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Lineage-Determining Transcription Factor TCF-1 Initiates the Epigenetic Identity of T Cells
Open accessAbstract
T cell development is orchestrated by transcription factors that regulate the expression of genes initially buried within inaccessible chromatin, but the transcription factors that establish the regulatory landscape of the T cell lineage remain unknown. Profiling chromatin accessibility at eight stages of T cell development revealed the selective enrichment of TCF-1 at genomic regions that became accessible at the earliest stages of development. TCF-1 was further required for the accessibility of these regulatory elements and at the single-cell level, it dictated a coordinate opening of chromatin in T cells. TCF-1 expression in fibroblasts generated de novo chromatin accessibility even at chromatin regions with repressive marks, inducing the expression of T cell-restricted genes. These results indicate that a mechanism by which TCF-1 controls T cell fate is through its widespread ability to target silent chromatin and establish the epigenetic identity of T cells.
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“PU.1 recognition motifs are the most highly enriched of all defined motifs at sites that start out highly accessible in early pro-T cell stages, when PU.1 is present, and lose accessibility during commitment, i.e., as PU.1 levels decline (44, 85, 95).”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [95]
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Citations
Cites
R: A Language and Environment for Statistical Computing
R Core Team (2000) · doi:10.32614/r.manuals · Cited by 355,893
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
Love, M. I., Huber, W., & Anders, S. (2014) · Genome Biology · doi:10.1186/s13059-014-0550-8 · Cited by 95,106
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506580102 · Cited by 53,625
STAR: ultrafast universal RNA-seq aligner
Dobin, A., Davis, C. A., Schlesinger, F., Drenkow, J., Zaleski, C., Jha, S., Batut, P., Chaisson, M., & Gingeras, T. R. (2013) · Bioinformatics · doi:10.1093/bioinformatics/bts635 · Cited by 51,709
BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437
HTSeq—a Python framework to work with high-throughput sequencing data
Anders, S., Pyl, P. T., & Huber, W. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btu638 · Cited by 21,464
Model-based Analysis of ChIP-Seq (MACS)
Zhang, Y., Liu, T., Meyer, C. A., Eeckhoute, J., Johnson, D. S., Bernstein, B. E., Nusbaum, C., Myers, R. M., Brown, M., Li, W., et al. (2008) · Genome Biology · doi:10.1186/gb-2008-9-9-r137 · Cited by 18,386
Heinz, S., Benner, C., Spann, N., Bertolino, E., Lin, Y. C., Laslo, P., Cheng, J. X., Murre, C., Singh, H., & Glass, C. K. (2010) · Molecular Cell · doi:10.1016/j.molcel.2010.05.004 · Cited by 13,382
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y., & Greenleaf, W. J. (2013) · Nature Methods · doi:10.1038/nmeth.2688 · Cited by 6,422
FIMO: scanning for occurrences of a given motif
Grant, C. E., Bailey, T. L., & Noble, W. S. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr064 · Cited by 4,247
Single-cell chromatin accessibility reveals principles of regulatory variation
Buenrostro, J. D., Wu, B., Litzenburger, U. M., Ruff, D., Gonzales, M. L., Snyder, M. P., Chang, H. Y., & Greenleaf, W. J. (2015) · Nature · doi:10.1038/nature14590 · Cited by 2,308
Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy
Im, S. J., Hashimoto, M., Gerner, M. Y., Lee, J., Kissick, H. T., Burger, M. C., Shan, Q., Hale, J. S., Lee, J., Nasti, T. H., et al. (2016) · Nature · doi:10.1038/nature19330 · Cited by 2,070
The Immunological Genome Project: networks of gene expression in immune cells
The Immunological Genome Project Consortium, Heng, T. S. P., Painter, M. W., Elpek, K., Lukacs-Kornek, V., Mauermann, N., Turley, S. J., Koller, D., Kim, F. S., Wagers, A. J., et al. (2008) · Nature Immunology · doi:10.1038/ni1008-1091 · Cited by 1,864
chromVAR: inferring transcription-factor-associated accessibility from single-cell epigenomic data
Schep, A. N., Wu, B., Buenrostro, J. D., & Greenleaf, W. J. (2017) · Nature Methods · doi:10.1038/nmeth.4401 · Cited by 1,680
Pioneer transcription factors: establishing competence for gene expression
Zaret, K. S., & Carroll, J. S. (2011) · Genes & Development · doi:10.1101/gad.176826.111 · Cited by 1,589
Epigenetic stability of exhausted T cells limits durability of reinvigoration by PD-1 blockade
Pauken, K. E., Sammons, M. A., Odorizzi, P. M., Manne, S., Godec, J., Khan, O., Drake, A. M., Chen, Z., Sen, D. R., Kurachi, M., et al. (2016) · Science · doi:10.1126/science.aaf2807 · Cited by 1,348 · cited 2×
“, 2012) and CD8 T effector responses (Gray et al., 2017; Pauken et al., 2016; Yu et al., 2017), and reports on the dynamics of histone modifications during T cell development (Dose et al.”
