Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity
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T cell development comprises a stepwise process of commitment from a multipotent precursor. To define molecular mechanisms controlling this progression, we probed five stages spanning the commitment process using RNA-seq and ChIP-seq to track genome-wide shifts in transcription, cohorts of active transcription factor genes, histone modifications at diverse classes of cis-regulatory elements, and binding repertoire of GATA-3 and PU.1, transcription factors with complementary roles in T cell development. The results highlight potential promoter-distal cis-regulatory elements in play and reveal both activation sites and diverse mechanisms of repression that silence genes used in alternative lineages. Histone marking is dynamic and reversible, and though permissive marks anticipate, repressive marks often lag behind changes in transcription. In vivo binding of PU.1 and GATA-3 relative to epigenetic marking reveals distinctive factor-specific rules for recruitment of these crucial transcription factors to different subsets of their potential sites, dependent on dose and developmental context.
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PU.1 binding sites and binding partners are not the same in early T-cell precursors as in myeloid cells or B lineage cells.
“PU.1 binding sites and PU.1 binding partners are not the same in early T-cell precursors as in myeloid cells or B lineage cells (13, 80, 84, 85)”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [84]
The Results section, “Early T-cell specific sites for PU.1: a positive role” (page not available), says PU.1 binding sites in early T-cell precursors differ from those reported in B cells and macrophages. It also reports different preferred sequence motifs, but does not establish that PU.1’s binding partners differ between those cell types. (LLM, conf=0.86)
Experimental — accuracy not yet measuredPU.1 occupancy of genomic sites declines as development proceeds, but is still detectable through T-lineage commitment at approximately 5,000 sites before disappearing.
“Although PU.1 occupancy of genomic sites declines as development proceeds, PU.1 occupancy is still detectable through T-lineage commitment at ~5,000 sites before disappearing (84).”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [84]
The Results section, “Early T-cell specific sites for PU.1: a positive role” (page unavailable), reports reduced PU.1 binding intensity in FLDN2b cells at T-lineage commitment and absence of PU.1 in later DP cells. It does not report approximately 5,000 occupied sites at commitment; the site count it gives is approximately 34,000 in DN T cells. (LLM, conf=0.88)
Experimental — accuracy not yet measuredAdditional factors probably collaborate with PU.1 to fine-tune the responses of Mef2c and Lmo2, because they are already declining by the end of ETP stage, multiple cell cycles before DN2b stage when PU.1 itself declines.
“Additional factors also probably collaborate with PU.1 to fine-tune the responses of Mef2c and Lmo2, for they are already declining by the end of ETP stage, multiple cell cycles before DN2b stage when PU.1 itself declines (65, 67, 84, 121, 124) (Figure 8A).”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [84]
The Results section on transcription-factor expression dynamics reports that Mef2c, Lmo2, and Sfpi1 (PU.1) decrease between FLDN1 and FLDN2b. The Results section on early T-cell-specific PU.1 sites says PU.1 is markedly downregulated at DN2b, and the binding-dynamics section suggests PU.1 can act through combinations of binding complexes. Our copy does not establish that Mef2c and Lmo2 begin declining by the end of ETP, multiple cell cycles before PU.1, or that other factors specifically collaborate with PU.1 to regulate those two genes. (LLM, conf=0.83)
Experimental — accuracy not yet measuredPU.1 binds to more than 30,000 genomic sites in early T-cell precursors at the earliest stages.
“PU.1 was found binding to >30,000 genomic sites in these cells at the earliest stages (84)”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [84]
Endogenous, naturally expressed PU.1 is a prominent actor across the genome in T-cell precursors before commitment.
“With the advent of ChIP-seq data, though, it was confirmed that endogenous, naturally expressed PU.1 is indeed a prominent actor across the genome in T-cell precursors before commitment.”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [84]
PU.1 appears to be excluded from genomic regions packaged in Polycomb Repressive Complex 2-modified chromatin, marked by H3K27me3.
“Notably, PU.1 appears to be excluded from genomic regions that are packaged in Polycomb Repressive Complex 2-modified chromatin, as marked by trimethylation of Histone H3 Lysine 27 (H3K27me3) (84).”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [84]
The progression of cells through T-cell commitment involves the ordered downregulation of a substantial set of progenitor-specific Phase 1 transcription factors concomitant with the upregulation of T-lineage affiliated factors.
“It has become clear that the progression of cells through T-cell commitment involves the ordered downregulation of a substantial set of progenitor-specific transcription factors, called “Phase 1” factors in this context, concomitant with the upregulation of T-lineage affiliated factors (34, 65, 84, 121, 122).”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [84]
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Cites
Mapping and quantifying mammalian transcriptomes by RNA-Seq
Mortazavi, A., Williams, B. A., McCue, K., Schaeffer, L., & Wold, B. (2008) · Nature Methods · doi:10.1038/nmeth.1226 · Cited by 13,696 · see citing works
Self-citationHeinz, 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 · see citing works
Chromatin modifications and their function
Kouzarides, T. (2007) · Cell · doi:10.1016/j.cell.2007.02.005 · Cited by 10,883 · see citing works
High-Resolution Profiling of Histone Methylations in the Human Genome
Barski, A., Cuddapah, S., Cui, K., Roh, T.-Y., Schones, D. E., Wang, Z., Wei, G., Chepelev, I., & Zhao, K. (2007) · Cell · doi:10.1016/j.cell.2007.05.009 · Cited by 6,845 · see citing works
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data
Wang, L., Feng, Z., Wang, X., Wang, X., & Zhang, X. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp612 · Cited by 4,553 · see citing works
Heintzman, N. D., Stuart, R. K., Hon, G., Fu, Y., Ching, C. W., Hawkins, R. D., Barrera, L. O., Van Calcar, S., Qu, C., Ching, K. A., et al. (2007) · Nature Genetics · doi:10.1038/ng1966 · Cited by 3,398 · cited 2× · see citing works
“…activation at transcriptional start sites (TSSs), H3K27me3 is used in one mechanism for transcriptional silencing, and H3K4me2 is associated with activation, poising for activation or repression, or repression (Orford et al., 2008; Barski et al., 2007; Johnson et al., 2007; Heintzman et al., 2007).”
