The DOI matches its Crossref record; 70 of the 70 references it cites were found in a registry or an index.
Transformation of Accessible Chromatin and 3D Nucleome Underlies Lineage Commitment of Early T Cells
Open accessAbstract
How chromatin reorganization coordinates differentiation and lineage commitment from hematopoietic stem and progenitor cells (HSPCs) to mature immune cells has not been well understood. Here, we carried out an integrative analysis of chromatin accessibility, topologically associating domains, AB compartments, and gene expression from HSPCs to CD4+CD8+ T cells. We found that abrupt genome-wide changes at all three levels of chromatin organization occur during the transition from double-negative stage 2 (DN2) to DN3, accompanying the T lineage commitment. The transcription factor BCL11B, a critical regulator of T cell commitment, is associated with increased chromatin interaction, and Bcl11b deletion compromised chromatin interaction at its target genes. We propose that these large-scale and concerted changes in chromatin organization present an energy barrier to prevent the cell from reversing its fate to earlier stages or redirecting to alternatives and thus lock the cell fate into the T lineages.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“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 [44]
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“This is part of a general downregulation of stem/progenitor associated regulatory genes (“phase 1 genes”) (34, 43) and a major reorganization of active chromatin and chromatin interactions, genome-wide, that occurs during this transition (44).”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [44]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast gapped-read alignment with Bowtie 2
Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400
Robinson, M. D., McCarthy, D. J., & Smyth, G. K. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btp616 · Cited by 41,364
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890
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
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
A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
Rao, S. S. P., Huntley, M. H., Durand, N. C., Stamenova, E. K., Bochkov, I. D., Robinson, J. T., Sanborn, A. L., Machol, I., Omer, A. D., Lander, E. S., et al. (2014) · Cell · doi:10.1016/j.cell.2014.11.021 · Cited by 9,212
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
Lieberman-Aiden, E., van Berkum, N. L., Williams, L., Imakaev, M., Ragoczy, T., Telling, A., Amit, I., Lajoie, B. R., Sabo, P. J., Dorschner, M. O., et al. (2009) · Science · doi:10.1126/science.1181369 · Cited by 8,898
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
Self-citationTopological domains in mammalian genomes identified by analysis of chromatin interactions
Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829
TM4: a free, open-source system for microarray data management and analysis
Saeed, A. I., Sharov, V., White, J., Li, J., Liang, W., Bhagabati, N., Braisted, J., Klapa, M., Currier, T., Thiagarajan, M., et al. (2003) · BioTechniques · doi:10.2144/03342mt01 · Cited by 4,837
Cited by
Sorted by citations
Transcription factors and 3D genome conformation in cell-fate decisions
Stadhouders, R., Filion, G. J. P., & Graf, T. (2019) · Nature · doi:10.1038/s41586-019-1182-7 · Cited by 530
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
TCF1 in T cell immunity: a broadened frontier
Zhao, X., Shan, Q., & Xue, H. (2021) · Nature reviews. Immunology · doi:10.1038/s41577-021-00563-6 · Cited by 252
How transcription factors drive choice of the T cell fate
Hosokawa, H., & Rothenberg, E. V. (2020) · Nature reviews. Immunology · doi:10.1038/s41577-020-00426-6 · Cited by 250
Self-citationVilarrasa‐Blasi, R., Soler-Vila, P., Verdaguer-Dot, N., Russiñol, N., Stefano, M. D., Chapaprieta, V., Clot, G., Farabella, I., Cuscó, P., Kulis, M., et al. (2021) · Nature Communications · doi:10.1038/s41467-020-20849-y · Cited by 146
Helix–loop–helix proteins and the advent of cellular diversity: 30 years of discoveryPreprint
Murre, C. (2019) · Genes & Development · doi:10.1101/gad.320663.118 · Cited by 145
Epigenetic mechanisms regulating T-cell responses
Schmidl, C., Delacher, M., Huehn, J., & Feuerer, M. (2018) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2018.07.014 · Cited by 153
Paradoxical association of TET loss of function with genome-wide DNA hypomethylation
López-Moyado, I. F., Tsagaratou, A., Yuita, H., Seo, H., Delatte, B., Heinz, S., Benner, C. W., & Rao, A. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1903059116 · Cited by 130
Transcription-factor-mediated supervision of global genome architecture maintains B cell identity
Johanson, T. M., Lun, A. T. L., Coughlan, H. D., Tan, T., Smyth, G. K., Nutt, S. L., & Allan, R. S. (2018) · Nature Immunology · doi:10.1038/s41590-018-0234-8 · Cited by 109
Bcl11b sets pro-T cell fate by site-specific cofactor recruitment and by repressing Id2 and Zbtb16
Hosokawa, H., Romero-Wolf, M., Yui, M. A., Ungerbäck, J., Quiloan, M. L. G., Matsumoto, M., Nakayama, K. I., Tanaka, T., & Rothenberg, E. V. (2018) · Nature Immunology · doi:10.1038/s41590-018-0238-4 · Cited by 110
Self-citationZhou, 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 101
Self-citationControl of Lymphocyte Fate, Infection, and Tumor Immunity by TCF-1
Raghu, D., Xue, H., & Mielke, L. A. (2019) · Trends in Immunology · doi:10.1016/j.it.2019.10.006 · Cited by 98
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
“This is part of a general downregulation of stem/progenitor associated regulatory genes (“phase 1 genes”) (34, 43) and a major reorganization of active chromatin and chromatin interactions, genome-wide, that occurs during this transition (44).”
