Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig
Abstract
:Simple Summary
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals and Sample Collection
2.2. RNA Isolation, Library Construction, and RNA-seq
2.3. Identification and Classification of LncRNAs
2.4. Differential Expression Analysis and Functional Enrichment
2.5. Time-Series Analysis
2.6. Co-Expression Networks
2.7. Quantitative Real-Time PCR Analysis
3. Results
3.1. Identification and Classification of lncRNAs in Ningxiang Pig Liver
3.2. Identification of Differentially Expressed Protein-Coding Genes and lncRNAs
3.3. Time-Series Analysis of Protein-Coding Genes and LncRNAs
3.4. Co-Expression Network of Protein-Coding Genes and LncRNAs
3.5. RT-qPCR Quantification of LncRNAs
4. Discussion
4.1. Differentially Expressed Protein-Coding Genes and lncRNAs
4.2. Time-Series Analysis of Protein-Coding Genes and LncRNAs
4.3. Co-Expression Network of Protein-Coding Genes and LncRNAs
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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Name | Sequence (5’ to 3’) |
---|---|
MSTRG.1053.3-F | ACTTGGGAAGAAAGCAATTTTAAGA |
MSTRG.1053.3-R | TGTAGTCCCAGCTACTCGGG |
MSTRG.11451.1-F | AGACATCCGAGCCTGGGATA |
MSTRG.11451.1-R | CGTTTCAGAAAGCGTTGGAAGT |
MSTRG.8339.1-F | GGCATATGGAGGTTCCCAGG |
MSTRG.8339.1-R | GCGCAGTGGTTAACGAATCC |
MSTRG.10861.1-F | GAGCCTGATTCCTCCAGCTC |
MSTRG.10861.1-R | CCAGCCACAGCAATCAGAGA |
MSTRG.1054.2-F | TGTAGTCCCAGCTACTCGGG |
MSTRG.1054.2-R | ACAGGGTCTCGCTATGTTGC |
Sample | Raw Reads | Raw Bases | Clean Reads | Clean Bases | Error Rate (%) | Q20 (%) | Q30 (%) | GC Content (%) |
---|---|---|---|---|---|---|---|---|
30d-1 | 110,376,466 | 16,666,846,366 | 108,613,548 | 14,971,657,073 | 0.0241 | 98.25 | 95.24 | 55.15 |
30d-2 | 113,435,178 | 17,128,711,878 | 111,741,648 | 15,445,970,217 | 0.0241 | 98.27 | 95.16 | 54.05 |
30d-3 | 115,191,290 | 17,393,884,790 | 113,234,706 | 15,440,805,570 | 0.0242 | 98.22 | 95.10 | 54.40 |
90d-1 | 111,744,756 | 16,873,458,156 | 110,334,062 | 14,899,645,712 | 0.0237 | 98.48 | 95.60 | 51.03 |
90d-2 | 112,938,114 | 17,053,655,214 | 111,212,336 | 15,058,781,243 | 0.0237 | 98.47 | 95.59 | 52.15 |
90d-3 | 108,509,032 | 16,384,863,832 | 107,067,364 | 14,561,278,014 | 0.0237 | 98.48 | 95.53 | 51.38 |
150d-1 | 92,416,686 | 13,954,919,586 | 90,822,938 | 12,377,703,789 | 0.0239 | 98.38 | 95.32 | 50.39 |
150d-2 | 92,911,502 | 14,029,636,802 | 91,797,388 | 12,720,267,538 | 0.0238 | 98.44 | 95.40 | 49.73 |
150d-3 | 84,857,708 | 12,813,513,908 | 83,747,750 | 11,702,176,288 | 0.0241 | 98.34 | 95.16 | 49.99 |
210d-1 | 103,579,630 | 15,640,524,130 | 102,245,470 | 14,008,181,654 | 0.0237 | 98.51 | 95.54 | 49.84 |
210d-2 | 101,318,164 | 15,299,042,764 | 99,445,274 | 13,643,601,019 | 0.0237 | 98.45 | 95.52 | 52.12 |
210d-3 | 106,488,022 | 16,079,691,322 | 104,848,812 | 14,255,190,000 | 0.0237 | 98.45 | 95.56 | 50.78 |
Sample | Clean Reads | Mapped Reads | Mapping Rate (%) |
---|---|---|---|
30d-1 | 108,613,548 | 100,520,492 | 92.55 |
30d-2 | 111,741,648 | 103,608,606 | 92.72 |
30d-3 | 113,234,706 | 104,826,456 | 92.57 |
90d-1 | 110,334,062 | 104,211,698 | 94.45 |
90d-2 | 111,212,336 | 105,230,225 | 94.62 |
90d-3 | 107,067,364 | 101,424,972 | 94.73 |