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
Johnson, D. S., Mortazavi, A., Myers, R. M., & Wold, B. (2007) · Science · doi:10.1126/science.1141319 · Cited by 2,927 · see citing works
Self-citationThe 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 · see citing works
Wei, G., Wei, L., Zhu, J., Zang, C., Hu-Li, J., Yao, Z., Cui, K., Kanno, Y., Roh, T.-Y., Watford, W. T., et al. (2009) · Immunity · doi:10.1016/j.immuni.2008.12.009 · Cited by 1,152 · see citing works
Systematic Protein Location Mapping Reveals Five Principal Chromatin Types in Drosophila Cells
Filion, G. J. P., van Bemmel, J. G., Braunschweig, U., Talhout, W., Kind, J., Ward, L. D., Brugman, W., de Castro, I. J., Kerkhoven, R. M., Bussemaker, H. J., et al. (2010) · Cell · doi:10.1016/j.cell.2010.09.009 · Cited by 963 · see citing works
Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis
Novershtern, N., Subramanian, A., Lawton, L. N., Mak, R. H., Haining, W. N., McConkey, M. E., Habib, N., Yosef, N., Chang, C. Y., Shay, T., et al. (2011) · Cell · doi:10.1016/j.cell.2011.01.004 · Cited by 942 · see citing works
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 · see citing works
Comprehensive methylome map of lineage commitment from haematopoietic progenitors
Ji, H., Ehrlich, L. I. R., Seita, J., Murakami, P. N., Doi, A., Lindau, P., Lee, H.-J., Aryee, M. J., Irizarry, R. A., Kim, K., et al. (2010) · Nature · doi:10.1038/nature09367 · Cited by 636 · see citing works
Computation for ChIP-seq and RNA-seq studies
Pepke, S., Wold, B. J., & Mortazavi, A. (2009) · Nature Methods · doi:10.1038/nmeth.1371 · Cited by 553 · see citing works
Self-citationWetering, M., Oosterwegel, M., Dooijes, D., & Clevers, H. (1991) · EMBO Journal · doi:10.1002/j.1460-2075.1991.tb07928.x · Cited by 546 · see citing works
Lin, Y. C., Jhunjhunwala, S., Benner, C. W., Heinz, S., Welinder, E., Månsson, R., Sigvardsson, M., Hagman, J. R., Espinoza, C. A., Dutkowski, J., et al. (2010) · Nature Immunology · doi:10.1038/ni.1891 · Cited by 502 · see citing works
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 475 · see citing works
Self-citationReprogramming Factor Expression Initiates Widespread Targeted Chromatin Remodeling
Koche, R. P., Smith, Z. D., Adli, M., Gu, H., Ku, M., Gnirke, A., Bernstein, B., & Meissner, A. (2011) · Cell stem cell · doi:10.1016/j.stem.2010.12.001 · Cited by 367 · see citing works
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 · see citing works
PU.1 Regulates Expression of the Interleukin-7 Receptor in Lymphoid Progenitors
DeKoter, R. P., Lee, H.-J., & Singh, H. (2002) · Immunity · doi:10.1016/s1074-7613(02)00269-8 · Cited by 319 · see citing works
Schebesta, A., McManus, S., Salvagiotto, G., Delogu, A., Busslinger, G. A., & Busslinger, M. (2007) · Immunity · doi:10.1016/j.immuni.2007.05.019 · Cited by 306 · see citing works
Rosenbauer, F., Owens, B. M., Yu, L., Tumang, J. R., Steidl, U., Kutok, J. L., Clayton, L. K., Wagner, K., Scheller, M., Iwasaki, H., et al. (2006) · Nature Genetics · doi:10.1038/ng1679 · Cited by 237 · see citing works
The Lmo2 Oncogene Initiates Leukemia in Mice by Inducing Thymocyte Self-Renewal
McCormack, M. P., Young, L. F., Vasudevan, S., de Graaf, C. A., Codrington, R., Rabbitts, T. H., Jane, S. M., & Curtis, D. J. (2010) · Science · doi:10.1126/science.1182378 · Cited by 231 · see citing works
Maintaining Cell Identity through Global Control of Genomic Organization
Natoli, G. (2010) · Immunity · doi:10.1016/j.immuni.2010.07.006 · Cited by 199 · see citing works
Taghon, T., Yui, M. A., & Rothenberg, E. V. (2007) · Nature Immunology · doi:10.1038/ni1486 · Cited by 195 · see citing works
Self-citationDecker, T., di Magliano, M. P., McManus, S., Sun, Q., Bonifer, C., Tagoh, H., & Busslinger, M. (2009) · Immunity · doi:10.1016/j.immuni.2009.01.012 · Cited by 194 · see citing works
From the cradle to the grave: activities of GATA‐3 throughout T‐cell development and differentiation
Hosoya, T., Maillard, I. P., & Engel, J. D. (2010) · Immunological Reviews · doi:10.1111/j.1600-065x.2010.00954.x · Cited by 157 · see citing works
Differential H3K4 Methylation Identifies Developmentally Poised Hematopoietic Genes
Orford, K. W., Kharchenko, P. V., Lai, W. R., Dao, M. C., Worhunsky, D. J., Ferro, A., Janzen, V., Park, P. J., & Scadden, D. T. (2008) · Developmental Cell · doi:10.1016/j.devcel.2008.04.002 · Cited by 154 · see citing works
GATA-3 is required for early T lineage progenitor development
Hosoya, T., Kuroha, T., Moriguchi, T., Cummings, D. R., Maillard, I. P., Lim, K.-C., & Engel, J. D. (2009) · The Journal of Experimental Medicine · doi:10.1084/jem.20090934 · Cited by 154 · see citing works
Delayed, asynchronous, and reversible T-lineage specification induced by Notch/Delta signalingPreprint
