Role of the <i>Egr2</i> Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape
<b>Background</b>: Schwann cells (SCs) and their plasticity contribute to the peripheral nervous system’s capacity for nerve regeneration after injury. The <i>Egr2/Krox20</i> promoter antisense RNA (Egr2-AS) recruits chromatin remodeling complexes to inhibit <i>Egr2<...
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2024-11-01
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| author | Margot Martinez Moreno David Karambizi Hyeyeon Hwang Kristen Fregoso Madison J. Michles Eduardo Fajardo Andras Fiser Nikos Tapinos |
| author_facet | Margot Martinez Moreno David Karambizi Hyeyeon Hwang Kristen Fregoso Madison J. Michles Eduardo Fajardo Andras Fiser Nikos Tapinos |
| author_sort | Margot Martinez Moreno |
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| description | <b>Background</b>: Schwann cells (SCs) and their plasticity contribute to the peripheral nervous system’s capacity for nerve regeneration after injury. The <i>Egr2/Krox20</i> promoter antisense RNA (Egr2-AS) recruits chromatin remodeling complexes to inhibit <i>Egr2</i> transcription following peripheral nerve injury. <b>Methods</b>: RNA-seq and ATAC-seq were performed on control cells, Lenti-GFP-transduced cells, and cells overexpressing Egr2-AS (Lenti-AS). Egr2 AS-RNA was cloned into the pLVX-DsRed-Express2-N1 lentiviral expression vector (Clontech, Mountain View, CA, USA), and the levels of AS-RNA expression were determined. Ezh2 and Wdr5 were immunoprecipitated from rat SCs and RT-qPCR was performed against AS-Egr2 RNA. ChIP followed by DNA purification columns was used to perform qPCR for relevant promoters. Hi-C, HiC-DC+, R, Bioconductor, and TOBIAS were used for significant and differential loop analysis, identifications of COREs and CORE-promotor loops, comparisons of TF activity at promoter sites, and identification of site-specific TF footprints. OnTAD was used to detect TADs, and Juicer was used to identify A/B compartments. <b>Results</b>: Here we show that a Neuregulin-ErbB2/3 signaling axis mediates binding of the Egr2-AS to YY1<sup>Ser184</sup> and regulates its expression. Egr2-AS modulates the chromatin accessibility of Schwann cells and interacts with two distinct histone modification complexes. It binds to EZH2 and WDR5 and enables targeting of H3K27me3 and H3K4me3 to promoters of <i>Egr2</i> and <i>C-JUN,</i> respectively. Expression of the Egr2-AS results in reorganization of the global chromatin landscape and quantitative changes in the loop formation and contact frequency at domain boundaries exhibiting enrichment for AP-1 genes. In addition, the Egr2-AS induces changes in the hierarchical TADs and increases transcription factor binding scores on an inter-TAD loop between a super-enhancer regulatory hub and the promoter of <i>mTOR</i>. <b>Conclusions</b>: Our results show that Neuregulin-ErbB2/3-YY1 regulates the expression of Egr2-AS, which mediates remodeling of the chromatin landscape in Schwann cells. |
| format | Article |
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| publishDate | 2024-11-01 |
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| spelling | doaj-art-1ff3e42373414a449b8d2d35e3c8dac52025-08-20T01:53:49ZengMDPI AGBiomedicines2227-90592024-11-011211259410.3390/biomedicines12112594Role of the <i>Egr2</i> Promoter Antisense RNA in Modulating the Schwann Cell Chromatin LandscapeMargot Martinez Moreno0David Karambizi1Hyeyeon Hwang2Kristen Fregoso3Madison J. Michles4Eduardo Fajardo5Andras Fiser6Nikos Tapinos7Department of Neurosurgery, Brown University, Rhode Island Hospital, Providence, RI 02903, USALaboratory of Cancer Epigenetics and Plasticity, Brown University, Providence, RI 02903, USALaboratory of Cancer Epigenetics and Plasticity, Brown