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Distinct super-enhancer elements differentially control Il2ra gene expression in a cell-type specific fashion

Spolski, Rosanne and Li, Peng and Chandra, Vivek and Shin, Boyoung and Liu, Chengyu and Oh, Jangsuk and Ren, Min and Enomoto, Yutaka and West, Erin E. and Christensen, Stephen and Wan, Edwin C. K. and Ge, Meili and Lin, Jian-Xin and Vijayanand, Pandurangan and Rothenberg, Ellen V. and Leonard, Warren J. (2022) Distinct super-enhancer elements differentially control Il2ra gene expression in a cell-type specific fashion. . (Unpublished)

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The IL-2 receptor α-chain (IL-2Rα/CD25) is constitutively expressed on DN2/DN3 thymocytes and Treg cells but induced by IL-2 on mature T and NK cells. Il2ra expression is regulated by a super-enhancer extensively bound by STAT5 in mature T cells. Here, we demonstrate that STAT5 cooperates with Notch to induce/maintain Il2ra/CD25 expression in DN2/DN3 cells. Moreover, we systematically investigated CD25 regulation using a series of mice with deletions spanning STAT5 binding elements. Deleting the upstream super-enhancer region mainly affected constitutive CD25 expression on DN2/DN3 thymocytes and Tregs, whereas deleting an intronic region primarily decreased IL-2-induced CD25 on peripheral T and NK cells. Thus, distinct elements preferentially control constitutive versus inducible expression in a cell-type-specific manner, with the MED1 coactivator co-localizing with specific STAT5 binding sites. Moreover, the intronic region was a dominant element whose deletion altered the structure throughout the super-enhancer in mature T cells. These results demonstrate differential functions for distinct super-enhancer elements, thereby indicating ways to manipulate CD25 expression in a cell-type specific fashion.

Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription Paper
Chandra, Vivek0000-0002-4047-015X
Shin, Boyoung0000-0001-7926-5527
Liu, Chengyu0000-0002-5136-9225
Enomoto, Yutaka0000-0002-6346-9362
West, Erin E.0000-0002-7103-8394
Christensen, Stephen0000-0002-3618-6420
Wan, Edwin C. K.0000-0003-4783-3029
Vijayanand, Pandurangan0000-0001-7067-9723
Rothenberg, Ellen V.0000-0002-3901-347X
Leonard, Warren J.0000-0002-5740-7448
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. This article is a US Government work. It is not subject to copyright under 17 USC 105 and is also made available for use under a CC0 license. This work was supported by the Division of Intramural Research, National Heart, Lung, and Blood Institutes, NHLBI (W.J.L); NIH grants R01AI135200 and R01HD100039 (E.V.R.); R24AI108564, R01AI121426 and R01HL114093 (V.P.). B.S. was supported by a Cancer Research Institute-Irvington Postdoctoral Fellowship. For ChIP-Seq and RNA-Seq analysis, DNA sequencing was performed in the NHLBI DNA Sequencing Core. We thank Dr. Ning Du for help with mast cell STAT5 ChIP-Seq studies. Author Contributions. R.S. and P.L. designed the project, performed experiments, interpreted data, and wrote the manuscript. V.C. and P.V performed HiChIP experiments and analyzed the data. P.L and S.C. performed computational analysis. B.S. and E.V.R. performed the DN thymocyte in vitro experiments and ChIP-Seq experiments and analyzed data and wrote the manuscript. C.L. and J.O. designed and constructed mouse deletion mutants. M.R, Y.E, E.E.W., E.W., J.O., M.G., and J.L. contributed to in vitro cloning, animal experiments, and ChIP-Seq experiments. W.J.L. supervised the project and wrote the manuscript. Accession numbers: For the RNA expression in control and Stat5a;Stat5b double knockout DN2 cells, the GSE accession number is GSE184845 ( For the RNA-Seq data from IL-2-induced CD8+ T cells (Hermans et al., 2020), the GSE accession number is GSE143903. Other data can be viewed at and raw data will be deposited in GEO database prior to publication. The authors have declared no competing interest.
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National Heart, Lung, and Blood InstituteUNSPECIFIED
Cancer Research InstituteUNSPECIFIED
Record Number:CaltechAUTHORS:20230316-182834000.67
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Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:120175
Deposited By: George Porter
Deposited On:17 Mar 2023 23:05
Last Modified:17 Mar 2023 23:05

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