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Transcriptional dynamics and epigenetic regulation of E and ID protein encoding genes during human T cell development

Juliette Roels (UGent) , Jolien Van Hulle (UGent) , Marieke Lavaert, Anna Kuchmiy (UGent) , Steven Strubbe, Tom Putteman (UGent) , Bart Vandekerckhove (UGent) , Georges Leclercq (UGent) , Filip Van Nieuwerburgh (UGent) , Lena Boehme (UGent) , et al.
(2022) FRONTIERS IN IMMUNOLOGY. 13.
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Abstract
T cells are generated from hematopoietic stem cells through a highly organized developmental process, in which stage-specific molecular events drive maturation towards alpha beta and gamma delta T cells. Although many of the mechanisms that control alpha beta- and gamma delta-lineage differentiation are shared between human and mouse, important differences have also been observed. Here, we studied the regulatory dynamics of the E and ID protein encoding genes during pediatric human T cell development by evaluating changes in chromatin accessibility, histone modifications and bulk and single cell gene expression. We profiled patterns of ID/E protein activity and identified up- and downstream regulators and targets, respectively. In addition, we compared transcription of E and ID protein encoding genes in human versus mouse to predict both shared and unique activities in these species, and in prenatal versus pediatric human T cell differentiation to identify regulatory changes during development. This analysis showed a putative involvement of TCF3/E2A in the development of gamma delta T cells. In contrast, in alpha beta T cell precursors a pivotal pre-TCR-driven population with high ID gene expression and low predicted E protein activity was identified. Finally, in prenatal but not postnatal thymocytes, high HEB/TCF12 levels were found to counteract high ID levels to sustain thymic development. In summary, we uncovered novel insights in the regulation of E and ID proteins on a cross-species and cross-developmental level.

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MLA
Roels, Juliette, et al. “Transcriptional Dynamics and Epigenetic Regulation of E and ID Protein Encoding Genes during Human T Cell Development.” FRONTIERS IN IMMUNOLOGY, vol. 13, 2022, doi:10.3389/fimmu.2022.960918.
APA
Roels, J., Van Hulle, J., Lavaert, M., Kuchmiy, A., Strubbe, S., Putteman, T., … Taghon, T. (2022). Transcriptional dynamics and epigenetic regulation of E and ID protein encoding genes during human T cell development. FRONTIERS IN IMMUNOLOGY, 13. https://doi.org/10.3389/fimmu.2022.960918
Chicago author-date
Roels, Juliette, Jolien Van Hulle, Marieke Lavaert, Anna Kuchmiy, Steven Strubbe, Tom Putteman, Bart Vandekerckhove, et al. 2022. “Transcriptional Dynamics and Epigenetic Regulation of E and ID Protein Encoding Genes during Human T Cell Development.” FRONTIERS IN IMMUNOLOGY 13. https://doi.org/10.3389/fimmu.2022.960918.
Chicago author-date (all authors)
Roels, Juliette, Jolien Van Hulle, Marieke Lavaert, Anna Kuchmiy, Steven Strubbe, Tom Putteman, Bart Vandekerckhove, Georges Leclercq, Filip Van Nieuwerburgh, Lena Boehme, and Tom Taghon. 2022. “Transcriptional Dynamics and Epigenetic Regulation of E and ID Protein Encoding Genes during Human T Cell Development.” FRONTIERS IN IMMUNOLOGY 13. doi:10.3389/fimmu.2022.960918.
Vancouver
1.
Roels J, Van Hulle J, Lavaert M, Kuchmiy A, Strubbe S, Putteman T, et al. Transcriptional dynamics and epigenetic regulation of E and ID protein encoding genes during human T cell development. FRONTIERS IN IMMUNOLOGY. 2022;13.
IEEE
[1]
J. Roels et al., “Transcriptional dynamics and epigenetic regulation of E and ID protein encoding genes during human T cell development,” FRONTIERS IN IMMUNOLOGY, vol. 13, 2022.
@article{01GMBG1EPBDDDJ50VKDS6MPA7Y,
  abstract     = {{T cells are generated from hematopoietic stem cells through a highly organized developmental process, in which stage-specific molecular events drive maturation towards alpha beta and gamma delta T cells. Although many of the mechanisms that control alpha beta- and gamma delta-lineage differentiation are shared between human and mouse, important differences have also been observed. Here, we studied the regulatory dynamics of the E and ID protein encoding genes during pediatric human T cell development by evaluating changes in chromatin accessibility, histone modifications and bulk and single cell gene expression. We profiled patterns of ID/E protein activity and identified up- and downstream regulators and targets, respectively. In addition, we compared transcription of E and ID protein encoding genes in human versus mouse to predict both shared and unique activities in these species, and in prenatal versus pediatric human T cell differentiation to identify regulatory changes during development. This analysis showed a putative involvement of TCF3/E2A in the development of gamma delta T cells. In contrast, in alpha beta T cell precursors a pivotal pre-TCR-driven population with high ID gene expression and low predicted E protein activity was identified. Finally, in prenatal but not postnatal thymocytes, high HEB/TCF12 levels were found to counteract high ID levels to sustain thymic development. In summary, we uncovered novel insights in the regulation of E and ID proteins on a cross-species and cross-developmental level.}},
  articleno    = {{960918}},
  author       = {{Roels, Juliette and Van Hulle, Jolien and Lavaert, Marieke and Kuchmiy, Anna and Strubbe, Steven and Putteman, Tom and Vandekerckhove, Bart and Leclercq, Georges and Van Nieuwerburgh, Filip and Boehme, Lena and Taghon, Tom}},
  issn         = {{1664-3224}},
  journal      = {{FRONTIERS IN IMMUNOLOGY}},
  language     = {{eng}},
  pages        = {{24}},
  title        = {{Transcriptional dynamics and epigenetic regulation of E and ID protein encoding genes during human T cell development}},
  url          = {{http://doi.org/10.3389/fimmu.2022.960918}},
  volume       = {{13}},
  year         = {{2022}},
}
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