Comprehensive Transcriptomic Profiling of m6A Modification in Age-Related Hearing Loss
Abstract
1. Introduction
2. Materials and Methods
2.1. Animals
2.2. Auditory Brainstem Response (ABR) Analysis
2.3. RNA Extraction and qRT–PCR
2.4. m6A Quantification
2.5. Western Blot Analysis
2.6. MeRIP-Seq and Data Analysis
2.7. RNA-Seq and Data Analysis
2.8. MeRIP-qPCR
3. Results
3.1. Increased Hearing Thresholds and Decreased Cochlear m6A Modification in Ageing Mice
3.2. Changes in m6A-Related Modification Enzymes in the Cochleae of 6 w and 12 m Mice
3.3. General Characteristics of m6A Methylation Modification in ARHL
3.4. Functional Enrichment and Pathway Analysis of Differentially m6A-Methylated Genes
3.5. Combined Analysis of MeRIP-Seq and RNA-Seq Data
3.6. Validation of Differentially m6A-Modified Genes by MeRIP-qPCR and qRT–PCR
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
Abbreviations
Appendix A
Gene | Forward and Reverse Primer |
---|---|
WTAP | F: 5′ GAAGGAGACACGACAGCAGTTGG 3′ |
R: 5′ GCTTGTGACCTCTGCCTGATCTAC 3′ | |
METTL3 | F: 5′ CGCTGCCTCCGATGTTGATCTG 3′ |
R: 5′ CTGACTGACCTTCTTGCTCTGCTG 3′ | |
FTO | F: 5′ ATGAAGACGCTGTGCCACTGTG 3′ |
R: 5′ CACGTTGTAGGCTGCTCTGCTC 3′ | |
ALKBH5 | F: 5′ GCAAGGTGAAGAGCGGCATCC 3′ |
R: 5′GTCCACCGTGTGCTCGTTGTAC 3′ | |
RAPGEF6 | F: 5′ AGCTGTCAGGACCAAAGTCG 3′ |
R: 5′ CGCTCAGGTGTTGCCTTGAT 3′ | |
BIRC6 | F: 5′ TGCAGAGGCTCAAAGTAGCC 3′ |
R: 5′ GGAACAGAATGCCCATTGGA 3′ | |
RPS6KA3 | F: 5′ GACAGCGCGGAGAATGGACA 3′ |
R: 5′ CCGAACACGGTCTCGAACTT 3′ | |
SH2D1B1 | F: 5′ TGTGCCTCTGTGTCTCGTTTA 3′ |
R: 5′ TTGTCCAATGTCCTTGTCTTCA 3′ | |
β-ACTIN | F: 5′ AGTGTGACGTTGACATCCGT 3′ |
R: 5′ TGCTAGGAGCCAGAGCAGTA 3′ |
Gene | Forward and Reverse Primer |
---|---|
RAPGEF6 | F: 5′ CAGGGGATATGGAGCAGGC 3′ |
R: 5′ CAGGCCTCCGTCACTAAATAG 3′ | |
BIRC6 | F: 5′ GCCTCCTCTCTCTTCCTTGG 3′ |
R: 5′ AATCAGCACCCCAGTAGTCA 3′ | |
RPS6KA3 | F: 5′ GGCGTCCTCCTTTATACAATGC 3′ |
R: 5′ GTCCTTTGCTGTGTCTGAAAC 3′ | |
SH2D1B1 | F: 5′ TGACCAAGCGAGAGTGTGAA 3′ |
R: 5′ GAGACACAGAGGCACAGGG 3′ |
ID | Gene | M6a Fold Change | m6A p Value | Gene Log FC | Gene p Value | Change |
---|---|---|---|---|---|---|
ENSMUSG00000029661 | COL1A2 | 231.2 | 1.38075 × 10−10 | −1.6059902 | 0.04229598 | Hypo-down |
ENSMUSG00000055737 | GHR | 11.7 | 4.29725 × 10−11 | −3.0214016 | 0.03698555 | Hypo-down |
ENSMUSG00000003882 | IL7R | 5.1 | 8.2386 × 10−8 | −8.2804095 | 0.03681321 | Hypo-down |
ENSMUSG00000027111 | ITGA6 | 2.9 | 1.19754 × 10−7 | −5.6042221 | 0.00835887 | Hyper-down |
ENSMUSG00000038668 | LPAR1 | 4.4 | 4.55964 × 10−7 | −2.5137438 | 0.0377013 | Hypo-down |
ENSMUSG00000021702 | THBS4 | 1044.7 | 2.7696 × 10−12 | −3.5606082 | 0.02895484 | Hypo-down |
ENSMUSG00000005871 | APC | 7.7 | 1.8278 × 10−8 | −9.4020705 | 0.01765319 | Hypo-down |
ENSMUSG00000020538 | SREBF1 | 2.3 | 2.8006 × 10−10 | 1.68543898 | 0.04796545 | Hyper-up |
ENSMUSG00000020122 | EGFR | 6.3 | 2.51291 × 10−6 | −3.4024714 | 0.04096643 | Hyper-down |
