Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration
Injured sensory neurons activate a transcriptional program necessary for robust axon regeneration and eventual target reinnervation. Understanding the transcriptional regulators that govern this axon regenerative response may guide therapeutic strategies to promote axon regeneration in the injured n...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-08-01
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| Series: | Frontiers in Molecular Neuroscience |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fnmol.2022.967472/full |
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| author | Oshri Avraham Jimmy Le Kathleen Leahy Tiandao Li Tiandao Li Guoyan Zhao Guoyan Zhao Valeria Cavalli Valeria Cavalli Valeria Cavalli |
| author_facet | Oshri Avraham Jimmy Le Kathleen Leahy Tiandao Li Tiandao Li Guoyan Zhao Guoyan Zhao Valeria Cavalli Valeria Cavalli Valeria Cavalli |
| author_sort | Oshri Avraham |
| collection | DOAJ |
| description | Injured sensory neurons activate a transcriptional program necessary for robust axon regeneration and eventual target reinnervation. Understanding the transcriptional regulators that govern this axon regenerative response may guide therapeutic strategies to promote axon regeneration in the injured nervous system. Here, we used cultured dorsal root ganglia neurons to identify pro-regenerative transcription factors. Using RNA sequencing, we first characterized this neuronal culture and determined that embryonic day 13.5 DRG (eDRG) neurons cultured for 7 days are similar to e15.5 DRG neurons in vivo and that all neuronal subtypes are represented. This eDRG neuronal culture does not contain other non-neuronal cell types. Next, we performed RNA sequencing at different time points after in vitro axotomy. Analysis of differentially expressed genes revealed upregulation of known regeneration associated transcription factors, including Jun, Atf3 and Rest, paralleling the axon injury response in vivo. Analysis of transcription factor binding sites in differentially expressed genes revealed other known transcription factors promoting axon regeneration, such as Myc, Hif1α, Pparγ, Ascl1a, Srf, and Ctcf, as well as other transcription factors not yet characterized in axon regeneration. We next tested if overexpression of novel candidate transcription factors alone or in combination promotes axon regeneration in vitro. Our results demonstrate that expression of Ctcf with Yy1 or E2f2 enhances in vitro axon regeneration. Our analysis highlights that transcription factor interaction and chromatin architecture play important roles as a regulator of axon regeneration. |
| first_indexed | 2024-04-13T18:26:21Z |
| format | Article |
| id | doaj.art-29cf98a2918d40af959f2d48e8148f1e |
| institution | Directory Open Access Journal |
| issn | 1662-5099 |
| language | English |
| last_indexed | 2024-04-13T18:26:21Z |
| publishDate | 2022-08-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Molecular Neuroscience |
| spelling | doaj.art-29cf98a2918d40af959f2d48e8148f1e2022-12-22T02:35:13ZengFrontiers Media S.A.Frontiers in Molecular Neuroscience1662-50992022-08-011510.3389/fnmol.2022.967472967472Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regenerationOshri Avraham0Jimmy Le1Kathleen Leahy2Tiandao Li3Tiandao Li4Guoyan Zhao5Guoyan Zhao6Valeria Cavalli7Valeria Cavalli8Valeria Cavalli9Department of Neuroscience, Washington University School of Medicine, St. Louis, MO, United StatesDepartment of Neuroscience, Washington University School of Medicine, St. Louis, MO, United StatesDepartment of Neuroscience, Washington University School of Medicine, St. Louis, MO, United StatesDepartment of Developmental Biology, Washington University School of Medicine, St. Louis, MO, United StatesCenter of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United StatesDepartment of Neuroscience, Washington University School of Medicine, St. Louis, MO, United StatesDepartment of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, United StatesDepartment of Neuroscience, Washington University School of Medicine, St. Louis, MO, United StatesCenter of Regenerative Medicine, Washington University School of Medicine, St. Louis, MO, United StatesHope Center for Neurological Disorders, Washington University School of Medicine, St. Louis, MO, United StatesInjured sensory neurons activate a transcriptional program necessary for robust axon regeneration and eventual target reinnervation. Understanding the transcriptional regulators that govern this axon regenerative response may guide therapeutic strategies to promote axon regeneration in the injured nervous system. Here, we used cultured dorsal root ganglia neurons to identify pro-regenerative transcription factors. Using RNA sequencing, we first characterized this neuronal culture and determined that embryonic day 13.5 DRG (eDRG) neurons cultured for 7 days are similar to e15.5 DRG neurons in vivo and that all neuronal subtypes are represented. This eDRG neuronal culture does not contain other non-neuronal cell types. Next, we performed RNA sequencing at different time points after in vitro axotomy. Analysis of differentially expressed genes revealed upregulation of known regeneration associated transcription factors, including Jun, Atf3 and Rest, paralleling the axon injury response in vivo. Analysis of transcription factor binding sites in differentially expressed genes revealed other known transcription factors promoting axon regeneration, such as Myc, Hif1α, Pparγ, Ascl1a, Srf, and Ctcf, as well as other transcription factors not yet characterized in axon regeneration. We next tested if overexpression of novel candidate transcription factors alone or in combination promotes axon regeneration in vitro. Our results demonstrate that expression of Ctcf with Yy1 or E2f2 enhances in vitro axon regeneration. Our analysis highlights that transcription factor interaction and chromatin architecture play important roles as a regulator of axon regeneration.https://www.frontiersin.org/articles/10.3389/fnmol.2022.967472/fullaxon regenerationsensory neuronstranscription factorsbioinformatics analysesCTCFYY1 |
| spellingShingle | Oshri Avraham Jimmy Le Kathleen Leahy Tiandao Li Tiandao Li Guoyan Zhao Guoyan Zhao Valeria Cavalli Valeria Cavalli Valeria Cavalli Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration Frontiers in Molecular Neuroscience axon regeneration sensory neurons transcription factors bioinformatics analyses CTCF YY1 |
| title | Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration |
| title_full | Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration |
| title_fullStr | Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration |
| title_full_unstemmed | Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration |
| title_short | Analysis of neuronal injury transcriptional response identifies CTCF and YY1 as co-operating factors regulating axon regeneration |
| title_sort | analysis of neuronal injury transcriptional response identifies ctcf and yy1 as co operating factors regulating axon regeneration |
| topic | axon regeneration sensory neurons transcription factors bioinformatics analyses CTCF YY1 |
| url | https://www.frontiersin.org/articles/10.3389/fnmol.2022.967472/full |
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