Taghon, T., David‐Fung, E., Zúñiga‐Pflücker, J. C., & Rothenberg, E. V. (2005) · Genes & Development · doi:10.1101/gad.1298305 · Cited by 154 · see citing works
Self-citationFine-Scale Staging of T Cell Lineage Commitment in Adult Mouse Thymus
Yui, M. A., Feng, N., & Rothenberg, E. V. (2010) · The Journal of Immunology · doi:10.4049/jimmunol.1000679 · Cited by 152 · see citing works
Self-citationGA binding protein regulates interleukin 7 receptor α-chain gene expression in T cells
Xue, H., Bollenbacher, J., Rovella, V., Tripuraneni, R., Du, Y., Liu, C., Williams, A., McCoy, J. P., & Leonard, W. J. (2004) · Nature Immunology · doi:10.1038/ni1117 · Cited by 140 · see citing works
Yang, Q., Bell, J. J., & Bhandoola, A. (2010) · Immunological Reviews · doi:10.1111/j.1600-065x.2010.00956.x · Cited by 116 · see citing works
Notch/Delta signaling constrains reengineering of pro-T cells by PU.1
Franco, C. B., Scripture-Adams, D. D., Proekt, I., Taghon, T., Weiss, A. H., Yui, M. A., Adams, S. L., Diamond, R. A., & Rothenberg, E. V. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601188103 · Cited by 109 · see citing works
Self-citationHeinzel, K., Benz, C., Martins, V. C., Haidl, I. D., & Bleul, C. C. (2007) · The Journal of Immunology · doi:10.4049/jimmunol.178.2.858 · Cited by 99 · see citing works
T Cell Lineage Commitment: Identity and Renunciation
Rothenberg, E. V. (2011) · The Journal of Immunology · doi:10.4049/jimmunol.1003703 · Cited by 90 · see citing works
Self-citationArco, P. G., Kashiwagi, M., Jackson, A. F., Naito, T., Zhang, J., Liu, F., Kee, B. L., Vooijs, M., Radtke, F., Redondo, J. M., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.11.008 · Cited by 89 · see citing works
Self-citationYannoutsos, N., Barreto, V. M., Misulovin, Z., Gazumyan, A., Yu, W., Rajewsky, N., Peixoto, B. R., Eisenreich, T., & Nussenzweig, M. C. (2004) · Nature Immunology · doi:10.1038/ni1053 · Cited by 87 · see citing works
Donaldson, I. J., Chapman, M., Kinston, S., Landry, J., Knezevic, K., Piltz, S., Buckley, N. J., Green, A. R., & Göttgens, B. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi056 · Cited by 78 · see citing works
Georgopoulos, K., van den Elsen, P. J., Bier, E., Maxam, A. M., & Terhorst, C. (1988) · The EMBO Journal · doi:10.1002/j.1460-2075.1988.tb03085.x · Cited by 78 · see citing works
T Cell Lineage Determination Precedes the Initiation of <i>TCR</i> β Gene Rearrangement
Masuda, K., Kakugawa, K., Nakayama, T., Minato, N., Katsura, Y., & Kawamoto, H. (2007) · The Journal of Immunology · doi:10.4049/jimmunol.179.6.3699 · Cited by 77 · see citing works
Transcription factor expression dynamics of early T-lymphocyte specification and commitment
David‐Fung, E., Butler, R. R., Buzi, G., Yui, M. A., Diamond, R. A., Anderson, M. K., Rowen, L., & Rothenberg, E. V. (2008) · Developmental Biology · doi:10.1016/j.ydbio.2008.10.021 · Cited by 68 · see citing works
Self-citationProgression of regulatory gene expression states in fetal and adult pro-T-cell development
David‐Fung, E., Yui, M. A., Morales, M., Wang, H., Taghon, T., Diamond, R. A., & Rothenberg, E. V. (2006) · Immunological Reviews · doi:10.1111/j.0105-2896.2006.00355.x · Cited by 60 · see citing works
Self-citationZarnegar, M. A., Chen, J., & Rothenberg, E. V. (2010) · Molecular and Cellular Biology · doi:10.1128/mcb.00354-10 · Cited by 52 · see citing works
Self-citationCompetition and collaboration: GATA-3, PU.1, and Notch signaling in early T-cell fate determination
Rothenberg, E. V., & Scripture-Adams, D. D. (2008) · Seminars in Immunology · doi:10.1016/j.smim.2008.07.006 · Cited by 43 · see citing works
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Sorted by citations
Chromatin states define tumour-specific T cell dysfunction and reprogramming
Philip, M., Fairchild, L., Sun, L., Horste, E. L., Camara, S., Shakiba, M., Scott, A. C., Viale, A., Lauer, P., Merghoub, T., et al. (2017) · Nature · doi:10.1038/nature22367 · Cited by 933 · see citing works
Dynamic and Coordinated Epigenetic Regulation of Developmental Transitions in the Cardiac Lineage
Wamstad, J. A., Alexander, J. M., Truty, R., Shrikumar, A., Li, F., Eilertson, K. E., Ding, H., Wylie, J. N., Pico, A. R., Capra, J. A., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.035 · Cited by 603 · see citing works
Absence of a simple code: how transcription factors read the genome
Slattery, M., Zhou, T., Yang, L., Dantas Machado, A. C., Gordân, R., & Rohs, R. (2014) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2014.07.002 · Cited by 537 · see citing works
Transcriptional and Epigenetic Dynamics during Specification of Human Embryonic Stem Cells
