1
|
Bernardi C, Maurer G, Ye T, Marchal P, Jost B, Wissler M, Maurer U, Kastner P, Chan S, Charvet C. CD4 + T cells require Ikaros to inhibit their differentiation toward a pathogenic cell fate. Proc Natl Acad Sci U S A 2021; 118:e2023172118. [PMID: 33893236 PMCID: PMC8092604 DOI: 10.1073/pnas.2023172118] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The production of proinflammatory cytokines, particularly granulocyte-macrophage colony-stimulating factor (GM-CSF), by pathogenic CD4+ T cells is central for mediating tissue injury in inflammatory and autoimmune diseases. However, the factors regulating the T cell pathogenic gene expression program remain unclear. Here, we investigated how the Ikaros transcription factor regulates the global gene expression and chromatin accessibility changes in murine T cells during Th17 polarization and after activation via the T cell receptor (TCR) and CD28. We found that, in both conditions, Ikaros represses the expression of genes from the pathogenic signature, particularly Csf2, which encodes GM-CSF. We show that, in TCR/CD28-activated T cells, Ikaros binds a critical enhancer downstream of Csf2 and is required to regulate chromatin accessibility at multiple regions across this locus. Genome-wide Ikaros binding is associated with more compact chromatin, notably at multiple sites containing NFκB or STAT5 target motifs, and STAT5 or NFκB inhibition prevents GM-CSF production in Ikaros-deficient cells. Importantly, Ikaros also limits GM-CSF production in TCR/CD28-activated human T cells. Our data therefore highlight a critical conserved transcriptional mechanism that antagonizes GM-CSF expression in T cells.
Collapse
Affiliation(s)
- Chiara Bernardi
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Gaëtan Maurer
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Tao Ye
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
- Plateforme GenomEast, Infrastructure France Génomique, 67404 Illkirch, France
| | - Patricia Marchal
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Bernard Jost
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
- Plateforme GenomEast, Infrastructure France Génomique, 67404 Illkirch, France
| | - Manuela Wissler
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
| | - Ulrich Maurer
- Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
- Spemann Graduate School of Biology and Medicine, Albert-Ludwigs-University of Freiburg, 79104 Freiburg, Germany
- BIOSS, Centre for Biological Signalling Studies, 79104 Freiburg, Germany
| | - Philippe Kastner
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
- Faculté de Médecine, Université de Strasbourg, 67000 Strasbourg, France
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| | - Céline Charvet
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, 67404 Illkirch, France;
- Centre National de la Recherche Scientifique, UMR7104, 67404 Illkirch, France
- Institut National de la Santé et de la Recherche Médicale, U1258, 67404 Illkirch, France
- Université de Strasbourg, 67000 Strasbourg, France
| |
Collapse
|
2
|
Wang Z, Liu S, Tao Y. Regulation of chromatin remodeling through RNA polymerase II stalling in the immune system. Mol Immunol 2019; 108:75-80. [PMID: 30784765 DOI: 10.1016/j.molimm.2019.02.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 02/13/2019] [Accepted: 02/14/2019] [Indexed: 12/11/2022]
Abstract
RNA polymerase II (Pol II) binds to promoter-proximal regions of inducible target genes that are controlled and not transcribed by several negative elongation factors, which is known as Pol II stalling. The occurrence of stalling is due to particular modification signatures and structural conformations of chromatin that affect Pol II elongation. The existence and physiological importance of Pol II stalling implies that there is a dynamic balance in chromatin regulation prior to endogenous or exogenous stimulation. In this review, we discuss the effects of ATP-dependent chromatin remodeling complexes and histone modification via transcriptional machinery Pol II C-terminal domain phosphorylated at serine 5 (S5P RNAPII) initiation and S2P RNAPII elongation on the expression or silence of specific genes after the production of activated or differentiated signals or cytokines. The response occurs immediately during immune cell development and function, and it also includes the generation of immunological memories. This summary suggests that the host immune response genes involve a novel mechanism of selectively regulatory chromatin remodeling, a fundamental and crucial aspect of epigenetic regulation.
Collapse
Affiliation(s)
- Zuli Wang
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China; Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China; Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China
| | - Shuang Liu
- Institute of Medical Sciences, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China.
| | - Yongguang Tao
- Key Laboratory of Carcinogenesis and Cancer Invasion, Ministry of Education, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan, 410008, China; Key Laboratory of Carcinogenesis, Ministry of Health, Cancer Research Institute, Central South University, 110 Xiangya Road, Changsha, Hunan, 410078, China; Department of Thoracic Surgery, Second Xiangya Hospital, Central South University, Changsha, China.
| |
Collapse
|
4
|
Bevington SL, Cauchy P, Cockerill PN. Chromatin priming elements establish immunological memory in T cells without activating transcription: T cell memory is maintained by DNA elements which stably prime inducible genes without activating steady state transcription. Bioessays 2016; 39. [PMID: 28026028 DOI: 10.1002/bies.201600184] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We have identified a simple epigenetic mechanism underlying the establishment and maintenance of immunological memory in T cells. By studying the transcriptional regulation of inducible genes we found that a single cycle of activation of inducible factors is sufficient to initiate stable binding of pre-existing transcription factors to thousands of newly activated distal regulatory elements within inducible genes. These events lead to the creation of islands of active chromatin encompassing nearby enhancers, thereby supporting the accelerated activation of inducible genes, without changing steady state levels of transcription in memory T cells. These studies also highlighted the need for more sophisticated definitions of gene regulatory elements. The chromatin priming elements defined here are distinct from classical enhancers because they function by maintaining chromatin accessibility rather than directly activating transcription. We propose that these priming elements are members of a wider class of genomic elements that support correct developmentally regulated gene expression.
Collapse
Affiliation(s)
- Sarah L Bevington
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
| | - Pierre Cauchy
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
| | - Peter N Cockerill
- Institute of Cancer and Genomic Sciences, Institute of Biomedical Research, University of Birmingham, Birmingham, West Midlands, UK
| |
Collapse
|
5
|
Anthony K, More A, Zhang X. Activation of silenced cytokine gene promoters by the synergistic effect of TBP-TALE and VP64-TALE activators. PLoS One 2014; 9:e95790. [PMID: 24755922 PMCID: PMC3995891 DOI: 10.1371/journal.pone.0095790] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 03/29/2014] [Indexed: 11/19/2022] Open
Abstract
Recent work has shown that the combinatorial use of multiple TALE activators can selectively activate certain cellular genes in inaccessible chromatin regions. In this study, we aimed to interrogate the activation potential of TALEs upon transcriptionally silenced immune genes in the context of non-immune cells. We designed a unique strategy, in which a single TALE fused to the TATA-box binding protein (TBP-TALE) is coupled with multiple VP64-TALE activators. We found that our strategy is significantly more potent than multiple TALE activators alone in activating expression of IL-2 and GM-CSF in diverse cell origins in which both genes are otherwise completely silenced. Chromatin analysis revealed that the gene activation was due in part to displacement of a distinctly positioned nucleosome. These studies provide a novel epigenetic mechanism for artificial gene induction and have important implications for targeted cancer immunotherapy, DNA vaccine development, as well as rational design of TALE activators.
Collapse
Affiliation(s)
- Kim Anthony
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, United States of America
| | - Abhijit More
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
| | - Xiaoliu Zhang
- Department of Biology and Biochemistry, University of Houston, Houston, Texas, United States of America
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, United States of America
- * E-mail:
| |
Collapse
|