Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Sequencing
2.2. Separation of RNA from Tissues
2.3. Library Construction and RNA Sequencing
2.4. Read Alignment to the Reference Sus Scrofa 11.1 Genome
2.5. Alternative Splicing Events in Pig Transcriptome
2.6. Comparison of Novel and Known Protein Domains
2.7. SNP Compared with Alternative Splicing Variations
2.8. Known and Novel AS Validation Using Quantitative Reverse Transcription PCR
2.9. Protein Extraction and Western Blotting
3. Results
3.1. Identification of Novel Transcripts in 34 Different Pig Tissues
3.2. Classification of Alternative Splicing Types
3.3. Tissue Specificity of Alternative Splicing in Different Tissues
3.4. Potential Effect of Novel Alternative Splicing on the Pig Proteome
3.5. Conserved Alternative Splicing between Pig and Human
3.6. Effect of Single Nucleotide Polymorphism on Pig Alternative Splicing
3.7. Validation of Known and Novel Transcripts Using RT-qPCR and Western Blotting
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
References
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Tissue | AS with Gene | Exon Skip** | Alternative 5′ Splice Site | Alternative 3′ Splice Site | Intron Retention |
---|---|---|---|---|---|
Brain_A | 147 | 113 | 60 | 52 | 58 |
Breast | 126 | 92 | 80 | 71 | 63 |
Testis_I | 150 | 80 | 71 | 70 | 99 |
Lung | 202 | 94 | 95 | 75 | 225 |
Placenta | 167 | 141 | 102 | 83 | 99 |
Stomach | 89 | 48 | 56 | 48 | 34 |
Gut_A | 144 | 76 | 111 | 54 | 86 |
PBMC | 551 | 402 | 303 | 212 | 716 |
Fat | 132 | 78 | 72 | 63 | 81 |
Lymph | 317 | 133 | 497 | 116 | 479 |
Prostate | 132 | 61 | 58 | 75 | 105 |
Thymus | 238 | 215 | 194 | 118 | 224 |
Heart_A | 116 | 89 | 55 | 72 | 56 |
Brain_I | 192 | 101 | 54 | 81 | 116 |
Gall | 175 | 78 | 70 | 64 | 146 |
Nasopharynx | 157 | 84 | 87 | 82 | 92 |
Retina | 252 | 192 | 113 | 104 | 228 |
Thyroid | 316 | 114 | 82 | 79 | 350 |
Liver_A | 108 | 97 | 69 | 66 | 45 |
Gut_I | 150 | 77 | 69 | 77 | 107 |
Oesophagus | 95 | 86 | 63 | 32 | 57 |
Salivary | 143 | 67 | 128 | 48 | 117 |
Urinary | 152 | 70 | 40 | 61 | 136 |
Testis_A | 459 | 359 | 322 | 172 | 313 |
Heart_I | 119 | 102 | 38 | 52 | 56 |
Kidney | 140 | 156 | 113 | 88 | 78 |
Ovary | 157 | 91 | 69 | 65 | 127 |
Spinal | 170 | 84 | 84 | 80 | 102 |
Uterus | 276 | 102 | 62 | 101 | 286 |
Adrenal | 127 | 99 | 56 | 49 | 84 |
Liver_I | 131 | 131 | 85 | 69 | 68 |
Longissimus | 122 | 91 | 90 | 53 | 58 |
Pancreas | 58 | 41 | 33 | 19 | 40 |
Spleen | 128 | 117 | 56 | 64 | 75 |
Position | Type | Canonical | Aberrant | Gene | Mutation | Detail |
---|---|---|---|---|---|---|
chr7: 22889860 | Novel | T28228 | T2132 | TMP-CH242-74M17.2 | Non-synonymous | ENSSSCT00000001330 |
C188 | C17845 | ENSSSCG00000001229 | exon3:c.A395G:p.H132R | |||
chr7: 22889835 | Novel | A27034 | A1996 | TMP-CH242-74M17.2 | Non-synonymous | ENSSSCT00000001329 |
C0 | C2429 | ENSSSCG00000001229 | exon3:c.T370G | |||
chr7: 22825399 | Novel | T2495 | T2956 | SLA-1 | Non-synonymous | ENSSSCT00000036412 |
C0 | C2075 | ENSSSCG00000001231 | exon3:c.A404G:p.D135G | |||
chr1: 236442561 | Novel | G2635 | G1216 | TLN1 | Non-synonymous | ENSSSCT00000005856 |
T0 | T722 | ENSSSCG00000005317 | exon8:c.C745A:p.H249N | |||
chr9: 67827403 | Novel | G1128 | G7 | C4BPA | Non-synonymous | ENSSSCT00000017061 |
T593 | T7237 | ENSSSCG00000015663 | exon4:c.C605T:p.T202I | |||
chr9: 67827383 | Novel | G1506 | G16 | C4BPA | Synonymous | ENSSSCT00000017061 |
A520 | A8310 | ENSSSCG00000015663 | exon4:c.G585A:p.K195K | |||
chr4: 90572872 | Semi-canonical | C17145 | C27 | TAGLN2 | Synonymous | ENSSSCT00000007008 |
T7513 | T785 | ENSSSCG00000006395 | exon3:c.G246A:p.G82G | |||
chr7: 1955628 | Semi-canonical | A6919 | A26 | TUBB2B | Synonymous | ENSSSCT00000001098 |
G5 | G4623 | ENSSSCG00000001006 | exon1:c.T42C:p.N14N | |||
chr6: 103414552 | Novel | A6090 | A79 | LOC733637 | Synonymous | ENSSSCT00000025362 |
G14 | G325 | ENSSSCG00000003692 | exon4:c.T495C:p.F165F | |||
chrX: 13203809 | Novel | T21856 | G0 | SYAP1 | Non-synonymous | ENSSSCT00000040956.2 |
G0 | T4538 | ENSSSCG00000012148 | exon8:c.G970T:p.D295Y | |||
chr7: 24913889 | Semi-canonical | C17224 | C14 | SLA-DRB1 | Synonymous | ENSSSCT00000001612 |
T61 | T1190 | ENSSSCG00000001455 | exon1:c.G39A:p.A13A | |||
chr6: 103414681 | Novel | A19996 | A114 | LOC733637 | Synonymous | ENSSSCT00000025362 |
G481 | G332 | ENSSSCG00000003692 | exon4:c.T366C:p.G122G | |||
chr7: 23636509 | Novel | C9015 | C3066 | SLA-7 | Synonymous | ENSSSCT00000035331 |
T2779 | T2870 | ENSSSCG00000024161 | exon4:c.C852T:p.H284H |
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Feng, W.; Zhao, P.; Zheng, X.; Hu, Z.; Liu, J. Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation. Genes 2020, 11, 1405. https://doi.org/10.3390/genes11121405
Feng W, Zhao P, Zheng X, Hu Z, Liu J. Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation. Genes. 2020; 11(12):1405. https://doi.org/10.3390/genes11121405
Chicago/Turabian StyleFeng, Wen, Pengju Zhao, **anrui Zheng, Zhengzheng Hu, and Jianfeng Liu. 2020. "Profiling Novel Alternative Splicing within Multiple Tissues Provides Useful Insights into Porcine Genome Annotation" Genes 11, no. 12: 1405. https://doi.org/10.3390/genes11121405