Gifford, C. A., Ziller, M. J., Gu, H., Trapnell, C., Donaghey, J., Tsankov, A., Shalek, A. K., Kelley, D. R., Shishkin, A. A., Issner, R., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.037 · Cited by 435 · see citing works
CD4 + T-cell subsets in inflammatory diseases: beyond the T h 1/T h 2 paradigm
Hirahara, K., & Nakayama, T. (2016) · International Immunology · doi:10.1093/intimm/dxw006 · Cited by 417 · see citing works
Amit, I., Winter, D. R., & Jung, S. (2015) · Nature Immunology · doi:10.1038/ni.3325 · Cited by 406 · see citing works
Shi, W., Liao, Y., Willis, S. N., Taubenheim, N., Inouye, M., Tarlinton, D. M., Smyth, G. K., Hodgkin, P. D., Nutt, S. L., & Corcoran, L. M. (2015) · Nature Immunology · doi:10.1038/ni.3154 · Cited by 381 · see citing works
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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 365 · see citing works
Seitan, V. C., Faure, A. J., Zhan, Y., McCord, R. P., Lajoie, B. R., Ing-Simmons, E., Lenhard, B., Giorgetti, L., Heard, E., Fisher, A. G., et al. (2013) · Genome Research · doi:10.1101/gr.161620.113 · Cited by 318 · see citing works
Developmental gene networks: a triathlon on the course to T cell identity
Yui, M. A., & Rothenberg, E. V. (2014) · Nature Reviews Immunology · doi:10.1038/nri3702 · Cited by 342 · see citing works
Self-citationEpigenetic modulation of antitumor immunity for improved cancer immunotherapy
Dai, E., Zhu, Z., Wahed, S., Qu, Z., Storkus, W. J., & Guo, Z. S. (2021) · Molecular Cancer · doi:10.1186/s12943-021-01464-x · Cited by 332 · see citing works
Isoda, T., Moore, A. J., He, Z., Chandra, V. K., Aida, M., Denholtz, M., van Hamburg, J. P., Fisch, K. M., Chang, A. N., Fahl, S. P., et al. (2017) · Cell · doi:10.1016/j.cell.2017.09.001 · Cited by 311 · see citing works
Positive Feedback Between PU.1 and the Cell Cycle Controls Myeloid Differentiation
Kueh, H. Y., Champhekar, A., Nutt, S. L., Elowitz, M. B., & Rothenberg, E. V. (2013) · Science · doi:10.1126/science.1240831 · Cited by 273 · see citing works
Self-citationEpigenetic Regulation of Pluripotency and Differentiation
Boland, M. J., Nazor, K. L., & Loring, J. F. (2014) · Circulation Research · doi:10.1161/circresaha.115.301517 · Cited by 266 · see citing works
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Mingueneau, M., Kreslavsky, T., Gray, D. H. D., Heng, T. S. P., Cruse, R., Ericson, J., Bendall, S. C., Spitzer, M. H., Nolan, G. P., Kobayashi, K. S., et al. (2013) · Nature Immunology · doi:10.1038/ni.2590 · Cited by 267 · see citing works
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Tindemans, I., Serafini, N., Santo, J. P. D., & Hendriks, R. W. (2014) · Immunity · doi:10.1016/j.immuni.2014.06.006 · Cited by 258 · see citing works
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Wan, Y. Y. (2014) · Trends in Immunology · doi:10.1016/j.it.2014.04.002 · Cited by 248 · see citing works
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Hosokawa, H., & Rothenberg, E. V. (2020) · Nature reviews. Immunology · doi:10.1038/s41577-020-00426-6 · Cited by 239 · see citing works
Self-citationGray, 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 245 · see citing works
Laurenti, E., Doulatov, S. R., Zandi, S., Plumb, I., Chen, J., April, C., Fan, J., & Dick, J. E. (2013) · Nature Immunology · doi:10.1038/ni.2615 · Cited by 224 · see citing works
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Self-citationWolterink, R. G. J. K., Serafini, N., van Nimwegen, M., Vosshenrich, C. A. J., de Bruijn, M. J. W., Fonseca‐Pereira, D., Veiga‐Fernandes, H., Hendriks, R. W., & Santo, J. P. D. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1217158110 · Cited by 226 · see citing works
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Johnson, J. L., Georgakilas, G., Petrovic, J., Kurachi, M., Cai, S., Harly, C., Pear, W. S., Bhandoola, A., Wherry, E. J., & Vahedi, G. (2018) · Immunity · doi:10.1016/j.immuni.2018.01.012 · Cited by 226 · see citing works
Russ, B. E., Olshanksy, M., Smallwood, H. S., Li, J., Denton, A. E., Prier, J. E., Stock, A. T., McQuilten, H. A., Cullen, J. G., Nguyen, M. L. T., et al. (2014) · Immunity · doi:10.1016/j.immuni.2014.11.001 · Cited by 222 · see citing works
de la Rica, L., Rodríguez-Ubreva, J., García, M., Islam, A. B., Urquiza, J. M., Hernando, H., Christensen, J., Helin, K., Gómez-Vaquero, C., & Ballestar, E. (2013) · Genome Biology · doi:10.1186/gb-2013-14-9-r99 · Cited by 211 · see citing works
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 · see citing works
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DeVorkin, L., Pavey, N., Carleton, G., Comber, A., Ho, C., Lim, J., McNamara, E., Huang, H., Kim, P., Zacharias, L. G., et al. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.03.037 · Cited by 185 · see citing works
Circadian Entrainment Triggers Maturation of Human In Vitro Islets