BackgroundSelf-citationA Validated Regulatory Network for Th17 Cell Specification
Ciofani, M., Madar, A., Galan, C., Sellars, M., Mace, K., Pauli, F., Agarwal, A., Huang, W., Parkurst, C. N., Muratet, M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.09.016 · Cited by 1,160
Measuring reproducibility of high-throughput experiments
Li, Q., Brown, J. B., Huang, H., & Bickel, P. J. (2011) · The Annals of Applied Statistics · doi:10.1214/11-aoas466 · Cited by 1,032
Soufi, A., Donahue, G., & Zaret, K. S. (2012) · Cell · doi:10.1016/j.cell.2012.09.045 · Cited by 933
Measuring reproducibility of high-throughput experiments
Li, Q., Brown, J. B., Huang, H., & Bickel, P. J. (2010) · UC Berkeley · Cited by 915
The UCSC Genome Browser database: 2015 update
Rosenbloom, K. R., Armstrong, J. C., Barber, G. P., Casper, J., Clawson, H., Diekhans, M., Dreszer, T. R., Fujita, P. A., Guruvadoo, L., Haeussler, M., et al. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku1177 · Cited by 883
Pioneer Transcription Factors Target Partial DNA Motifs on Nucleosomes to Initiate Reprogramming
Soufi, A., Garcia, M. F., Jaroszewicz, A., Osman, N., Pellegrini, M., & Zaret, K. S. (2015) · Cell · doi:10.1016/j.cell.2015.03.017 · Cited by 780 · cited 4×
“The extent to which TCF-1 bound to nucleosome-occupied regions in fibroblasts was comparable to reprogramming transcription factors such as OCT4 (85%), SOX2 (80%), and KLF4 (65%) (Soufi et al., 2015).”