150d-1 | 90,822,938 | 85,849,715 | 94.52 |
150d-2 | 91,797,388 | 85,907,029 | 93.58 |
150d-3 | 83,747,750 | 78,654,116 | 93.92 |
210d-1 | 102,245,470 | 95,722,450 | 93.62 |
210d-2 | 99,445,274 | 92,960,760 | 93.48 |
210d-3 | 104,848,812 | 98,178,592 | 93.64 |
Groups | Total DEmRNAs | Upregulated | Downregulated |
---|---|---|---|
30 vs. 90 d | 7345 | 3473 | 3872 |
30 vs. 150 d | 7971 | 4039 | 3932 |
30 vs. 210 d | 7634 | 3761 | 3873 |
90 vs. 150 d | 2309 | 1434 | 873 |
90 vs. 210 d | 2754 | 1518 | 1236 |
150 vs. 210 d | 1717 | 479 | 1238 |
Groups | Total DElncRNAs | Upregulated | Downregulated |
---|---|---|---|
30 vs. 90 d | 734 | 646 | 88 |
30 vs. 150 d | 600 | 521 | 79 |
30 vs. 210 d | 456 | 195 | 261 |
90 vs. 150 d | 135 | 64 | 71 |
90 vs. 210 d | 671 | 29 | 642 |
150 vs. 210 d | 576 | 24 | 552 |
mRNA | Module | Function of mRNA | Associated lncRNAs |
---|---|---|---|
MED24 | Molecular function | Interact with RNA polymerase II to promote formation of transcriptional pre-initiation complex to induce gene expression [17] | MSTRG.2158.2 MSTRG.34993.2 MSTRG.16183.1 MSTRG.17517.2 |
ANO6 | Molecular function | Essential component for calcium-dependent exposure of phosphatidylserine on cell surface, essential for triggering clotting system and deposition in bone mineralization [18] | MSTRG.31383.3 MSTRG.9728.2 MSTRG.33542.1 MSTRG.25050.1 MSTRG.40598.2 MSTRG.18175.1 MSTRG.42141.2 MSTRG.860.1 MSTRG.24048.3 MSTRG.13083.1 |
ZC4H2 | Molecular function | ZC4H2 may improve channel activity and turnover of plasma membrane and is identified as potential candidate for X-linked mental retardation [19] | MSTRG.33542.1 MSTRG.40598.2 MSTRG.11929.4 MSTRG.3259.4 |
TBPL1 | Cellular component | TBPL1 may play an important role in transcription by RNA polymerase II as a component of the transcription factor complex [20] | None |
MOGS | Biological process | MOGS may cleave distal alpha-1,2-linked glucose residue from Glc(3)-Man(9)-GlcNAc(2) oligosaccharide precursor [21] | MSTRG.3283.1 |
ACADSB | Biological process | Catalyze dehydrogenation of short branched chain acyl-CoA derivatives in metabolism of fatty acids [22,23] | MSTRG.6256.1 MSTRG.22802.1 MSTRG.11451.1 MSTRG.24004.1 MSTRG.26481.9 MSTRG.32831.1 MSTRG.29185.1 MSTRG.3444.1 |
DNAJC25 | Biological process | DNAJC25 may play an important role in cell protection, protein folding, refolding, aggregation and degradation, and protein translocation [24] | MSTRG.3827.1 MSTRG.8329.3 MSTRG.20562.1 |
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Gong, Y.; Zhang, Y.; Li, B.; Xiao, Y.; Zeng, Q.; Xu, K.; Duan, Y.; He, J.; Ma, H. Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig. Biology 2021, 10, 310. https://doi.org/10.3390/biology10040310
Gong Y, Zhang Y, Li B, Xiao Y, Zeng Q, Xu K, Duan Y, He J, Ma H. Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig. Biology. 2021; 10(4):310. https://doi.org/10.3390/biology10040310
Chicago/Turabian StyleGong, Yan, Yuebo Zhang, Biao Li, Yu Xiao, Qinghua Zeng, Kang Xu, Yehui Duan, Jianhua He, and Haiming Ma. 2021. "Insight into Liver lncRNA and mRNA Profiling at Four Developmental Stages in Ningxiang Pig" Biology 10, no. 4: 310. https://doi.org/10.3390/biology10040310