Alvarez-Dominguez, J. R., Donaghey, J., Rasouli, N., Kenty, J. H. R., Helman, A., Charlton, J., Straubhaar, J. R., Meissner, A., & Melton, D. A. (2020) · Cell Stem Cell · doi:10.1016/j.stem.2019.11.011 · Cited by 189 · see citing works
Enhancer Hijacking Drives Oncogenic BCL11B Expression in Lineage-Ambiguous Stem Cell Leukemia
Montefiori, L. E., Bendig, S., Gu, Z., Chen, X., Pölönen, P., Ma, X., Murison, A., Zeng, A. G. X., García‐Prat, L., Dickerson, K. M., et al. (2021) · Cancer Discovery · doi:10.1158/2159-8290.cd-21-0145 · Cited by 178 · see citing works
Self-citationThe Regulation of IL-10 Expression
Gabryšová, L., Howes, A., Saraiva, M., & O’Garra, A. (2014) · Current topics in microbiology and immunology · doi:10.1007/978-3-662-43492-5_8 · Cited by 181 · see citing works
Seumois, G., Chávez, L., Gerasimova, A. V., Lienhard, M., Omran, N., Kalinke, L., Vedanayagam, M., Ganesan, A. P. V., Chawla, A., Djukanović, R., et al. (2014) · Nature Immunology · doi:10.1038/ni.2937 · Cited by 172 · see citing works
Dissecting the dynamic changes of 5-hydroxymethylcytosine in T-cell development and differentiation
Tsagaratou, A., Äijö, T., Lio, C. J., Yue, X., Huang, Y., Jacobsen, S. E., Lähdesmäki, H. J., & Rao, A. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1412327111 · Cited by 172 · see citing works
Expression and regulation of C/EBPα in normal myelopoiesis and in malignant transformation
Avellino, R., & Delwel, R. (2017) · Blood · doi:10.1182/blood-2016-09-687822 · Cited by 165 · see citing works
Spatial enhancer clustering and regulation of enhancer-proximal genes by cohesin
Ing-Simmons, E., Seitan, V. C., Faure, A. J., Flicek, P., Carroll, T., Dekker, J., Fisher, A. G., Lenhard, B., & Merkenschlager, M. (2015) · Genome Research · doi:10.1101/gr.184986.114 · Cited by 167 · see citing works
Transcriptional Regulation of Innate and Adaptive Lymphocyte Lineages
Obaldia, M. E. D., & Bhandoola, A. (2015) · Annual Review of Immunology · doi:10.1146/annurev-immunol-032414-112032 · Cited by 163 · see citing works
Mechanisms underlying helper T-cell plasticity: Implications for immune-mediated disease
Hirahara, K., Poholek, A. C., Vahedi, G., Laurence, A. D. J., Kanno, Y., Milner, J. D., & O’Shea, J. J. (2013) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2013.03.015 · Cited by 162 · see citing works
Epigenomic profiling of primary gastric adenocarcinoma reveals super-enhancer heterogeneity
Ooi, W. F., Xing, M., Xu, C., Yao, X., Ramlee, M. K., Lim, M. C., Cao, F., Lim, K. J., Babu, D., Poon, L.-F., et al. (2016) · Nature Communications · doi:10.1038/ncomms12983 · Cited by 146 · see citing works
Wu, H., Whitfield, T. W., Gordon, J. A. R., Dobson, J. R., Tai, P. W. L., van Wijnen, A. J., Stein, J. L., Stein, G. S., & Lian, J. B. (2014) · Genome biology · doi:10.1186/gb-2014-15-3-r52 · Cited by 146 · see citing works
Unifying immunology with informatics and multiscale biology
Kidd, B. A., Peters, L. A., Schadt, E. E., & Dudley, J. T. (2014) · Nature Immunology · doi:10.1038/ni.2787 · Cited by 142 · see citing works
Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment
Kueh, H. Y., Yui, M. A., Ng, K. K. H., Pease, S., Zhang, J. A., Damle, S. S., Freedman, G., Siu, S., Bernstein, I. D., Elowitz, M. B., et al. (2016) · Nature Immunology · doi:10.1038/ni.3514 · Cited by 134 · see citing works
Self-citationRecurrent SPI1 (PU.1) fusions in high-risk pediatric T cell acute lymphoblastic leukemia
Seki, M., Kimura, S., Isobe, T., Yoshida, K., Ueno, H., Nakajima-Takagi, Y., Wang, C., Lin, L., Kon, A., Suzuki, H., et al. (2017) · Nature Genetics · doi:10.1038/ng.3900 · Cited by 138 · see citing works
Mansour, M. R., Sanda, T., Lawton, L. N., Li, X., Kreslavsky, T., Novina, C. D., Brand, M., Gutiérrez, A., Kelliher, M. A., Jamieson, C. H. M., et al. (2013) · The Journal of Experimental Medicine · doi:10.1084/jem.20122516 · Cited by 135 · see citing works
Hosokawa, H., Ungerbäck, J., Wang, X., Matsumoto, M., Nakayama, K. I., Cohen, S. M., Tanaka, T., & Rothenberg, E. V. (2018) · Immunity · doi:10.1016/j.immuni.2018.04.024 · Cited by 116 · see citing works
Self-citationDevelopment of invariant natural killer T cells
Gapin, L. (2016) · Current Opinion in Immunology · doi:10.1016/j.coi.2016.01.001 · Cited by 124 · see citing works
Invariant Natural Killer T Cell Subsets—More Than Just Developmental Intermediates
Krovi, S. H., & Gapin, L. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.01393 · Cited by 119 · see citing works
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 · see citing works
Self-citationHistone H3 Lysine 27 demethylases Jmjd3 and Utx are required for T-cell differentiation
