Intrinsically disordered domain of transcription factor TCF-1 is required for T cell developmental fidelity.


Journal

Nature immunology
ISSN: 1529-2916
Titre abrégé: Nat Immunol
Pays: United States
ID NLM: 100941354

Informations de publication

Date de publication:
10 2023
Historique:
received: 11 10 2022
accepted: 20 07 2023
medline: 23 10 2023
pubmed: 18 8 2023
entrez: 17 8 2023
Statut: ppublish

Résumé

In development, pioneer transcription factors access silent chromatin to reveal lineage-specific gene programs. The structured DNA-binding domains of pioneer factors have been well characterized, but whether and how intrinsically disordered regions affect chromatin and control cell fate is unclear. Here, we report that deletion of an intrinsically disordered region of the pioneer factor TCF-1 (termed L1) leads to an early developmental block in T cells. The few T cells that develop from progenitors expressing TCF-1 lacking L1 exhibit lineage infidelity distinct from the lineage diversion of TCF-1-deficient cells. Mechanistically, L1 is required for activation of T cell genes and repression of GATA2-driven genes, normally reserved to the mast cell and dendritic cell lineages. Underlying this lineage diversion, L1 mediates binding of TCF-1 to its earliest target genes, which are subject to repression as T cells develop. These data suggest that the intrinsically disordered N terminus of TCF-1 maintains T cell lineage fidelity.

Identifiants

pubmed: 37592014
doi: 10.1038/s41590-023-01599-7
pii: 10.1038/s41590-023-01599-7
doi:

Substances chimiques

Transcription Factors 0
T Cell Transcription Factor 1 0
Chromatin 0

Types de publication

Journal Article Research Support, N.I.H., Extramural Research Support, Non-U.S. Gov't

Langues

eng

Sous-ensembles de citation

IM

Pagination

1698-1710

Subventions

Organisme : NHLBI NIH HHS
ID : R01 HL145754
Pays : United States
Organisme : NCI NIH HHS
ID : P30 CA016520
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA248041
Pays : United States
Organisme : NIAID NIH HHS
ID : F30 AI161873
Pays : United States
Organisme : NIDDK NIH HHS
ID : UC4 DK112217
Pays : United States
Organisme : NIDDK NIH HHS
ID : U01 DK112217
Pays : United States
Organisme : NCI NIH HHS
ID : R01 CA230800
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI091627
Pays : United States
Organisme : NIAID NIH HHS
ID : F30 AI174776
Pays : United States
Organisme : NIDA NIH HHS
ID : U01 DA052715
Pays : United States
Organisme : NIDDK NIH HHS
ID : U01 DK127768
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI168240
Pays : United States
Organisme : NIAID NIH HHS
ID : R01 AI168136
Pays : United States

Informations de copyright

© 2023. The Author(s), under exclusive licence to Springer Nature America, Inc.

