The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells

Semir Beyaz, Ji Hyung Kim, Luca Pinello, Michael E. Xifaras, Yu Hu, Jialiang Huang, Marc A. Kerenyi, Partha P Das, R. Anthony Barnitz, Aurelie Herault, Rizkullah Dogum, W. Nicholas Haining, Ömer H. Yilmaz, Emmanuelle Passegue, Guo Cheng Yuan, Stuart H. Orkin, Florian Winau

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20 Citations (Scopus)

Abstract

Invariant natural killer T cells (iNKT cells) are innate-like lymphocytes that protect against infection, autoimmune disease and cancer. However, little is known about the epigenetic regulation of iNKT cell development. Here we found that the H3K27me3 histone demethylase UTX was an essential cell-intrinsic factor that controlled an iNKT-cell lineage-specific gene-expression program and epigenetic landscape in a demethylase-Activity-dependent manner. UTX-deficient iNKT cells exhibited impaired expression of iNKT cell signature genes due to a decrease in activation-Associated H3K4me3 marks and an increase in repressive H3K27me3 marks within the promoters occupied by UTX. We found that JunB regulated iNKT cell development and that the expression of genes that were targets of both JunB and the iNKT cell master transcription factor PLZF was UTX dependent. We identified iNKT cell super-enhancers and demonstrated that UTX-mediated regulation of super-enhancer accessibility was a key mechanism for commitment to the iNKT cell lineage. Our findings reveal how UTX regulates the development of iNKT cells through multiple epigenetic mechanisms.

Original languageEnglish
Pages (from-to)184-195
Number of pages12
JournalNature Immunology
Volume18
Issue number2
DOIs
Publication statusPublished - 1 Feb 2017
Externally publishedYes

Keywords

  • epigenetics in immune cells
  • NKT cells

Cite this

Beyaz, S., Kim, J. H., Pinello, L., Xifaras, M. E., Hu, Y., Huang, J., ... Winau, F. (2017). The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. Nature Immunology, 18(2), 184-195. https://doi.org/10.1038/ni.3644
Beyaz, Semir ; Kim, Ji Hyung ; Pinello, Luca ; Xifaras, Michael E. ; Hu, Yu ; Huang, Jialiang ; Kerenyi, Marc A. ; Das, Partha P ; Barnitz, R. Anthony ; Herault, Aurelie ; Dogum, Rizkullah ; Haining, W. Nicholas ; Yilmaz, Ömer H. ; Passegue, Emmanuelle ; Yuan, Guo Cheng ; Orkin, Stuart H. ; Winau, Florian. / The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. In: Nature Immunology. 2017 ; Vol. 18, No. 2. pp. 184-195.
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abstract = "Invariant natural killer T cells (iNKT cells) are innate-like lymphocytes that protect against infection, autoimmune disease and cancer. However, little is known about the epigenetic regulation of iNKT cell development. Here we found that the H3K27me3 histone demethylase UTX was an essential cell-intrinsic factor that controlled an iNKT-cell lineage-specific gene-expression program and epigenetic landscape in a demethylase-Activity-dependent manner. UTX-deficient iNKT cells exhibited impaired expression of iNKT cell signature genes due to a decrease in activation-Associated H3K4me3 marks and an increase in repressive H3K27me3 marks within the promoters occupied by UTX. We found that JunB regulated iNKT cell development and that the expression of genes that were targets of both JunB and the iNKT cell master transcription factor PLZF was UTX dependent. We identified iNKT cell super-enhancers and demonstrated that UTX-mediated regulation of super-enhancer accessibility was a key mechanism for commitment to the iNKT cell lineage. Our findings reveal how UTX regulates the development of iNKT cells through multiple epigenetic mechanisms.",
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author = "Semir Beyaz and Kim, {Ji Hyung} and Luca Pinello and Xifaras, {Michael E.} and Yu Hu and Jialiang Huang and Kerenyi, {Marc A.} and Das, {Partha P} and Barnitz, {R. Anthony} and Aurelie Herault and Rizkullah Dogum and Haining, {W. Nicholas} and Yilmaz, {{\"O}mer H.} and Emmanuelle Passegue and Yuan, {Guo Cheng} and Orkin, {Stuart H.} and Florian Winau",
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Beyaz, S, Kim, JH, Pinello, L, Xifaras, ME, Hu, Y, Huang, J, Kerenyi, MA, Das, PP, Barnitz, RA, Herault, A, Dogum, R, Haining, WN, Yilmaz, ÖH, Passegue, E, Yuan, GC, Orkin, SH & Winau, F 2017, 'The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells', Nature Immunology, vol. 18, no. 2, pp. 184-195. https://doi.org/10.1038/ni.3644

The histone demethylase UTX regulates the lineage-specific epigenetic program of invariant natural killer T cells. / Beyaz, Semir; Kim, Ji Hyung; Pinello, Luca; Xifaras, Michael E.; Hu, Yu; Huang, Jialiang; Kerenyi, Marc A.; Das, Partha P; Barnitz, R. Anthony; Herault, Aurelie; Dogum, Rizkullah; Haining, W. Nicholas; Yilmaz, Ömer H.; Passegue, Emmanuelle; Yuan, Guo Cheng; Orkin, Stuart H.; Winau, Florian.

In: Nature Immunology, Vol. 18, No. 2, 01.02.2017, p. 184-195.

Research output: Contribution to journalArticleResearchpeer-review

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AU - Beyaz, Semir

AU - Kim, Ji Hyung

AU - Pinello, Luca

AU - Xifaras, Michael E.

AU - Hu, Yu

AU - Huang, Jialiang

AU - Kerenyi, Marc A.

AU - Das, Partha P

AU - Barnitz, R. Anthony

AU - Herault, Aurelie

AU - Dogum, Rizkullah

AU - Haining, W. Nicholas

AU - Yilmaz, Ömer H.

AU - Passegue, Emmanuelle

AU - Yuan, Guo Cheng

AU - Orkin, Stuart H.

AU - Winau, Florian

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N2 - Invariant natural killer T cells (iNKT cells) are innate-like lymphocytes that protect against infection, autoimmune disease and cancer. However, little is known about the epigenetic regulation of iNKT cell development. Here we found that the H3K27me3 histone demethylase UTX was an essential cell-intrinsic factor that controlled an iNKT-cell lineage-specific gene-expression program and epigenetic landscape in a demethylase-Activity-dependent manner. UTX-deficient iNKT cells exhibited impaired expression of iNKT cell signature genes due to a decrease in activation-Associated H3K4me3 marks and an increase in repressive H3K27me3 marks within the promoters occupied by UTX. We found that JunB regulated iNKT cell development and that the expression of genes that were targets of both JunB and the iNKT cell master transcription factor PLZF was UTX dependent. We identified iNKT cell super-enhancers and demonstrated that UTX-mediated regulation of super-enhancer accessibility was a key mechanism for commitment to the iNKT cell lineage. Our findings reveal how UTX regulates the development of iNKT cells through multiple epigenetic mechanisms.

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