Manna, S., Kim, J. K., Baugé, C., Cam, M. C., Zhao, Y., Shetty, J., Vacchio, M. S., Castro, E., Tran, B. Q., Tessarollo, L., et al. (2015) · Nature Communications · doi:10.1038/ncomms9152 · Cited by 113 · see citing works
Dynamic Gene Regulatory Networks of Human Myeloid Differentiation
Ramírez, R. N., El-Ali, N. C., Mager, M. A., Wyman, D., Conesa, A., & Mortazavi, A. (2017) · Cell Systems · doi:10.1016/j.cels.2017.03.005 · Cited by 114 · see citing works
Self-citationDivergent 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 111 · see citing works
Lun, A. T. L., & Smyth, G. K. (2014) · Nucleic Acids Research · doi:10.1093/nar/gku351 · Cited by 113 · see citing works
Mechanisms of in vivo binding site selection of the hematopoietic master transcription factor PU.1
Pham, T.-H., Minderjahn, J., Schmidl, C., Hoffmeister, H., Schmidhofer, S., Chen, W., Längst, G., Benner, C., & Rehli, M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt355 · Cited by 102 · see citing works
Helper T‐cell identity and evolution of differential transcriptomes and epigenomes
Vahedi, G., Poholek, A. C., Hand, T. W., Laurence, A. D. J., Kanno, Y., O’Shea, J. J., & Hirahara, K. (2013) · Immunological Reviews · doi:10.1111/imr.12037 · Cited by 109 · see citing works
Huijskens, M. J. A. J., Walczak, M., Koller, N., Briedé, J. J., Senden-Gijsbers, B. L. M. G., Schnijderberg, M. C. A., Bos, G. M. J., & Germeraad, W. T. V. (2014) · Journal of Leukocyte Biology · doi:10.1189/jlb.1ta0214-121rr · Cited by 109 · see citing works
Zhou, W., Yui, M. A., Williams, B. A., Yun, J., Wold, B. J., Cai, L., & Rothenberg, E. V. (2019) · Cell Systems · doi:10.1016/j.cels.2019.09.008 · Cited by 100 · see citing works
Self-citationGATA-3 promotes T-cell specification by repressing B-cell potential in pro–T cells in mice
García‐Ojeda, M. E., Wolterink, R. G. J. K., Lemaı̂tre, F., Goff, O. R.-L., Hasan, M., Hendriks, R. W., Cumano, A., & Santo, J. P. D. (2013) · Blood · doi:10.1182/blood-2012-06-440065 · Cited by 105 · see citing works
Obaldia, M. E. D., Bell, J. J., Wang, X., Harly, C., Yashiro–Ohtani, Y., DeLong, J. H., Zlotoff, D. A., Sultana, D. A., Pear, W. S., & Bhandoola, A. (2013) · Nature Immunology · doi:10.1038/ni.2760 · Cited by 101 · see citing works
Next-Generation Sequencing in Acute Lymphoblastic Leukemia
Coccaro, N., Anelli, L., Zagaria, A., Specchia, G., & Albano, F. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20122929 · Cited by 99 · see citing works
Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development
Rothenberg, E. V., Hosokawa, H., & Ungerbäck, J. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.00228 · Cited by 99 · see citing works
Self-citationArchitecture of a lymphomyeloid developmental switch controlled by PU.1, Notch and Gata3
Del Real, M. M., & Rothenberg, E. V. (2013) · Development · doi:10.1242/dev.088559 · Cited by 95 · see citing works
Self-citationThe RUNX1–PU.1 axis in the control of hematopoiesis
Imperato, M. R., Cauchy, P., Obier, N., & Bonifer, C. (2015) · International Journal of Hematology · doi:10.1007/s12185-015-1762-8 · Cited by 94 · see citing works
Hawkins, R. D., Larjo, A., Tripathi, S. K., Wagner, U., Luu, Y., Lönnberg, T., Raghav, S. K., Lee, L. K., Lund, R., Ren, B., et al. (2013) · Immunity · doi:10.1016/j.immuni.2013.05.011 · Cited by 89 · see citing works
The RNA Pol II Elongation Factor Ell3 Marks Enhancers in ES Cells and Primes Future Gene Activation
Lin, C., Garruss, A. S., Luo, Z., Guo, F., & Shilatifard, A. (2012) · Cell · doi:10.1016/j.cell.2012.12.015 · Cited by 92 · see citing works
Epigenetic regulation of T‐helper cell differentiation, memory, and plasticity in allergic asthma
Tumes, D. J., Papadopoulos, M., Endo, Y., Onodera, A., Hirahara, K., & Nakayama, T. (2017) · Immunological Reviews · doi:10.1111/imr.12560 · Cited by 90 · see citing works
Bcl11b and combinatorial resolution of cell fate in the T-cell gene regulatory network
Longabaugh, W. J. R., Zeng, W., Zhang, J. A., Hosokawa, H., Jansen, C. S., Li, L., Romero-Wolf, M., Liu, P., Kueh, H. Y., Mortazavi, A., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1610617114 · Cited by 89 · see citing works
Self-citationTranscription factor interplay in T helper cell differentiation
Evans, C. M., & Jenner, R. G. (2013) · Briefings in Functional Genomics · doi:10.1093/bfgp/elt025 · Cited by 91 · see citing works
RORα is a critical checkpoint for T cell and ILC2 commitment in the embryonic thymus
Ferreira, A. C. F., Szeto, A. C. H., Heycock, M. W. D., Clark, P. A., Walker, J. A., Crisp, A., Barlow, J. L., Kitching, S., Lim, A., Gogoi, M., et al. (2021) · Nature Immunology · doi:10.1038/s41590-020-00833-w · Cited by 86 · see citing works
From thymus to periphery: Molecular basis of effector γδ‐T cell differentiation
Fiala, G. J., Gomes, A. Q., & Silva‐Santos, B. (2020) · Immunological Reviews · doi:10.1111/imr.12918 · Cited by 82 · see citing works