Références

Cirillo, L. A. et al. Opening of compacted chromatin by early developmental transcription factors HNF3 (FoxA) and GATA-4. Mol. Cell 9, 279–289 (2002).
pubmed: 11864602
Zaret, K. S. & Carroll, J. S. Pioneer transcription factors: establishing competence for gene expression. Genes Dev. 25, 2227–2241 (2011).
pubmed: 22056668 pmcid: 3219227
Lambert, S. A. et al. The human transcription factors. Cell 172, 650–665 (2018).
pubmed: 29425488
Verbeek, S. et al. An HMG-box-containing T cell factor required for thymocyte differentiation. Nature 374, 70–74 (1995).
pubmed: 7870176
Johnson, J. L. et al. Lineage-determining transcription factor TCF-1 initiates the epigenetic identity of T cells. Immunity 48, 243–257 (2018).
pubmed: 29466756 pmcid: 5824646
Emmanuel, A. O. et al. TCF-1 and HEB cooperate to establish the epigenetic and transcription profiles of CD4
pubmed: 30420627 pmcid: 6867931
Wang, W. et al. TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors. Nat. Immunol. 23, 1052–1062 (2022).
pubmed: 35726060 pmcid: 9728953
Xu, Z. et al. Cutting edge: beta-catenin-interacting Tcf1 isoforms are essential for thymocyte survival but dispensable for thymic maturation transitions. J. Immunol. 198, 3404–3409 (2017).
pubmed: 28348272
Zhao, X., Shan, Q. & Xue, H. H. TCF1 in T cell immunity: a broadened frontier. Nat. Rev. Immunol. 22, 147–157 (2022).
pubmed: 34127847
Love, J. J. et al. Structural basis for DNA bending by the architectural transcription factor LEF-1. Nature 376, 791–795 (1995).
pubmed: 7651541
Xing, S. et al. Tcf1 and Lef1 transcription factors establish CD8
pubmed: 27111144 pmcid: 4873337
Wang, C., Uversky, V. N. & Kurgan, L. Disordered nucleiome: abundance of intrinsic disorder in the DNA- and RNA-binding proteins in 1121 species from Eukaryota, Bacteria and Archaea. Proteomics 16, 1486–1498 (2016).
pubmed: 27037624
Shin, Y. & Brangwynne, C. P. Liquid phase condensation in cell physiology and disease. Science https://doi.org/10.1126/science.aaf4382 (2017).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
pubmed: 34265844 pmcid: 8371605
Boija, A. et al. Transcription factors activate genes through the phase-separation capacity of their activation domains. Cell 175, 1842–1855 (2018).
pubmed: 30449618
Ben Chorin, A. et al. ConSurf-DB: an accessible repository for the evolutionary conservation patterns of the majority of PDB proteins. Protein Sci. 29, 258–267 (2020).
pubmed: 31702846
Peng, K., Radivojac, P., Vucetic, S., Dunker, A. K. & Obradovic, Z. Length-dependent prediction of protein intrinsic disorder. BMC Bioinformatics 7, 208 (2006).
pubmed: 16618368 pmcid: 1479845
Skinner, J. J., Lim, W. K., Bedard, S., Black, B. E. & Englander, S. W. Protein hydrogen exchange: testing current models. Protein Sci. 21, 987–995 (2012).
pubmed: 22544567 pmcid: 3403436
Bai, Y., Milne, J. S., Mayne, L. & Englander, S. W. Primary structure effects on peptide group hydrogen exchange. Proteins 17, 75–86 (1993).
pubmed: 8234246 pmcid: 3438223
Connelly, G. P., Bai, Y., Jeng, M. F. & Englander, S. W. Isotope effects in peptide group hydrogen exchange. Proteins 17, 87–92 (1993).
pubmed: 8234247
Hosokawa, H. et al. Stage-specific action of Runx1 and GATA3 controls silencing of PU.1 expression in mouse pro-T cells. J. Exp. Med. https://doi.org/10.1084/jem.20202648 (2021).
Hu, G. et al. Transformation of accessible chromatin and 3D nucleome underlies lineage commitment of early T cells. Immunity 48, 227–242 (2018).
pubmed: 29466755 pmcid: 5847274
Rothenberg, E. V., Hosokawa, H. & Ungerback, J. Mechanisms of action of hematopoietic transcription factor PU.1 in initiation of T cell development. Front Immunol. 10, 228 (2019).
pubmed: 30842770 pmcid: 6391351
Shin, B. et al. Runx1 and Runx3 drive progenitor to T-lineage transcriptome conversion in mouse T cell commitment via dynamic genomic site switching. Proc. Natl Acad. Sci. USA https://doi.org/10.1073/pnas.2019655118 (2021).
Ungerback, J. et al. Pioneering, chromatin remodeling, and epigenetic constraint in early T cell gene regulation by SPI1 (PU.1). Genome Res. 28, 1508–1519 (2018).
pubmed: 30171019 pmcid: 6169891
Zhou, W., Gao, F., Romero-Wolf, M., Jo, S. & Rothenberg, E. V. Single-cell deletion analyses show control of pro-T cell developmental speed and pathways by Tcf7, Spi1, Gata3, Bcl11a, Erg, and Bcl11b. Sci. Immunol. 7, eabm1920 (2022).
pubmed: 35594339 pmcid: 9273332
Zhou, W. et al. Single-cell analysis reveals regulatory gene expression dynamics leading to lineage commitment in early T cell development. Cell Syst. 9, 321–337 (2019).
pubmed: 31629685 pmcid: 6932747
Schmitt, T. M. & Zuniga-Pflucker, J. C. T cell development, doing it in a dish. Immunol. Rev. 209, 95–102 (2006).
pubmed: 16448536
Schmitt, T. M. & Zuniga-Pflucker, J. C. Induction of T cell development from hematopoietic progenitor cells by delta-like-1 in vitro. Immunity 17, 749–756 (2002).
pubmed: 12479821
de Boer, J. et al. Transgenic mice with hematopoietic and lymphoid specific expression of Cre. Eur. J. Immunol. 33, 314–325 (2003).
