Unique tRNA Fragment Upregulation with SARS-CoV-2 but Not with SARS-CoV Infection
Abstract
:1. Introduction
2. Results
2.1. Uniquely Upregulated tRF5s with CoV2 Infection
2.2. More Downregulated Genes with CoV2 Infection Than with CoV Infection
2.3. Enriched Neural Functions of Theoretical Targets of Upregulated tRF5s
3. Discussion
4. Materials and Methods
4.1. Downloading Fastq Files from a GEO Dataset
4.2. Aligning Sequencing to Transcripts
4.3. Differential Expression Analysis
4.4. Involving Student Scientists
4.5. tRNA Methyltransferase Collection
4.6. Candidate Target Prediction
4.7. Enrichment Testing of tRF5 Targets
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Gene Symbol | SARS-CoV Infection | SARS-CoV-2 Infection | ||
---|---|---|---|---|
Log2FC | p-Value | Log2FC | p-Value | |
tRNA Methyltransferase | ||||
FTSJ1 | −0.41 | 0.058 | −0.70 | 2.3 × 10−4 |
METTL1 | −0.54 | 0.026 | −0.17 | 0.53 |
METTL8 | −0.53 | 0.052 | −0.81 | 7.7 × 10−4 |
THUMPD3 | 0.24 | 0.17 | 0.36 | 0.022 |
TRDMT1 | −0.30 | 0.41 | −1.43 | 3.2 × 10−5 |
TRMT2B | −0.57 | 0.026 | −0.37 | 0.13 |
TRMT44 | 0.59 | 0.036 | 0.67 | 0.60 |
TRMT61A | −0.56 | 0.0039 | −0.15 | 0.49 |
TRMT9B | 0.07 | 0.89 | 0.63 | 0.049 |
TYW3 | −0.22 | 0.36 | −0.42 | 0.033 |
Demethylase | ||||
ALKBH3 | −0.77 | 0.0022 | −0.56 | 0.019 |
Ribonuclease 1 | ||||
DICER1 | 1.18 | 3.0 × 10−29 | 1.75 | 2.8 × 10−69 |
KEGG ID | KEGG Description | Observed Gene Count | Background Gene Count | False Discovery Rate |
---|---|---|---|---|
Commonly downregulated genes | ||||
hsa03010 | Ribosome | 83 | 130 | 9.43 × 10−36 |
hsa01100 | Metabolic pathways | 209 | 1447 | 5.57× 10−12 |
hsa00190 | Oxidative phosphorylation | 45 | 130 | 1.83 × 10−11 |
hsa04714 | Thermogenesis | 61 | 229 | 1.83 × 10−11 |
hsa05012 | Parkinson disease | 57 | 240 | 3.47 × 10−9 |
hsa05014 | Amyotrophic lateral sclerosis | 68 | 352 | 9.68 × 10−8 |
hsa05010 | Alzheimer disease | 68 | 355 | 1.12 × 10−7 |
hsa05016 | Huntington disease | 60 | 298 | 1.75 × 10−7 |
hsa05020 | Prion disease | 52 | 265 | 3.40 × 10−6 |
hsa04142 | Lysosome | 29 | 126 | 0.00015 |
hsa04510 | Focal adhesion | 36 | 198 | 0.0011 |
hsa01212 | Fatty acid metabolism | 16 | 54 | 0.0015 |
hsa04932 | Non-alcoholic fatty liver disease | 29 | 148 | 0.0016 |
hsa03060 | Protein export | 10 | 23 | 0.0026 |
hsa04260 | Cardiac muscle contraction | 20 | 87 | 0.003 |
hsa00062 | Fatty acid elongation | 10 | 25 | 0.0039 |
hsa05110 | Vibrio cholerae infection | 13 | 48 | 0.0105 |
hsa05100 | Bacterial invasion of epithelial cells | 16 | 70 | 0.012 |
hsa01200 | Carbon metabolism | 22 | 117 | 0.013 |
hsa04810 | Regulation of actin cytoskeleton | 32 | 209 | 0.0219 |
hsa03008 | Ribosome biogenesis in eukaryotes | 16 | 77 | 0.0246 |
hsa05205 | Proteoglycans in cancer | 30 | 196 | 0.0279 |
hsa04146 | Peroxisome | 16 | 79 | 0.0282 |
hsa00010 | Glycolysis/Gluconeogenesis | 14 | 65 | 0.031 |
hsa04910 | Insulin signaling pathway | 22 | 133 | 0.0415 |
Downregulated only in SARS-CoV | ||||
hsa03010 | Ribosome | 19 | 130 | 0.00021 |
hsa05012 | Parkinson disease | 26 | 240 | 0.00021 |
hsa05016 | Huntington disease | 30 | 298 | 0.00021 |
hsa05020 | Prion disease | 28 | 265 | 0.00021 |
hsa05014 | Amyotrophic lateral sclerosis | 30 | 352 | 0.0011 |
hsa01100 | Metabolic pathways | 81 | 1447 | 0.0015 |
hsa05010 | Alzheimer disease | 28 | 355 | 0.0051 |
hsa03050 | Proteasome | 8 | 43 | 0.0116 |
hsa00190 | Oxidative phosphorylation | 14 | 130 | 0.0134 |
hsa04932 | Non-alcoholic fatty liver disease | 15 | 148 | 0.0137 |
Downregulated only in SARS-CoV-2 | ||||
hsa01100 | Metabolic pathways | 149 | 1447 | 4.78 × 10−14 |