Ikaros mediates gene silencing in T cells through Polycomb repressive complex 2
Oravecz, A., Apostolov, A., Polak, K., Jost, B., Gras, S. L., Chan, S. H., & Kastner, P. (2015) · Nature Communications · doi:10.1038/ncomms9823 · Cited by 80 · see citing works
Regulatory network control of blood stem cells
Göttgens, B. (2015) · Blood · doi:10.1182/blood-2014-08-570226 · Cited by 82 · see citing works
From thymus to tissues and tumors: A review of T-cell biology
Chopp, L. B., Redmond, C., O’Shea, J. J., & Schwartz, D. M. (2022) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2022.10.011 · Cited by 85 · see citing works
GATA-3 Dose-Dependent Checkpoints in Early T Cell Commitment
Scripture-Adams, D. D., Damle, S. S., Li, L., Elihu, K. J., Qin, S., Arias, A. M., Butler, R. R., Champhekar, A., Zhang, J. A., & Rothenberg, E. V. (2014) · The Journal of Immunology · doi:10.4049/jimmunol.1301663 · Cited by 81 · see citing works
Self-citationTranscriptional drivers of the T-cell lineage program
Rothenberg, E. V. (2012) · Current Opinion in Immunology · doi:10.1016/j.coi.2011.12.012 · Cited by 80 · see citing works
Self-citationCytokines, Transcription Factors, and the Initiation of T-Cell DevelopmentPreprint
Hosokawa, H., & Rothenberg, E. V. (2017) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a028621 · Cited by 79 · see citing works
Self-citationA stochastic epigenetic switch controls the dynamics of T-cell lineage commitment
Ng, K. K. H., Yui, M. A., Mehta, A., Siu, S., Irwin, B., Pease, S., Hirose, S., Elowitz, M. B., Rothenberg, E. V., & Kueh, H. Y. (2018) · eLife · doi:10.7554/elife.37851 · Cited by 77 · see citing works
Self-citationDevelopmental programming of natural killer and innate lymphoid cells
Vosshenrich, C. A. J., & Santo, J. P. D. (2013) · Current Opinion in Immunology · doi:10.1016/j.coi.2013.02.002 · Cited by 76 · see citing works
Ungerbäck, J., Hosokawa, H., Wang, X., Strid, T., Williams, B. A., Sigvardsson, M., & Rothenberg, E. V. (2018) · Genome Research · doi:10.1101/gr.231423.117 · Cited by 77 · see citing works
Self-citationProgramming for T-lymphocyte fates: modularity and mechanismsPreprint
Rothenberg, E. V. (2019) · Genes & Development · doi:10.1101/gad.327163.119 · Cited by 74 · see citing works
Self-citationTCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors
Wang, W., Chandra, A., Goldman, N., Yoon, S., Ferrari, E. K., Nguyen, S. C., Joyce, E. F., & Vahedi, G. (2022) · Nature Immunology · doi:10.1038/s41590-022-01232-z · Cited by 72 · see citing works
Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells
Allison, K. A., Sajti, E., Collier, J. G., Gosselin, D., Troutman, T. D., Stone, E. L., Hedrick, S. Μ., & Glass, C. K. (2016) · eLife · doi:10.7554/elife.10134 · Cited by 74 · see citing works
Champhekar, A., Damle, S. S., Freedman, G., Carotta, S., Nutt, S. L., & Rothenberg, E. V. (2015) · Genes & Development · doi:10.1101/gad.259879.115 · Cited by 74 · see citing works
Self-citationKuang, Z., Cai, L., Zhang, X., Ji, H., Tu, B. P., & Boeke, J. D. (2014) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.2881 · Cited by 73 · see citing works
Requirement for Lyl1 in a model of Lmo2-driven early T-cell precursor ALL
McCormack, M. P., Shields, B. J., Jackson, J. T., Nasa, C., Shi, W., Slater, N. J., Tremblay, C. S., Rabbitts, T. H., & Curtis, D. J. (2013) · Blood · doi:10.1182/blood-2012-09-458570 · Cited by 69 · see citing works
E2A transcription factors limit expression of Gata3 to facilitate T lymphocyte lineage commitment
Xu, W., Carr, T. M., Ramirez, K., McGregor, S. M., Sigvardsson, M., & Kee, B. L. (2013) · Blood · doi:10.1182/blood-2012-08-449447 · Cited by 73 · see citing works
Transcriptional Repression of Gata3 Is Essential for Early B Cell Commitment
Banerjee, A., Northrup, D. L., Boukarabila, H., Jacobsen, S. E. W., & Allman, D. (2013) · Immunity · doi:10.1016/j.immuni.2013.01.014 · Cited by 72 · see citing works
The T-ALL related gene BCL11B regulates the initial stages of human T-cell differentiation
Ha, V. L., Luong, A., Li, F., Casero, D., Malvar, J., Kim, Y. M., Bhatia, R., Crooks, G. M., & Parekh, C. (2017) · Leukemia · doi:10.1038/leu.2017.70 · Cited by 70 · see citing works
Regulation of germinal center responses and B-cell memory by the chromatin modifier MOZ
Good-Jacobson, K. L., Chen, Y., Voss, A. K., Smyth, G. K., Thomas, T., & Tarlinton, D. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1402485111 · Cited by 64 · see citing works
The chromatin landscape and transcription factors in T cell programming
Rothenberg, E. V. (2014) · Trends in Immunology · doi:10.1016/j.it.2014.03.001 · Cited by 70 · see citing works
Self-citationEpigenetic program and transcription factor circuitry of dendritic cell development