BackgroundInfluentialThe pCL vector system: rapid production of helper-free, high-titer, recombinant retroviruses
Naviaux, R. K., Costanzi, E., Haas, M., & Verma, I. M. (1996) · Journal of Virology · doi:10.1128/jvi.70.8.5701-5705.1996 · Cited by 735
Differentiation and persistence of memory CD8+ T cells depend on T cell factor 1
Zhou, X.-Y., Yu, S.-Y., Zhao, D.-M., Harty, J., Badovinac, V., & Xue, H.-H. (2010) · Immunity · doi:10.1016/j.immuni.2010.08.002 · Cited by 689
Ghisletti, S., Barozzi, I., Mietton, F., Polletti, S., De Santa, F., Venturini, E., Gregory, L., Lonie, L., Chew, A., Wei, C.-L., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.02.008 · Cited by 666
An HMG-box-containing T-cell factor required for thymocyte differentiation
Verbeek, S., Izon, D., Hofhuis, F., Robanus-Maandag, E., Riele, H. T., van de Watering, M., Oosterwegel, M., Wilson, A., Macdonald, H., & Clevers, H. (1995) · Nature · doi:10.1038/374070a0 · Cited by 585
Structural basis for DNA bending by the architectural transcription factor LEF-1
Love, J. J., Li, X., Case, D. A., Giese, K., Grosschedl, R., & Wright, P. E. (1995) · Nature · doi:10.1038/376791a0 · Cited by 573
Launching the T-cell-lineage developmental programme
Rothenberg, E. V., Moore, J. E., & Yui, M. A. (2007) · Nature reviews. Immunology · doi:10.1038/nri2232 · Cited by 514
Fundamentally Different Logic of Gene Regulation in Eukaryotes and Prokaryotes
Struhl, K. (1999) · Cell · doi:10.1016/s0092-8674(00)80599-1 · Cited by 486
H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs
Chen, J., Liu, H., Liu, J., Qi, J., Wei, B., Yang, J., Liang, H., Chen, Y., Chen, J., Wu, Y., et al. (2013) · Nature Genetics · doi:10.1038/ng.2491 · Cited by 462
Chromatin Higher Order Folding--Wrapping up Transcription
Horn, P. J., & Peterson, C. L. (2002) · Science · doi:10.1126/science.1074200 · Cited by 448
DNA Sequence-Dependent Compartmentalization and Silencing of Chromatin at the Nuclear Lamina
Zullo, J., Demarco, I. A., Piqué-Regi, R., Gaffney, D. J., Epstein, C. B., Spooner, C. J., Luperchio, T. R., Bernstein, B., Pritchard, J. K., Reddy, K. L., et al. (2012) · Cell · doi:10.1016/j.cell.2012.04.035 · Cited by 448
A critical role for TCF-1 in T-lineage specification and differentiation
Weber, B., Chi, A. W. S., Chavez, A., Yashiro–Ohtani, Y., Yang, Q., Shestova, O. E., & Bhandoola, A. (2011) · Nature · doi:10.1038/nature10279 · Cited by 433
Self-citationDANPOS: Dynamic analysis of nucleosome position and occupancy by sequencingPreprint
Chen, K.-F., Xi, Y., Pan, X.-W., Li, Z.-Y., Kaestner, K., Tyler, J. K., Dent, S., He, X.-W., & Li, W. (2013) · Genome Research · doi:10.1101/gr.142067.112 · Cited by 415
STATs Shape the Active Enhancer Landscape of T Cell Populations
Vahedi, G., Takahashi, H., Nakayamada, S., Sun, H., Sartorelli, V., Kanno, Y., & O’Shea, J. J. (2012) · Cell · doi:10.1016/j.cell.2012.09.044 · Cited by 380
Self-citationSchep, A. N., Buenrostro, J. D., Denny, S. K., Schwartz, K., Sherlock, G., & Greenleaf, W. J. (2015) · Genome Research · doi:10.1101/gr.192294.115 · Cited by 375
Super-enhancers delineate disease-associated regulatory nodes in T cells
Vahedi, G., Kanno, Y., Furumoto, Y., Jiang, K., Parker, S. C. J., Erdos, M. R., Davis, S. R., Roychoudhuri, R., Restifo, N. P., Gadina, M., et al. (2015) · Nature · doi:10.1038/nature14154 · Cited by 369
Self-citationZhang, J. A., Mortazavi, A., Williams, B. A., Wold, B. J., & Rothenberg, E. V. (2012) · Cell · doi:10.1016/j.cell.2012.01.056 · Cited by 337