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ID | Gene | m6A Fold Change | m6A p-Value | Gene Log FC | Gene p-Value | Change |
---|---|---|---|---|---|---|
ENSMUSG00000037533 | RAPGEF6 | 433.2 | 1.2812 × 10−14 | −10.025374 | 0.00213148 | Hyper-down |
ENSMUSG00000024073 | BIRC6 | 800.7 | 5.0835 × 10−14 | −2.9943806 | 0.02636128 | Hyper-down |
ENSMUSG00000058997 | VWA8 | 201.1 | 7.6235 × 10−14 | −3.7058447 | 0.01945395 | Hyper-down |
ENSMUSG00000068036 | MLLT4 | 353.6 | 1.4383 × 10−13 | −1.9414922 | 0.04990249 | Hyper-down |
ENSMUSG00000022607 | PTK2 | 19.9 | 1.6866 × 10−13 | −3.4652058 | 0.01968117 | Hyper-down |
ENSMUSG00000032410 | XRN1 | 1434.8 | 2.9063 × 10−13 | −10.023874 | 0.00555607 | Hyper-down |
ENSMUSG00000003847 | NFAT5 | 8.6 | 3.6304 × 10−13 | −2.3516677 | 0.03805174 | Hyper-down |
ENSMUSG00000032555 | TOPBP1 | 11.8 | 8.4203 × 10−13 | −7.2946474 | 0.01763448 | Hyper-down |
ENSMUSG00000024672 | MS4A7 | 6.7 | 2.8421 × 10−12 | 1.83305783 | 0.04776993 | Hyper- up |
ENSMUSG00000029186 | PI4K2B | 3.5 | 2.8892 × 10−12 | −10.125856 | 0.02227473 | Hyper-down |
ENSMUSG00000067149 | IGJ | 312.9 | 1.4276 × 10−13 | 8.49015602 | 0.00112192 | Hypo-up |
ENSMUSG00000031309 | RPS6KA3 | 24.95 | 1.8979 × 10−13 | −5.2427937 | 0.00759645 | Hypo-down |
ENSMUSG00000096334 | SH2D1B1 | 412.2 | 3.1109 × 10−13 | 6.18769686 | 0.02234852 | Hypo-up |
ENSMUSG00000030231 | PLEKHA5 | 167.2 | 3.5733 × 10−13 | −6.9262512 | 0.00946439 | Hypo-down |
ENSMUSG00000024900 | CPT1A | 524.4 | 3.6441 × 10−13 | −2.580643 | 0.01844615 | Hypo-down |
ENSMUSG00000025278 | FLNB | 93.24 | 3.6648 × 10−13 | −3.7084202 | 0.03199615 | Hypo-down |
ENSMUSG00000030811 | FBXL19 | 470.7 | 3.9417 × 10−13 | −9.4987969 | 0.03882934 | Hypo-down |
ENSMUSG00000024749 | TMC1 | 543.7 | 5.0403 × 10−13 | −8.4734806 | 0.03470489 | Hypo-down |
ENSMUSG00000061080 | LSAMP | 554.1 | 5.7905 × 10−13 | 9.7209504 | 0.00629816 | Hypo-up |
ENSMUSG00000022297 | FZD6 | 698.6 | 6.9979 × 10−13 | −9.89231 | 0.0045972 | Hypo-down |
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Feng, M.; Zhou, X.; Hu, Y.; Zhang, J.; Yang, T.; Chen, Z.; Yuan, W. Comprehensive Transcriptomic Profiling of m6A Modification in Age-Related Hearing Loss. Biomolecules 2023, 13, 1537. https://doi.org/10.3390/biom13101537
Feng M, Zhou X, Hu Y, Zhang J, Yang T, Chen Z, Yuan W. Comprehensive Transcriptomic Profiling of m6A Modification in Age-Related Hearing Loss. Biomolecules. 2023; 13(10):1537. https://doi.org/10.3390/biom13101537
Chicago/Turabian StyleFeng, Menglong, Xiaoqing Zhou, Yaqin Hu, Juhong Zhang, Ting Yang, Zhiji Chen, and Wei Yuan. 2023. "Comprehensive Transcriptomic Profiling of m6A Modification in Age-Related Hearing Loss" Biomolecules 13, no. 10: 1537. https://doi.org/10.3390/biom13101537
APA StyleFeng, M., Zhou, X., Hu, Y., Zhang, J., Yang, T., Chen, Z., & Yuan, W. (2023). Comprehensive Transcriptomic Profiling of m6A Modification in Age-Related Hearing Loss. Biomolecules, 13(10), 1537. https://doi.org/10.3390/biom13101537