Small Non-Coding RNAome of Ageing Chondrocytes
Abstract
:1. Introduction
2. Materials and Methods
2.1. Sample Collection and Preparation
2.2. RNA Isolation, cDNA Library Preparation, and Small RNA Sequencing (RNA-seq)
2.3. Data Processing
2.4. Pathway Analysis
2.5. qRT-PCR Validation
2.6. tRNA Fragment Analysis
2.7. Novel snoRNA Analysis
2.8. Statistical Analysis
2.9. Human Sample Collection and Preparation
2.10. Removal of tRF Modifications from Human Cartilage RNA
2.11. tRF 3′ and 5′ Adaptor Ligation for Human Cartilage cDNA Synthesis
2.12. tRF and tRNA Human qPCR Arrays
3. Results
3.1. Preliminary Analysis of Small RNA-seq Data
3.2. Age-Related Differential Small Non-Coding RNA Gene Expression
3.3. Age Specific miRNA Interactome
3.4. Confirmation of Differential Gene Expression Using qRT-PCR
3.5. tRNA Fragment Changes in Equine Ageing
3.6. Human tRNA and tRF Profiles Compared to Equine tRNA and tRF Profiles
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Acknowledgments
Conflicts of Interest
Abbreviations
ECM | extracellular matrix |
OA | osteoarthritis |
sncRNAs | small non-coding RNAs |
miRNAs or miRs | microRNAs |
snRNAs | small nuclear RNAs |
snoRNAs | small nucleolar RNAs |
tRNAs | transfer RNAs |
mRNA | messenger RNA |
tiRNAs | tRNA halves |
ANG | angiogenin |
tRFs | tRNA-derived small RNA fragments |
PCA | principle component analysis |
logFC | log2 fold change |
FDR | False Discovery Rate |
IPA | Ingenuity Pathway Analysis |
RNA-seq | RNA sequencing |
qRT-PCR | real-time quantitative Polymerase Chain Reaction |
lncRNAs | long non-coding RNAs |
PCs | Principle components |
GP6 | glycoprotein 6 |
BMP | bone morphogenic protein |
FST | follistatin |
TNF | tumour necrosis factor |
TNFSF11 | TNF ligand superfamily member 11 |
RANKL | receptor activator of nuclear factor kappa-Β ligand |
ERK | extracellular signal-regulated kinase |
SMAD | mothers against decapentaplegic homolog |
MAPK | mitogen-activated protein kinase |
TGF-β | transforming growth factor beta |
IL | interleukin |
JAK3 | Janus Kinase 3 |
AGO | Argonaute |
RISC | RNA-induced silencing complex |
JAK-STAT | Janus Kinase and Signal Transducer and Activator of Transcription |
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Gene/Transcript Name | Gene Biotype | Log2 Fold Change |
---|---|---|
eca-miR-143 | miRNA | −1.3 |
eca-miR-145 | miRNA | −1.8 |
eca-miR-181b | miRNA | −1.8 |
eca-miR-122 | miRNA | 2.3 |
eca-miR-148a | miRNA | 1.3 |
snora71 | snoRNA | −3.2 |
snord113 | snoRNA | −2.4 |
snora46 | snoRNA | 1.0 |
snora77 | snoRNA | 2.0 |
snora47 | snoRNA | 2.5 |
snord29 | snoRNA | 2.5 |
ECABCGRLG0000003960 | novel snoRNA | −2.6 |
ECABCGRLG0000002980 | novel snoRNA | −2.5 |
ECABCGRLG0000006050 | novel snoRNA | −1.6 |
ECABCGRLG0000000640 | novel snoRNA | −1.1 |
ECABCGRLG0000002800 | novel snoRNA | −1.0 |
ECABCGRLG0000007680 | novel snoRNA | 1.8 |
ECABCGRLG0000008070 | novel snoRNA | 2.0 |
ECABCGRLG0000007010 | novel snoRNA | 2.5 |
ECABCGRLG0000008090 | novel snoRNA | 2.9 |
ECABCGRLG0000004470 | novel snoRNA | 3.0 |
ECABCGRLG0000005680 | novel snoRNA | 3.1 |
LOC111775808 | snRNA | −1.3 |
LOC111773055 | snRNA | 2.2 |
LOC111772636 | snRNA | 2.5 |
