Analysis of the Long Non-Coding and Messenger RNA Expression Profiles in the Skin Tissue of Super Merino and Small-Tailed Han Sheep
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Ethical Statement
2.2. Histomorphological Study
2.3. RNA Isolation, Library Preparation, and Sequencing
2.4. lncRNA Identification and Target Gene Prediction
2.5. Expression Analysis
2.6. Enrichment Analyses with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG)
2.7. Construction of PPI and lncRNA–mRNA Network
2.8. qRT-PCR Verification
2.9. Immunohistochemistry Study
2.10. Data Analysis
3. Results
3.1. Characterization of Sheep Wool and Follicle Traits
3.2. Sequencing Data Quality Control
3.3. Identification and Expression Analysis of lncRNA and mRNA
3.4. Comparative Analysis of lncRNA and mRNA Characteristics
3.5. PPI Network and Functional Analyses of DE mRNAs
3.6. GO and KEGG Analyses of DE lncRNA Target Genes
3.7. Regulatory Network
3.8. Validation of the RNA-Seq Data
3.9. Immunohistochemistry Data
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene | Primer Sequence 5′→3′ | Product Length (bp) |
---|---|---|
MSTRG.93521.1 (down) | CAGGCTCGGCTGAGGTTTGG AGTCTGTGGTTGTGTCCAGTGATG | 114 |
MSTRG.20995.1 (down) | GTGGGGAGCCAAAGAGGAAT AGGTCAACGGCGTGGTTAAA | 165 |
MSTRG.154129.25 (up) | TGGTTAGCTCAAGGTTCGAGA GCAGCAGGAGGAAACAACCTA | 141 |
MSTRG.96951.1 (down) | ACTCGCCTTGTTCCAACCTC AGTGTGTCCGAATCTGCCTC | 131 |
MSTRG.31806.12 (up) | AGCAAGAGCCAGTGGTACAATA ATAGCCTCCAGCAGACGAGG | 92 |
COL7A1 (up) | ATGATCCCTGTTCGCTTCCAC TCCGCAGCCACCATAGACGA | 122 |
CNN1 (down) | AGAACACCAACCACACGCAAG GCCCGATAATGTTCCGCCCTT | 159 |
KLK6 (up) | AGAGACTGCTCAGCCAACCAC TGCTTCTCATCCCCGGCACAC | 179 |
IGFBP5 (down) | CGCCACTCATTTCATCTCATGT TGCGACCTTGCCAGAGATTC | 94 |
CRABP1 (down) | ACGGGGACCAGTTCTACATCA TCCCAAGTGGGTAAGCTCCTG | 127 |
KRT10 (down) | AGCAGAAACTAGCTGGGATACT AGGACTCTACCATCAGGTGC | 81 |
GAPDH | GTGGACCTGACCTGCCGTCTAG GAGTGGGTGTCGCTGTTGAAGTC | 149 |
Traits | Super Merino (n = 6) | Small-Tailed Han Sheep (n = 6) |
---|---|---|
Skin thickness (µm) | 1355.37 ± 50.48 | 1616.57 ± 44.53 ** |
Hair follicle density (mm2) | 19.74 ± 2.04 ** | 11.59 ± 1.13 |
Diameter of primary dermal papilla (µm) | 122.35 ± 2.99 | 143.68 ± 5.46 ** |
Diameter of secondary dermal papilla (µm) | 49.26 ± 1.99 | 63.81 ± 3.24 ** |
S/P | 19.65 ± 2.90 ** | 5.46 ± 2.43 |
BMK-ID | Total Reads | Mapped Reads | Uniquely Mapped Reads | Multiple Mapped Reads | Q20 (%) | Q30 (%) |
---|---|---|---|---|---|---|
SM1 | 119,612,582 | 113,676,411 (95.04%) | 111,058,913 (92.85%) | 2,617,498 (2.19%) | 97.67 | 93.62 |
SM2 | 115,429,242 | 109,531,249 (94.89%) | 107,228,260 (92.90%) | 2,302,989 (2.00%) | 97.76 | 93.79 |
SM3 | 124,719,310 | 117,304,477 (94.05%) | 115,270,935 (92.42%) | 2,033,542 (1.63%) | 97.86 | 93.87 |
SM4 | 118,615,420 | 113,129,111 (95.37%) | 109,835,326 (92.60%) | 3,293,785 (2.78%) | 97.67 | 93.62 |
SM5 | 132,926,276 | 127,869,012 (96.20%) | 125,542,321 (94.45%) | 2,326,691 (1.75%) | 97.85 | 93.87 |
SM6 | 122,335,752 | 117,949,087 (96.41%) | 115,542,600 (94.45%) | 2,406,487 (1.97%) | 98.16 | 94.68 |
STH1 | 127,399,620 | 123,042,683 (96.58%) | 120,295,753 (94.42%) | 2,746,930 (2.16%) | 98.08 | 94.52 |
STH2 | 127,087,066 | 122,677,440 (96.53%) | 119,419,027 (93.97%) | 3,258,413 (2.56%) | 98.18 | 94.80 |
STH3 | 128,176,154 | 123,199,306 (96.12%) | 119,827,700 (93.49%) | 3,371,606 (2.63%) | 98.07 | 94.45 |
STH4 | 132,012,936 | 126,513,200 (95.83%) | 123,006,721 (93.18%) | 3,506,479 (2.66%) | 97.84 | 93.88 |
STH5 | 117,224,636 | 112,912,295 (96.32%) | 110,197,340 (94.01%) | 2,714,955 (2.32%) | 97.89 | 93.96 |
STH6 | 114,176,126 | 109,862,331 (96.22%) | 107,334,555 (94.01%) | 2,527,776 (2.21%) | 98.02 | 94.38 |
ID | RNA-seq (Regulated) | qRT-PCR (Regulated) |
---|---|---|
MSTRG.96951.1 | down | down |
MSTRG.31806.12 | up | up |
MSTRG.20995.1 | down | down |
MSTRG.93521.1 | down | down |
MSTRG.154129.25 | up | up |
CRABP1 | down | down |
KRT10 | down | down |
CNN1 | down | down |
COL7A1 | up | up |
KLK6 | up | up |
IGFBP5 | down | down |
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Fu, J.; Zhang, X.; Wang, D.; Liu, W.; Zhang, C.; Wang, W.; Fan, W.; Zhang, L.; Sun, F. Analysis of the Long Non-Coding and Messenger RNA Expression Profiles in the Skin Tissue of Super Merino and Small-Tailed Han Sheep. Curr. Issues Mol. Biol. 2024, 46, 9588-9606. https://doi.org/10.3390/cimb46090570
Fu J, Zhang X, Wang D, Liu W, Zhang C, Wang W, Fan W, Zhang L, Sun F. Analysis of the Long Non-Coding and Messenger RNA Expression Profiles in the Skin Tissue of Super Merino and Small-Tailed Han Sheep. Current Issues in Molecular Biology. 2024; 46(9):9588-9606. https://doi.org/10.3390/cimb46090570
Chicago/Turabian StyleFu, Jiaqi, Xinyu Zhang, Dan Wang, Wenqing Liu, Caihong Zhang, Wei Wang, Wei Fan, Lichun Zhang, and Fuliang Sun. 2024. "Analysis of the Long Non-Coding and Messenger RNA Expression Profiles in the Skin Tissue of Super Merino and Small-Tailed Han Sheep" Current Issues in Molecular Biology 46, no. 9: 9588-9606. https://doi.org/10.3390/cimb46090570