Genome-wide Analyses of Transcription Factor GATA3-Mediated Gene Regulation in Distinct T Cell Types
Wei, G., Abraham, B. J., Yagi, R., Jothi, R., Cui, K., Sharma, S., Narlikar, L., Northrup, D. L., Tang, Q., Paul, W. E., et al. (2011) · Immunity · doi:10.1016/j.immuni.2011.08.007 · Cited by 337
Developmental Acquisition of Regulomes Underlies Innate Lymphoid Cell Functionality
Shih, H.-Y., Sciumè, G., Mikami, Y., Guo, L., Sun, H.-W., Brooks, S. R., Urban, J. F., Davis, F. P., Kanno, Y., & O’Shea, J. J. (2016) · Cell · doi:10.1016/j.cell.2016.04.029 · Cited by 334
Exhaustion-associated regulatory regions in CD8 + tumor-infiltrating T cells
Mognol, G. P., Spreafico, R., Wong, V., Scott-Browne, J. P., Togher, S., Hoffmann, A., Hogan, P. G., Rao, A., & Trifari, S. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620498114 · Cited by 324
Genome-wide nucleosome positioning during embryonic stem cell development
Teif, V. B., Vainshtein, Y., Caudron‐Herger, M., Mallm, J., Marth, C., Höfer, T., & Rippe, K. (2012) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2419 · Cited by 263
Epigenetic landscapes reveal transcription factors that regulate CD8+ T cell differentiation
Yu, B., Zhang, K., Milner, J. J., Toma, C., Chen, R., Scott-Browne, J. P., Pereira, R. M., Crotty, S., Chang, J. T., Pipkin, M. E., et al. (2017) · Nature Immunology · doi:10.1038/ni.3706 · Cited by 248
Gray, S. M., Amezquita, R. A., Guan, T., Kleinstein, S. H., & Kaech, S. M. (2017) · Immunity · doi:10.1016/j.immuni.2017.03.012 · Cited by 240
Tcf1 and Lef1 transcription factors establish CD8+ T cell identity through intrinsic HDAC activity
Xing, S., Li, F., Zeng, Z., Zhao, Y., Yu, S., Shan, Q., Li, Y., Phillips, F. C., Maina, P. K., Qi, H. H., et al. (2016) · Nature Immunology · doi:10.1038/ni.3456 · Cited by 226
T-cell factor 1 is a gatekeeper for T-cell specification in response to Notch signaling
Germar, K., Dose, M., Konstantinou, T., Zhang, J., Wang, H., Lobry, C., Arnett, K. L., Blacklow, S. C., Aifantis, I., Aster, J. C., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1110230108 · Cited by 225
Barozzi, I., Simonatto, M., Bonifacio, S., Yang, L., Rohs, R., Ghisletti, S., & Natoli, G. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.04.006 · Cited by 209
C/EBPα poises B cells for rapid reprogramming into induced pluripotent stem cells
Stefano, B. D., Sardina, J. L., van Oevelen, C. J. C., Collombet, S., Kallin, E. M., Vicent, G. P., Lü, J., Thieffry, D., Beato, M., & Graf, T. (2013) · Nature · doi:10.1038/nature12885 · Cited by 208
Creating reference gene annotation for the mouse C57BL6/J genome assembly
Mudge, J. M., & Harrow, J. (2015) · Mammalian Genome · doi:10.1007/s00335-015-9583-x · Cited by 173
Boller, S., Ramamoorthy, S., Akbas, D., Nechanitzky, R., Burger, L., Murr, R., Schübeler, D., & Grosschedl, R. (2016) · Immunity · doi:10.1016/j.immuni.2016.02.021 · Cited by 133
Divergent transcription is associated with promoters of transcriptional regulators
Lepoivre, C., Belhocine, M., Bergon, A., Griffon, A., Yammine, M., Vanhille, L., Cabeza, J. Z., Garibal, M., Koch, F., Maqbool, M. A., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-914 · Cited by 125
A far downstream enhancer for murine Bcl11b controls its T-cell specific expression
Li, L., Zhang, J. A., Dose, M., Kueh, H. Y., Mosadeghi, R., Gounari, F., & Rothenberg, E. V. (2013) · Blood · doi:10.1182/blood-2012-08-447839 · Cited by 115