LOC111770368 | lncRNA | −3.4 |
LOC111768432 | lncRNA | −3.2 |
LOC102148414 | lncRNA | −3.2 |
LOC102149168 | lncRNA | −2.9 |
LOC111772155 | lncRNA | −2.5 |
LOC106783307 | lncRNA | −2.5 |
LOC111775319 | lncRNA | −2.5 |
LOC102148711 | lncRNA | −2.5 |
LOC111775759 | lncRNA | −2.5 |
LOC111774351 | lncRNA | −2.5 |
LOC102150704 | lncRNA | −2.5 |
LOC111775994 | lncRNA | −2.5 |
LOC102150027 | lncRNA | −2.5 |
LOC106781358 | lncRNA | −2.5 |
LOC102147393 | lncRNA | −2.5 |
LOC111776203 | lncRNA | −2.5 |
LOC111771286 | lncRNA | −1.3 |
LOC102149893 | lncRNA | 1.7 |
LOC111775969 | lncRNA | 1.7 |
LOC106781629 | lncRNA | 1.9 |
LOC111773181 | lncRNA | 2.0 |
LOC102149863 | lncRNA | 2.5 |
LOC102149361 | lncRNA | 2.5 |
LOC111770630 | lncRNA | 2.5 |
LOC102147707 | lncRNA | 2.5 |
LOC106783385 | lncRNA | 2.5 |
LOC102149569 | lncRNA | 2.5 |
LOC106782740 | lncRNA | 2.5 |
LOC111770896 | lncRNA | 2.5 |
LOC102150024 | lncRNA | 2.9 |
LOC102150338 | lncRNA | 2.9 |
TRNAR-ACG | tRNA | −3.4 |
TRNAR-CCU | tRNA | −3.2 |
TRNAS-AGA | tRNA | −3.2 |
TRNAS-GCU | tRNA | −3.1 |
TRNAA-UGC | tRNA | −3.0 |
TRNAP-AGG | tRNA | −2.9 |
TRNAQ-UUG | tRNA | −2.9 |
TRNAS-AGA | tRNA | −2.9 |
TRNAA-UGC | tRNA | −2.9 |
TRNAF-GAA | tRNA | −2.5 |
TRNAP-UGG | tRNA | −2.5 |
TRNAE-UUC | tRNA | −2.5 |
TRNAF-GAA | tRNA | −2.2 |
TRNAV-AAC | tRNA | −2.2 |
TRNAM-CAU | tRNA | −2.1 |
TRNAT-AGU | tRNA | −1.9 |
TRNAY-GUA | tRNA | −1.9 |
TRNAQ-CUG | tRNA | −1.4 |
TRNAN-GUU | tRNA | −1.4 |
TRNAY-GUA | tRNA | −1.4 |
TRNAY-GUA | tRNA | −1.2 |
TRNAV-AAC | tRNA | 1.9 |
TRNAP-CGG | tRNA | 2.2 |
TRNAA-UGC | tRNA | 2.4 |
TRNAC-GCA | tRNA | 2.5 |
TRNAI-AAU | tRNA | 2.9 |
TRNAD-GUC | tRNA | 3.4 |
a. Top Molecular and Cellular Functions | p-Value Range | Number of Molecules |
---|---|---|
Cellular Movement | 1.41 × 10−3–4.23 × 10−10 | 21 |
Cell Morphology | 1.37 × 10−3–3.52 × 10−8 | 16 |
Cellular Development | 1.42 × 10−3–4.94 × 10−7 | 24 |
Cell Death and Survival | 1.37 × 10−3–1.08 × 10−5 | 18 |
Cell-To-Cell Signalling and Interaction | 1.37 × 10−3–1.88 × 10−5 | 20 |
b. Top Diseases and Disorders | ||
Skeletal and Muscular Disorders | 1.50 × 10−3–1.22 × 10-9 | 16 |
Connective Tissue Disorders | 1.50 × 10−3–3.52 × 10-8 | 16 |
Organismal Injury and Abnormalities | 1.50 × 10−3–3.52 × 10-8 | 31 |
Cancer | 1.49 × 10−3–5.30 × 10-7 | 31 |
Developmental Disorder | 1.37 × 10−3–5.30 × 10-7 | 17 |
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Balaskas, P.; Green, J.A.; Haqqi, T.M.; Dyer, P.; Kharaz, Y.A.; Fang, Y.; Liu, X.; Welting, T.J.M.; Peffers, M.J. Small Non-Coding RNAome of Ageing Chondrocytes. Int. J. Mol. Sci. 2020, 21, 5675. https://doi.org/10.3390/ijms21165675
Balaskas P, Green JA, Haqqi TM, Dyer P, Kharaz YA, Fang Y, Liu X, Welting TJM, Peffers MJ. Small Non-Coding RNAome of Ageing Chondrocytes. International Journal of Molecular Sciences. 2020; 21(16):5675. https://doi.org/10.3390/ijms21165675
Chicago/Turabian StyleBalaskas, Panagiotis, Jonathan A. Green, Tariq M. Haqqi, Philip Dyer, Yalda A. Kharaz, Yongxiang Fang, Xuan Liu, Tim J.M. Welting, and Mandy J. Peffers. 2020. "Small Non-Coding RNAome of Ageing Chondrocytes" International Journal of Molecular Sciences 21, no. 16: 5675. https://doi.org/10.3390/ijms21165675