The Important Role of m6A-Modified circRNAs in the Differentiation of Intramuscular Adipocytes in Goats Based on MeRIP Sequencing Analysis
Abstract
:1. Introduction
2. Results
2.1. Identification of an Intramuscular Preadipocyte Differentiation Model in Goats
2.2. Overview of the circRNA-seq and MeRIP-seq Data
2.3. Characteristics of m6A-Modified circRNAs in the Intramuscular Adipocytes of Goats before and after Differentiation
2.4. Differential Expression of m6A-Modified circRNAs in Different Goat Adipocytes
2.5. Regulatory Network of the Differential m6A-circRNAs between IMA and IMPA Groups
2.6. Conjoint Analysis of circRNA-Seq and MeRIP-Seq
2.7. Verification of circRNA Expression Profiles Using qRT-PCR
3. Discussion
4. Materials and Methods
4.1. Isolation and Cell Culture of Goat Intramuscular Preadipocytes
4.2. Preadipocyte Differentiation Induction
4.3. Oil Red O and BODIPY Staining
4.4. RNA Extraction, Library Construction, and Sequencing
4.5. Sequencing Data Analysis
4.6. Bioinformatics Analysis and Statistical Analysis
4.7. Validation of Gene Expression by RT-qPCR Technique
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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Sample | Raw_Reads(M) | Clean_Reads(M) | Clean_Bases(G) | Valid_Bases(%) | Q30(%) | GC(%) |
---|---|---|---|---|---|---|
IMA1 | 50.38 | 49.57 | 14.17 | 93.75 | 94.08 | 60.94 |
IMA2 | 50.11 | 49.27 | 14.05 | 93.47 | 93.83 | 60.63 |
IMA3 | 50.3 | 49.49 | 14.22 | 94.24 | 93.82 | 60.74 |
IMPA1 | 49.83 | 49.01 | 13.99 | 93.58 | 94.03 | 61.13 |
IMPA2 | 49.37 | 48.62 | 14.02 | 94.66 | 94.02 | 60.68 |
IMPA3 | 50.31 | 49.49 | 14.11 | 93.49 | 93.89 | 61.01 |
IMA1_input | 47.97 | 47.05 | 13.23 | 91.94 | 95.93 | 57.21 |
IMA2_input | 49.37 | 48.39 | 13.51 | 91.21 | 96.04 | 56.96 |
IMA3_input | 47.29 | 46.34 | 12.98 | 91.49 | 96.1 | 57.41 |
IMPA1_input | 47.73 | 46.82 | 13.16 | 91.9 | 95.94 | 57.5 |
IMPA2_input | 48.35 | 47.44 | 13.31 | 91.77 | 95.99 | 56.77 |
IMPA3_input | 47.88 | 46.89 | 13.07 | 90.99 | 95.87 | 57.06 |
Sample | Total_Reads | Total_Mapped | Multiple_Mapped | Uniquely_Mapped |
---|---|---|---|---|
IMA1 | 99,139,058 | 95,401,484 (96.22%) | 4,848,347 (4.89%) | 90,553,137 (91.33%) |
IMA2 | 98,545,924 | 94,865,327 (96.26%) | 4,698,299 (4.76%) | 90,167,028 (91.49%) |
IMA3 | 98,984,968 | 95,084,400 (96.05%) | 5,016,142 (5.06%) | 90,068,258 (90.99%) |
IMPA1 | 98,018,414 | 94,268,208 (96.17%) | 5,241,506 (5.34%) | 89,026,702 (90.82%) |
IMPA2 | 97,232,168 | 93,538,409 (96.20%) | 4,702,985 (4.83%) | 88,835,424 (91.36%) |
IMPA3 | 98,974,940 | 95,109,577 (96.09%) | 5,017,553 (5.06%) | 90,092,024 (91.02%) |
IMA1_input | 94,096,060 | 89,868,600 (95.50%) | 10,729,437 (11.40%) | 79,139,163 (84.10%) |
IMA2_input | 96,775,848 | 92,699,532 (95.78%) | 10,800,206 (11.16%) | 81,899,326 (84.62%) |
IMA3_input | 92,682,072 | 88,584,369 (95.57%) | 10,356,897 (11.17%) | 78,227,472 (84.40%) |
IMPA1_input | 93,638,328 | 89376,862 (95.44%) | 10,923,483 (11.66%) | 78,453,379 (83.78%) |
IMPA2_input | 94,873,142 | 90,865,112 (95.77%) | 10,783,550 (11.36%) | 80,081,562 (84.40%) |
IMPA3_input | 93,789,268 | 89,386,330 (95.30%) | 10,808,685 (11.52%) | 78,577,645 (83.78%) |
Chr | Start | End | circRNA | Log2FC | p-Value | Regulation | Gene Name |
---|---|---|---|---|---|---|---|
Chr12 | 35,549,676 | 35,551,085 | circRNA_1055 | 3.32478924 | 3.12E-87 | Up | LMO7 |
