 0.26 | ITGAV |
Metabolic pathways | 0.66 | ARSB |
Module Color | KEGG Term | p-Value | Gene |
---|---|---|---|
Blue | Ubiquitin mediated proteolysis | 3.50 × 10−2 | FBXW7, HUWE1, BIRC6, UBE2Q2, UBA6 |
Ras signaling pathway | 4.40 × 10−2 | RAB5C, TIAM1, PDGFD, RRAS2, STK4 | |
Black | Leishmaniasis | 9.40 × 10−2 | TAB2, TGFB2 |
Brown | Wnt signaling pathway | 5.90 × 10−2 | APC, LRP6, ROCK2 |
Green | Focal adhesion | 3.20 × 10−2 | AKT3, DOCK1, ITGB1, LAMC1, MAPK1 |
Toxoplasmosis | 5.60 × 10−2 | AKT3, ITGB1, LAMC1, MAPK1 | |
mTOR signaling pathway | 1.30 × 10−2 | AKT3, RICTOR, MAPK1 | |
PI3K-Akt signaling pathway | 1.90 × 10−2 | AKT3, ITGB1, LAMC1, MAPK1, PPP2R2A | |
Estrogen signaling pathway | 3.50 × 10−2 | AKT3, FKBP5, MAPK1 | |
TNF signaling pathway | 4.20 × 10−2 | AKT3, MAPK1, RIPK1 | |
Turquoise | Endocytosis | 1.50 × 10−2 | WASL, LDLRAP1, NEDD4L, PSD3, RABEP1, STAM2 |
Insulin resistance | 2.70 × 10−2 | GFPT1, PPARA, PIK3R1, PRKAA2, PRKCE | |
Neurotrophin signaling pathway | 3.70 × 10−2 | ABL1, RAP1B, NTRK2, PIK3R1, RPS6KA5 | |
Fc gamma R-mediated phagocytosis | 5.60 × 10−2 | WASL, PIK3R1, PLPP1, PRKCE | |
Notch signaling pathway | 9.90 × 10−2 | NUMBL, SNW1, RBPJ | |
T cell receptor signaling pathway | 0.012 | FYN, SOS1, DLG1, TEC | |
Yellow | Focal adhesion | 0.018 | FYN, ARHGAP5, SOS1, IGF1R |
PI3K-Akt signaling pathway | 0.025 | RHEB, SOS1, GYS1, IGF1R | |
Adherens junction | 0.044 | FYN, IGF1R, PTPRM |
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Liu, A.; Chen, X.; Liu, M.; Zhang, L.; Ma, X.; Tian, S. Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep. Animals 2021, 11, 1863. https://doi.org/10.3390/ani11071863
Liu A, Chen X, Liu M, Zhang L, Ma X, Tian S. Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep. Animals. 2021; 11(7):1863. https://doi.org/10.3390/ani11071863
Chicago/Turabian StyleLiu, Aiju, Xiaoyong Chen, Menghe Liu, Limeng Zhang, Xiaofei Ma, and Shujun Tian. 2021. "Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep" Animals 11, no. 7: 1863. https://doi.org/10.3390/ani11071863