pubmed: 12548562
Yang, Q. et al. TCF-1 upregulation identifies early innate lymphoid progenitors in the bone marrow. Nat. Immunol. 16, 1044–1050 (2015).
pubmed: 26280998 pmcid: 4575643
Weber, B. N. et al. A critical role for TCF-1 in T-lineage specification and differentiation. Nature 476, 63–68 (2011).
pubmed: 21814277 pmcid: 3156435
Yoshida, H. et al. The cis-regulatory atlas of the mouse immune system. Cell 176, 897–912 (2019).
pubmed: 30686579 pmcid: 6785993
Ling, K. W. et al. GATA-2 plays two functionally distinct roles during the ontogeny of hematopoietic stem cells. J. Exp. Med. 200, 871–882 (2004).
pubmed: 15466621 pmcid: 2213282
Li, Y. et al. GATA2 regulates mast cell identity and responsiveness to antigenic stimulation by promoting chromatin remodeling at super-enhancers. Nat. Commun. 12, 494 (2021).
pubmed: 33479210 pmcid: 7820599
Onodera, K. et al. GATA2 regulates dendritic cell differentiation. Blood 128, 508–518 (2016).
pubmed: 27259979 pmcid: 5026465
Tsai, F. Y. & Orkin, S. H. Transcription factor GATA-2 is required for proliferation/survival of early hematopoietic cells and mast cell formation, but not for erythroid and myeloid terminal differentiation. Blood 89, 3636–3643 (1997).
pubmed: 9160668
Jin, W. et al. Critical POU domain residues confer Oct4 uniqueness in somatic cell reprogramming. Sci. Rep. 6, 20818 (2016).
pubmed: 26877091 pmcid: 4753506
Boller, S. et al. Pioneering activity of the C-terminal domain of EBF1 shapes the chromatin landscape for B cell programming. Immunity 44, 527–541 (2016).
pubmed: 26982363
Wang, Y. et al. A prion-like domain in transcription factor EBF1 promotes phase separation and enables B cell programming of progenitor chromatin. Immunity 53, 1151–1167 (2020).
pubmed: 33159853
de Bruijn, M. F. & Speck, N. A. Core-binding factors in hematopoiesis and immune function. Oncogene 23, 4238–4248 (2004).
pubmed: 15156179
Xing, S. et al. Tle corepressors are differentially partitioned to instruct CD8
pubmed: 30045946 pmcid: 6080905
Hosokawa, H. et al. Transcription factor PU.1 represses and activates gene expression in early T cells by redirecting partner transcription factor binding. Immunity 48, 1119–1134 (2018).
pubmed: 29924977 pmcid: 6063530
Frederick, M. A. et al. A pioneer factor locally opens compacted chromatin to enable targeted ATP-dependent nucleosome remodeling. Nat. Struct. Mol. Biol. 30, 31–37 (2023).
pubmed: 36536103
Minderjahn, J. et al. Mechanisms governing the pioneering and redistribution capabilities of the non-classical pioneer PU.1. Nat. Commun. 11, 402 (2020).
pubmed: 31964861 pmcid: 6972792
Xue, B., Dunbrack, R. L., Williams, R. W., Dunker, A. K. & Uversky, V. N. PONDR-FIT: a meta-predictor of intrinsically disordered amino acids. Biochim. Biophys. Acta 1804, 996–1010 (2010).
pubmed: 20100603 pmcid: 2882806
Nguyen, D., Mayne, L., Phillips, M. C. & Walter Englander, S. Reference parameters for protein hydrogen exchange rates. J. Am. Soc. Mass. Spectrom. 29, 1936–1939 (2018).
pubmed: 30022340 pmcid: 6087487
Carleton, M. et al. Signals transduced by CD3ε, but not by surface pre-TCR complexes, are able to induce maturation of an early thymic lymphoma in vitro. J. Immunol. 163, 2576–2585 (1999).
pubmed: 10452996
Ogilvy, S. et al. Promoter elements of vav drive transgene expression in vivo throughout the hematopoietic compartment. Blood 94, 1855–1863 (1999).
pubmed: 10477714
Shimshek, D. R. et al. Codon-improved Cre recombinase (iCre) expression in the mouse. Genesis 32, 19–26 (2002).
pubmed: 11835670
Dou, Z. et al. Autophagy mediates degradation of nuclear lamina. Nature 527, 105–109 (2015).
pubmed: 26524528 pmcid: 4824414
Schindelin, J. et al. Fiji: an open-source platform for biological-image analysis. Nat. Methods 9, 676–682 (2012).
pubmed: 22743772
Aguilan, J. T., Kulej, K. & Sidoli, S. Guide for protein fold change and P value calculation for non-experts in proteomics. Mol. Omics 16, 573–582 (2020).
pubmed: 32968743
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).
pubmed: 24097267 pmcid: 3959825
Fasolino, M. et al. Genetic variation in type 1 diabetes reconfigures the 3D chromatin organization of T cells and alters gene expression. Immunity 52, 257–274 (2020).
pubmed: 32049053 pmcid: 7152927
Stirling, D. R. et al. CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics 22, 433 (2021).
pubmed: 34507520 pmcid: 8431850
Mayne, L. Hydrogen exchange mass spectrometry. Methods Enzymol. 566, 335–356 (2016).
pubmed: 26791986
Mayne, L. et al. Many overlapping peptides for protein hydrogen exchange experiments by the fragment separation-mass spectrometry method. J. Am. Soc. Mass. Spectrom. 22, 1898–1905 (2011).
pubmed: 21952777 pmcid: 3396559
Kan, Z. Y., Ye, X., Skinner, J. J., Mayne, L. & Englander, S. W. ExMS2: an integrated solution for hydrogen–deuterium exchange mass spectrometry data analysis. Anal. Chem. 91, 7474–7481 (2019).
pubmed: 31082210
Glasoe, P. K. & Long, F. A. Use of glass electrodes to measure acidities in deuterium oxide. J. Phys. Chem. 64, 188–190 (1960).

