Neuronal Depolarization Induced RNA m<sup>5</sup>C Methylation Changes in Mouse Cortical Neurons
Neuronal activity is accomplished via substantial changes in gene expression, which may be accompanied by post-transcriptional modifications including RNA cytosine-5 methylation (m<sup>5</sup>C). Despite several reports on the transcriptome profiling of activated neurons, the dynamics of...
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MDPI AG
2022-06-01
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| Online Access: | https://www.mdpi.com/2079-7737/11/7/988 |
| _version_ | 1827619156938194944 |
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| author | Xiguang Xu Zachary Johnson Hehuang Xie |
| author_facet | Xiguang Xu Zachary Johnson Hehuang Xie |
| author_sort | Xiguang Xu |
| collection | DOAJ |
| description | Neuronal activity is accomplished via substantial changes in gene expression, which may be accompanied by post-transcriptional modifications including RNA cytosine-5 methylation (m<sup>5</sup>C). Despite several reports on the transcriptome profiling of activated neurons, the dynamics of neuronal mRNA m<sup>5</sup>C modification in response to environmental stimuli has not been explored. Here, we provide transcriptome-wide maps of m<sup>5</sup>C modification, together with gene expression profiles, for mouse cortical neurons at 0 h, 2 h, and 6 h upon membrane depolarization. Thousands of differentially expressed genes (DEGs) were identified during the neuronal depolarization process. In stimulated neurons, the majority of early response genes were found to serve as expression regulators of late response genes, which are involved in signaling pathways and diverse synaptic functions. With RNA bisulfite sequencing data, a union set of 439 m<sup>5</sup>C sites was identified with high confidence, and approximately 30% of them were shared by neurons at all three time points. Interestingly, over 41% of the m<sup>5</sup>C sites showed increased methylation upon neuronal activation and were enriched in transcripts coding for proteins with synaptic functions. In addition, a modest negative correlation was observed between RNA expression and methylation. In summary, our study provided dynamic transcriptome-wide landscapes of RNA m<sup>5</sup>C methylation in neurons, and revealed that mRNA m<sup>5</sup>C methylation is associated with the regulation of gene expression. |
| first_indexed | 2024-03-09T10:22:18Z |
| format | Article |
| id | doaj.art-764b7241861c458790c40779343810f5 |
| institution | Directory Open Access Journal |
| issn | 2079-7737 |
| language | English |
| last_indexed | 2024-03-09T10:22:18Z |
| publishDate | 2022-06-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biology |
| spelling | doaj.art-764b7241861c458790c40779343810f52023-12-01T21:54:20ZengMDPI AGBiology2079-77372022-06-0111798810.3390/biology11070988Neuronal Depolarization Induced RNA m<sup>5</sup>C Methylation Changes in Mouse Cortical NeuronsXiguang Xu0Zachary Johnson1Hehuang Xie2Epigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USAEpigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USAEpigenomics and Computational Biology Lab, Fralin Life Sciences Institute, Virginia Tech, Blacksburg, VA 24061, USANeuronal activity is accomplished via substantial changes in gene expression, which may be accompanied by post-transcriptional modifications including RNA cytosine-5 methylation (m<sup>5</sup>C). Despite several reports on the transcriptome profiling of activated neurons, the dynamics of neuronal mRNA m<sup>5</sup>C modification in response to environmental stimuli has not been explored. Here, we provide transcriptome-wide maps of m<sup>5</sup>C modification, together with gene expression profiles, for mouse cortical neurons at 0 h, 2 h, and 6 h upon membrane depolarization. Thousands of differentially expressed genes (DEGs) were identified during the neuronal depolarization process. In stimulated neurons, the majority of early response genes were found to serve as expression regulators of late response genes, which are involved in signaling pathways and diverse synaptic functions. With RNA bisulfite sequencing data, a union set of 439 m<sup>5</sup>C sites was identified with high confidence, and approximately 30% of them were shared by neurons at all three time points. Interestingly, over 41% of the m<sup>5</sup>C sites showed increased methylation upon neuronal activation and were enriched in transcripts coding for proteins with synaptic functions. In addition, a modest negative correlation was observed between RNA expression and methylation. In summary, our study provided dynamic transcriptome-wide landscapes of RNA m<sup>5</sup>C methylation in neurons, and revealed that mRNA m<sup>5</sup>C methylation is associated with the regulation of gene expression.https://www.mdpi.com/2079-7737/11/7/988neuronal depolarizationgene expressionRNA cytosine-5 methylationRNA bisulfite sequencingRNA-seq |
| spellingShingle | Xiguang Xu Zachary Johnson Hehuang Xie Neuronal Depolarization Induced RNA m<sup>5</sup>C Methylation Changes in Mouse Cortical Neurons Biology neuronal depolarization gene expression RNA cytosine-5 methylation RNA bisulfite sequencing RNA-seq |
| title | Neuronal Depolarization Induced RNA m<sup>5</sup>C Methylation Changes in Mouse Cortical Neurons |
| title_full | Neuronal Depolarization Induced RNA m<sup>5</sup>C Methylation Changes in Mouse Cortical Neurons |
| title_fullStr | Neuronal Depolarization Induced RNA m<sup>5</sup>C Methylation Changes in Mouse Cortical Neurons |
| title_full_unstemmed | Neuronal Depolarization Induced RNA m<sup>5</sup>C Methylation Changes in Mouse Cortical Neurons |
| title_short | Neuronal Depolarization Induced RNA m<sup>5</sup>C Methylation Changes in Mouse Cortical Neurons |
| title_sort | neuronal depolarization induced rna m sup 5 sup c methylation changes in mouse cortical neurons |
| topic | neuronal depolarization gene expression RNA cytosine-5 methylation RNA bisulfite sequencing RNA-seq |
| url | https://www.mdpi.com/2079-7737/11/7/988 |
| work_keys_str_mv | AT xiguangxu neuronaldepolarizationinducedrnamsup5supcmethylationchangesinmousecorticalneurons AT zacharyjohnson neuronaldepolarizationinducedrnamsup5supcmethylationchangesinmousecorticalneurons AT hehuangxie neuronaldepolarizationinducedrnamsup5supcmethylationchangesinmousecorticalneurons |