β-Catenin induces T-cell transformation by promoting genomic instability
Dose, M., Emmanuel, A. O., Chaumeil, J., Zhang, J., Sun, T., Germar, K., Aghajani, K., Davis, E. M., Keerthivasan, S., Bredemeyer, A. L., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1315752111 · Cited by 63
Wöhrle, S., Wallmen, B., & Hecht, A. (2007) · Molecular and Cellular Biology · doi:10.1128/mcb.00555-07 · Cited by 56
Regulation of antigen receptor gene assembly by genetic–epigenetic crosstalk
Osipovich, O. A., & Oltz, E. M. (2010) · Seminars in Immunology · doi:10.1016/j.smim.2010.07.001 · Cited by 25
Oestreich, K. J., & Weinmann, A. S. (2011) · Current topics in microbiology and immunology · doi:10.1007/82_2011_141 · Cited by 14
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Khan, O., Giles, J. R., McDonald, S., Manne, S., Ngiow, S. F., Patel, K. P., Werner, M. T., Huang, A. C., Alexander, K. A., Wu, J. E., et al. (2019) · Nature · doi:10.1038/s41586-019-1325-x · Cited by 1,646
Self-citationSatpathy, A. T., Granja, J. M., Yost, K. E., Qi, Y., Meschi, F., McDermott, G. P., Olsen, B. N., Mumbach, M. R., Pierce, S. E., Corces, M. R., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0206-z · Cited by 980
Sexual-dimorphism in human immune system aging
Márquez, E. J., Chung, C.-H., Marches, R., Rossi, R. J., Nehar-Belaid, D., Eroglu, A., Mellert, D. J., Kuchel, G. A., Banchereau, J., & Ucar, D. (2020) · Nature Communications · doi:10.1038/s41467-020-14396-9 · Cited by 584
The emerging role of epigenetic therapeutics in immuno-oncology
Topper, M. J., Vaz, M., Marrone, K. A., Brahmer, J. R., & Baylin, S. B. (2020) · Nature Reviews Clinical Oncology · doi:10.1038/s41571-019-0266-5 · Cited by 433
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Zaret, K. S. (2020) · Annual Review of Genetics · doi:10.1146/annurev-genet-030220-015007 · Cited by 409
Metadata
- Authors
- Johnson, J. L., Georgakilas, G., Petrovic, J., Kurachi, M., Cai, S., Harly, C., Pear, W. S., Bhandoola, A., Wherry, E. J., & Vahedi, G.
- Affiliations
- University of Pennsylvania (US)
- National Institutes of Health (US)
- Corresponding author
- Vahedi, Golnaz
- ORCID
- Venue
- Immunity
- Publisher
- Elsevier BV
- Published
- 2018-02
- Volume
- 48
- Issue
- 2
- Pages
- 243-257.e10
- ISSN
- 1074-7613 (ISSN-L)
- PMC
- PMC5824646
- OpenAlex
- W2788726131
- Cited by
- 226
- References
- 57
- Citations by year
- 2026: 12 · 2025: 17 · 2024: 23 · 2023: 37 · 2022: 37 · 2021: 37 · 2020: 36 · 2019: 12 · 2018: 15
- FWCI
- 8.89
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Immunity (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- HAL (submittedVersion)
- Funders
- National Cancer Institute (P01CA119070, R01CA215518)
- National Institute of Allergy and Infectious Diseases (R01AI115712, R01AI047833, R01AI105343, K22AI112570, U19AI117950, P01AI112521, R21AI117718, U19AI082630, P01AI108545)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Immunology and Microbiology › Immunology › T-cell and B-cell Immunology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- TCF1, T cell development, chromatin accessibility, transcription factors, lineage determination, chromatin opening, T cell fate
- MeSH terms
- Animals, Chromatin, Fibroblasts, T-Lymphocytes, Transcription, Genetic, Cell Lineage, NIH 3T3 Cells, Chromatin Assembly and Disassembly, Mice, Hepatocyte Nuclear Factor 1-alpha, T Cell Transcription Factor 1, Epigenomics
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