Lin, Q., Chauvistré, H., Costa, I. G., Gusmao, E. G., Mitzka, S., Hänzelmann, S., Baying, B., Klisch, T., Moriggl, R., Hennuy, B., et al. (2015) · Nucleic Acids Research · doi:10.1093/nar/gkv1056 · Cited by 68 · see citing works
SATB1 Plays a Critical Role in Establishment of Immune Tolerance
Kondo, M., Tanaka, Y., Kuwabara, T., Naito, T., Kohwi-shigematsu, T., & Watanabe, A. (2015) · The Journal of Immunology · doi:10.4049/jimmunol.1501429 · Cited by 67 · see citing works
SCL, LMO1 and Notch1 Reprogram Thymocytes into Self-Renewing Cells
Gerby, B., Tremblay, C., Tremblay, M., Rojas-Sutterlin, S., Herblot, S., Hébert, J., Sauvageau, G., Lemieux, S., Lécuyer, E., Veiga, D. F. T., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004768 · Cited by 66 · see citing works
GATA3 induces human T-cell commitment by restraining Notch activity and repressing NK-cell fate
de Walle, I. V., Dolens, A., Durinck, K., Katrien De Mulder, A., Loocke, W. V., Damle, S. S., Waegemans, E., Medts, J. D., Velghe, I., Smedt, M. D., et al. (2016) · Nature Communications · doi:10.1038/ncomms11171 · Cited by 65 · see citing works
Self-citationWu, H., Gordon, J. A. R., Whitfield, T. W., Tai, P. W. L., van Wijnen, A. J., Stein, J. L., Stein, G. S., & Lian, J. B. (2017) · Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms · doi:10.1016/j.bbagrm.2017.01.003 · Cited by 65 · see citing works
Russ, B. E., Olshansky, M., Li, J., Nguyen, M. L. T., Gearing, L. J., Nguyen, T. H. O., Olson, M. R., McQuilton, H. A., Nüssing, S., Khoury, G., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.11.097 · Cited by 65 · see citing works
Oncogenic enhancers drive esophageal squamous cell carcinogenesis and metastasis
Ye, B., Fan, D., Xiong, W., Li, M., Yuan, J., Jiang, Q., Zhao, Y., Lin, J., Liu, J., Lv, Y., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24813-2 · Cited by 64 · see citing works
T cell immunity as a tool for studying epigenetic regulation of cellular differentiation
Russ, B. E., Prier, J. E., Rao, S., & Turner, S. J. (2013) · Frontiers in Genetics · doi:10.3389/fgene.2013.00218 · Cited by 62 · see citing works
Genome-Wide Analysis of Histone Modifications in Human Endometrial Stromal Cells
Tamura, I., Ohkawa, Y., Sato, T., Suyama, M., Jozaki, K., Okada, M., Lee, L., Maekawa, R., Asada, H., Sato, S., et al. (2014) · Molecular Endocrinology · doi:10.1210/me.2014-1117 · Cited by 62 · see citing works
Danis, E., Yamauchi, T., Echanique, K. A., Zhang, X., Haladyna, J. N., Riedel, S. S., Zhu, N., Xie, H.-F., Orkin, S., Armstrong, S., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.01.064 · Cited by 58 · see citing works
Khanam, T., Sandmann, S., Seggewiß, J., Ruether, C., Zimmermann, M., Norvil, A. B., Bartenhagen, C., Randau, G., Mueller, S., Herbrueggen, H., et al. (2020) · Blood · doi:10.1182/blood.2020005381 · Cited by 62 · see citing works
Rothenberg, E. V., Ungerbäck, J., & Champhekar, A. (2016) · Advances in Immunology · doi:10.1016/bs.ai.2015.09.002 · Cited by 61 · see citing works
Self-citation
- Authors
- Zhang, J. A., Mortazavi, A., Williams, B. A., Wold, B. J., & Rothenberg, E. V.
- Affiliations
- California Institute of Technology (US)
- Corresponding author
- Rothenberg, Ellen V.
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2012-04
- Volume
- 149
- Issue
- 2
- Pages
- 467-482
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC3336965
- OpenAlex
- W2002424170
- Cited by
- 337
- References
- 45
- Citations by year
- 2026: 3 · 2025: 10 · 2024: 5 · 2023: 12 · 2022: 15 · 2021: 25 · 2020: 22 · 2019: 27 · 2018: 28 · 2017: 32 · 2016: 32 · 2015: 36 · 2014: 35 · 2013: 42 · 2012: 12
- FWCI
- 16.08
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Cell (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- National Institutes of Health
- National Heart, Lung, and Blood Institute (R33HL089123)
- National Cancer Institute (R01CA090233, RC2CA148278)
- National Institute of Allergy and Infectious Diseases (R01AI095943)
- 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 › Epigenetics and DNA Methylation
- Keywords
- T cell development, transcription factor binding, GATA3, PU.1, histone modifications, cis-regulatory elements, transcriptional repression, lineage commitment, epigenetic regulation, transcriptional regulation
- MeSH terms
- Proto-Oncogene Protein Spi-1, Animals, Cell Differentiation, Gene Expression Regulation, Mice, Inbred C57BL, Promoter Regions, Genetic, Proto-Oncogene Proteins, T-Lymphocytes, Transcription, Genetic, Signal Transduction, Trans-Activators, Histone Code, Epigenesis, Genetic, Regulatory Elements, Transcriptional, GATA3 Transcription Factor, Mice, Receptors, Notch, Genome-Wide Association Study
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