Chr18 | 56,511,885 | 56,517,614 | circRNA_1438 | 9.255672903 | 1.11E-62 | Up | NUCB1 |
Chr13 | 33,128,553 | 33,129,648 | circRNA_1119 | 2.485573285 | 5.46E-55 | Up | ZEB1 |
Chr10 | 21,218,634 | 21,218,882 | circRNA_0873 | 8.626127066 | 2.59E-44 | Up | SLC8A3 |
Chr10 | 16,161,014 | 16,161,210 | circRNA_0866 | 2.253712935 | 1.31E-42 | Up | LOC102187597 |
Chr3 | 10,437,366 | 10,437,666 | circRNA_0238 | 8.487830648 | 4.97E-41 | Up | ZMYM4 |
Chr11 | 74,783,037 | 74,799,539 | circRNA_1012 | 8.339699789 | 9.02E-38 | Up | ATAD2B |
Chr27 | 12,234,705 | 12,235,515 | circRNA_1944 | 8.329999645 | 1.44E-37 | Up | WHSC1L1 |
Chr13 | 61,360,331 | 61,366,664 | circRNA_1079 | 8.30930326 | 3.91E-37 | Up | DCLK1 |
Chr20 | 66,412,450 | 66,418,587 | circRNA_1583 | 1.733511924 | 3.03E-35 | Up | PAPD7 |
Chr18 | 23,020,758 | 23,021,057 | circRNA_1399 | 2.578567264 | 1.12E-51 | Down | CHD9 |
Chr13 | 75,314,614 | 75,354,619 | circRNA_1149 | 9.125673331 | 3.81E-49 | Down | ZMYND8 |
Chr19 | 53,784,636 | 53,812,138 | circRNA_1531 | 8.986718904 | 1.48E-45 | Down | SEPTIN9 |
Chr18 | 3,010,918 | 3,011,590 | circRNA_1385 | 2.205131135 | 2.40E-43 | Down | DDX19A |
Chr2 | 113,508,380 | 113,508,876 | circRNA_0178 | 2.756039782 | 4.60E-41 | Down | SP3 |
Chr26 | 11,981,485 | 11,988,759 | circRNA_1905 | 8.661060515 | 4.30E-38 | Down | SEC23IP |
Chr8 | 40,220,320 | 40,221,369 | circRNA_0743 | 2.262451821 | 3.39E-36 | Down | GLIS3 |
Chr8 | 76,948,426 | 76,949,174 | circRNA_0762 | 8.473007382 | 2.47E-34 | Down | KIF27 |
Chr20 | 13,792,302 | 13,792,500 | circRNA_1563 | 8.471672577 | 2.62E-34 | Down | NLN |
Chr17 | 9,726,962 | 9,729,487 | circRNA_1343 | 8.469304477 | 2.91E-34 | Down | LOC102190983 |
Gene Name | Primer Sequence | TM/°C | Product Length |
---|---|---|---|
UXT | GCAAGTGGATTTGGGCTGTAAC | 60 | 180 |
ATGGAGTCCTTGGTGAGGTTGT | 60 | ||
circRNA_LMO7 | TCAAAGTTAGTGTCTGGCAATG | 55.7 | 227 |
GTGCTGGACTTTTGTGGG | 55.6 | ||
circRNA_PAPD7 | TACATCCCAGCACCTAACC | 52.9 | 180 |
CATCGGTCTGTTCCATCC | 53 | ||
circRNA_CHD9 | ACTGCCAGTTCCCGTGACA | 59 | 235 |
GAAGGGGTTCGTAGCAGCG | 60.6 | ||
circRNA_SP3 | GGGTCCTTGTGGGGCTTAC | 59 | 237 |
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Wang, J.; Li, X.; Qubi, W.; Li, Y.; Wang, Y.; Wang, Y.; Lin, Y. The Important Role of m6A-Modified circRNAs in the Differentiation of Intramuscular Adipocytes in Goats Based on MeRIP Sequencing Analysis. Int. J. Mol. Sci. 2023, 24, 4817. https://doi.org/10.3390/ijms24054817
Wang J, Li X, Qubi W, Li Y, Wang Y, Wang Y, Lin Y. The Important Role of m6A-Modified circRNAs in the Differentiation of Intramuscular Adipocytes in Goats Based on MeRIP Sequencing Analysis. International Journal of Molecular Sciences. 2023; 24(5):4817. https://doi.org/10.3390/ijms24054817
Chicago/Turabian StyleWang, Jianmei, Xin Li, Wuqie Qubi, Yanyan Li, Yong Wang, Youli Wang, and Yaqiu Lin. 2023. "The Important Role of m6A-Modified circRNAs in the Differentiation of Intramuscular Adipocytes in Goats Based on MeRIP Sequencing Analysis" International Journal of Molecular Sciences 24, no. 5: 4817. https://doi.org/10.3390/ijms24054817
APA StyleWang, J., Li, X., Qubi, W., Li, Y., Wang, Y., Wang, Y., & Lin, Y. (2023). The Important Role of m6A-Modified circRNAs in the Differentiation of Intramuscular Adipocytes in Goats Based on MeRIP Sequencing Analysis. International Journal of Molecular Sciences, 24(5), 4817. https://doi.org/10.3390/ijms24054817