hsa00280 | Valine, leucine, and isoleucine degradation | 12 | 46 | 0.0021 |
hsa05132 | Salmonella infection | 27 | 209 | 0.0021 |
hsa00100 | Steroid biosynthesis | 8 | 20 | 0.0025 |
hsa00640 | Propanoate metabolism | 9 | 34 | 0.0094 |
hsa01200 | Carbon metabolism | 17 | 117 | 0.0099 |
hsa04723 | Retrograde endocannabinoid signaling | 19 | 145 | 0.012 |
hsa05031 | Amphetamine addiction | 12 | 66 | 0.012 |
hsa05110 | Vibrio cholerae infection | 10 | 48 | 0.0121 |
hsa04071 | Sphingolipid signaling pathway | 16 | 116 | 0.0153 |
hsa00020 | Citrate cycle (TCA cycle) | 7 | 29 | 0.036 |
hsa00190 | Oxidative phosphorylation | 16 | 130 | 0.036 |
hsa00340 | Histidine metabolism | 6 | 21 | 0.036 |
hsa00620 | Pyruvate metabolism | 8 | 38 | 0.036 |
hsa04728 | Dopaminergic synapse | 16 | 128 | 0.036 |
hsa04730 | Long-term depression | 10 | 59 | 0.036 |
hsa00564 | Glycerophospholipid metabolism | 13 | 97 | 0.0375 |
hsa04015 | Rap1 signaling pathway | 21 | 202 | 0.0375 |
hsa04962 | Vasopressin-regulated water reabsorption | 8 | 44 | 0.0478 |
Term ID | Term Description | tRF5 Name |
---|---|---|
GO:0001764 | Neuron migration | tRF5-Glu-CTC-2-1 |
GO:0007399 | Nervous system development | tRF5-Gln-CTG-2-1 |
tRF5-Glu-CTC-2-1 | ||
tRF5-Leu-AAG-3-1 | ||
GO:0007417 | Central nervous system development | tRF5-Glu-CTC-2-1 |
tRF5-Leu-AAG-3-1 | ||
GO:0010975 | Regulation of neuron projection development | tRF5-SeC-TCA-2-1 |
GO:0010976 | Positive regulation of neuron projection development | tRF5-Glu-CTC-2-1 |
GO:0022008 | Neurogenesis | tRF5-Gln-CTG-2-1 |
tRF5-Glu-CTC-2-1 | ||
GO:0030182 | Neuron differentiation | tRF5-Gln-CTG-2-1 |
tRF5-Glu-CTC-2-1 | ||
tRF5-Leu-AAG-3-1 | ||
GO:0031175 | Neuron projection development | tRF5-Leu-AAG-3-1 |
GO:0045664 | Regulation of neuron differentiation | tRF5-Glu-CTC-2-1 |
tRF5-SeC-TCA-2-1 | ||
GO:0045665 | Negative regulation of neuron differentiation | tRF5-Glu-CTC-2-1 |
GO:0045666 | Positive regulation of neuron differentiation | tRF5-Glu-CTC-2-1 |
GO:0048666 | Neuron development | tRF5-Gln-CTG-2-1 |
tRF5-Glu-CTC-2-1 | ||
tRF5-Leu-AAG-3-1 | ||
GO:0048699 | Generation of neurons | tRF5-Gln-CTG-2-1 |
tRF5-Glu-CTC-2-1 | ||
tRF5-Leu-AAG-3-1 | ||
GO:0048812 | Neuron projection morphogenesis | tRF5-Leu-AAG-3-1 |
GO:0050767 | Regulation of neurogenesis | tRF5-Glu-CTC-2-1 |
tRF5-Leu-AAG-3-1 | ||
GO:0050769 | Positive regulation of neurogenesis | tRF5-Glu-CTC-2-1 |
GO:0051960 | Regulation of nervous system development | tRF5-Gln-CTG-2-1 |
tRF5-Glu-CTC-2-1 | ||
tRF5-Leu-AAG-3-1 | ||
GO:0051962 | Positive regulation of nervous system development | tRF5-Glu-CTC-2-1 |
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Imirowicz, I.; Saifee, A.; Henry, L.; Tunkle, L.; Popescu, A.; Huang, P.; Jakpor, J.; Barbano, A.; Goru, R.; Gunawan, A.; et al. Unique tRNA Fragment Upregulation with SARS-CoV-2 but Not with SARS-CoV Infection. Int. J. Mol. Sci. 2024, 25, 399. https://doi.org/10.3390/ijms25010399
Imirowicz I, Saifee A, Henry L, Tunkle L, Popescu A, Huang P, Jakpor J, Barbano A, Goru R, Gunawan A, et al. Unique tRNA Fragment Upregulation with SARS-CoV-2 but Not with SARS-CoV Infection. International Journal of Molecular Sciences. 2024; 25(1):399. https://doi.org/10.3390/ijms25010399
Chicago/Turabian StyleImirowicz, Isabella, Azeem Saifee, Leanne Henry, Leo Tunkle, Alexander Popescu, Philip Huang, Jibiana Jakpor, Ava Barbano, Rohit Goru, Audrey Gunawan, and et al. 2024. "Unique tRNA Fragment Upregulation with SARS-CoV-2 but Not with SARS-CoV Infection" International Journal of Molecular Sciences 25, no. 1: 399. https://doi.org/10.3390/ijms25010399