University, Providence, RI 02903, USALaboratory of Cancer Epigenetics and Plasticity, Brown University, Providence, RI 02903, USADepartment of Neurosurgery, Brown University, Rhode Island Hospital, Providence, RI 02903, USADepartment of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USADepartment of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USADepartment of Neurosurgery, Brown University, Rhode Island Hospital, Providence, RI 02903, USA<b>Background</b>: Schwann cells (SCs) and their plasticity contribute to the peripheral nervous system’s capacity for nerve regeneration after injury. The <i>Egr2/Krox20</i> promoter antisense RNA (Egr2-AS) recruits chromatin remodeling complexes to inhibit <i>Egr2</i> transcription following peripheral nerve injury. <b>Methods</b>: RNA-seq and ATAC-seq were performed on control cells, Lenti-GFP-transduced cells, and cells overexpressing Egr2-AS (Lenti-AS). Egr2 AS-RNA was cloned into the pLVX-DsRed-Express2-N1 lentiviral expression vector (Clontech, Mountain View, CA, USA), and the levels of AS-RNA expression were determined. Ezh2 and Wdr5 were immunoprecipitated from rat SCs and RT-qPCR was performed against AS-Egr2 RNA. ChIP followed by DNA purification columns was used to perform qPCR for relevant promoters. Hi-C, HiC-DC+, R, Bioconductor, and TOBIAS were used for significant and differential loop analysis, identifications of COREs and CORE-promotor loops, comparisons of TF activity at promoter sites, and identification of site-specific TF footprints. OnTAD was used to detect TADs, and Juicer was used to identify A/B compartments. <b>Results</b>: Here we show that a Neuregulin-ErbB2/3 signaling axis mediates binding of the Egr2-AS to YY1<sup>Ser184</sup> and regulates its expression. Egr2-AS modulates the chromatin accessibility of Schwann cells and interacts with two distinct histone modification complexes. It binds to EZH2 and WDR5 and enables targeting of H3K27me3 and H3K4me3 to promoters of <i>Egr2</i> and <i>C-JUN,</i> respectively. Expression of the Egr2-AS results in reorganization of the global chromatin landscape and quantitative changes in the loop formation and contact frequency at domain boundaries exhibiting enrichment for AP-1 genes. In addition, the Egr2-AS induces changes in the hierarchical TADs and increases transcription factor binding scores on an inter-TAD loop between a super-enhancer regulatory hub and the promoter of <i>mTOR</i>. <b>Conclusions</b>: Our results show that Neuregulin-ErbB2/3-YY1 regulates the expression of Egr2-AS, which mediates remodeling of the chromatin landscape in Schwann cells.https://www.mdpi.com/2227-9059/12/11/2594promoter antisense-RNA<i>EGR2</i><i>C-JUN</i>EZH2WDR5AP-1 |
| spellingShingle | Margot Martinez Moreno David Karambizi Hyeyeon Hwang Kristen Fregoso Madison J. Michles Eduardo Fajardo Andras Fiser Nikos Tapinos Role of the <i>Egr2</i> Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape Biomedicines promoter antisense-RNA <i>EGR2</i> <i>C-JUN</i> EZH2 WDR5 AP-1 |
| title | Role of the <i>Egr2</i> Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape |
| title_full | Role of the <i>Egr2</i> Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape |
| title_fullStr | Role of the <i>Egr2</i> Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape |
| title_full_unstemmed | Role of the <i>Egr2</i> Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape |
| title_short | Role of the <i>Egr2</i> Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape |
| title_sort | role of the i egr2 i promoter antisense rna in modulating the schwann cell chromatin landscape |
| topic | promoter antisense-RNA <i>EGR2</i> <i>C-JUN</i> EZH2 WDR5 AP-1 |
| url | https://www.mdpi.com/2227-9059/12/11/2594 |
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