Auteurs

Naomi Goldman (N)

Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Aditi Chandra (A)

Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Isabelle Johnson (I)

Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Matthew A Sullivan (MA)

Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Graduate Group in Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Abhijeet R Patil (AR)

Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Ashley Vanderbeck (A)

Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Atishay Jay (A)

Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Department of Bioengineering, School of Engineering and Applied Sciences, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Yeqiao Zhou (Y)

Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Emily K Ferrari (EK)

Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Leland Mayne (L)

Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Jennifer Aguilan (J)

Department of Biochemistry, Albert Einstein School of Medicine, New York City, NY, USA.

Hai-Hui Xue (HH)

Center for Discovery and Innovation, Hackensack University Medical Center, Nutley, NJ, USA.
New Jersey Veterans Affairs Health Care System, East Orange, NJ, USA.

Robert B Faryabi (RB)

Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

E John Wherry (E)

Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Simone Sidoli (S)

Department of Biochemistry, Albert Einstein School of Medicine, New York City, NY, USA.

Ivan Maillard (I)

Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Division of Hematology-Oncology, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.
Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA.

Golnaz Vahedi (G)

Department of Genetics, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA. vahedi@pennmedicine.upenn.edu.
Institute for Immunology and Immune Health, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA. vahedi@pennmedicine.upenn.edu.
Epigenetics Institute, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA. vahedi@pennmedicine.upenn.edu.
Institute for Diabetes, Obesity and Metabolism, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA. vahedi@pennmedicine.upenn.edu.
Abramson Family Cancer Research Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Philadelphia, PA, USA. vahedi@pennmedicine.upenn.edu.

Articles similaires

Humans Receptors, Antigen, T-Cell Proto-Oncogene Proteins p21(ras) Pancreatic Neoplasms T-Lymphocytes

A key role for P2RX5 in brown adipocyte differentiation and energy homeostasis.

Maria Razzoli, Seth McGonigle, Bhavani Shankar Sahu et al.
1.00
Animals Adipocytes, Brown Mice Cell Differentiation Male
Triticum Transcription Factors Gene Expression Regulation, Plant Plant Proteins Salt Stress
Animals Humans Mice Neoplasms Tumor Microenvironment

Classifications MeSH