BackgroundSelf-citationTCF-1: a maverick in T cell development and function
Gounari, F., & Khazaie, K. (2022) · Nature Immunology · doi:10.1038/s41590-022-01194-2 · Cited by 95
Shan, Q., Li, X., Chen, X., Zeng, Z., Zhu, S., Gai, K., Peng, W., & Xue, H. (2021) · Nature Communications · doi:10.1038/s41467-021-26159-1 · Cited by 95
Zhong, C., Zheng, M., Cui, K., Martins, A. J., Hu, G., Li, D., Tessarollo, L., Kozlov, S. V., Keller, J. R., Tsang, J. S., et al. (2019) · Immunity · doi:10.1016/j.immuni.2019.12.001 · Cited by 94
Self-citationEpigenetic reprogramming of immune cells in injury, repair, and resolution
Placek, K., Schultze, J. L., & Aschenbrenner, A. C. (2019) · Journal of Clinical Investigation · doi:10.1172/jci124619 · Cited by 86
Multi-Omics Approaches in Immunological Research
Chu, X., Zhang, B., Koeken, V. A. C. M., Gupta, M. K., & Li, Y. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.668045 · Cited by 87
A 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 79
Self-citationSpatial Genome Re-organization between Fetal and Adult Hematopoietic Stem Cells
Chen, C., Yu, W., Tober, J. M., Gao, P., He, B., Lee, K., Trieu, T., Blobel, G. A., Speck, N. A., & Tan, K. (2019) · Cell Reports · doi:10.1016/j.celrep.2019.11.065 · Cited by 79
Epigenomic drivers of immune dysfunction in aging
Keenan, C. R., & Allan, R. S. (2018) · Aging Cell · doi:10.1111/acel.12878 · Cited by 80
Integrative multi-omics approaches to explore immune cell functions: Challenges and opportunities
Wang, X., Dian, F., Yang, Y., Gimple, R. C., & Zhou, S. (2023) · iScience · doi:10.1016/j.isci.2023.106359 · Cited by 87
Self-citationUngerbäck, 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
Self-citationProgramming for T-lymphocyte fates: modularity and mechanismsPreprint
Rothenberg, E. V. (2019) · Genes & Development · doi:10.1101/gad.327163.119 · Cited by 75
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
tagHi-C Reveals 3D Chromatin Architecture Dynamics during Mouse Hematopoiesis
Zhang, C., Xu, Z., Yang, S., Sun, G., Jia, L., Zheng, Z., Gu, Q., Tao, W., Cheng, T., Li, C., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.108206 · Cited by 75
Cell type–specific actions of Bcl11b in early T-lineage and group 2 innate lymphoid cells
Hosokawa, H., Romero-Wolf, M., Yang, Q., Motomura, Y., Levanon, D., Groner, Y., Moro, K., Tanaka, T., & Rothenberg, E. V. (2019) · The Journal of Experimental Medicine · doi:10.1084/jem.20190972 · Cited by 67
Self-citationWang, X., Shen, X., Chen, S., Liu, H., Hong, N., Zhong, H., Chen, X. X., & Jin, W. (2021) · The Journal of Immunology · doi:10.4049/jimmunol.2100581 · Cited by 67
Self-citationTcf1–CTCF cooperativity shapes genomic architecture to promote CD8+ T cell homeostasis
Shan, Q., Zhu, S., Chen, X., Liu, J., Yuan, S., Li, X., Peng, W., & Xue, H. (2022) · Nature Immunology · doi:10.1038/s41590-022-01263-6 · Cited by 62
Epigenetic and transcriptional mechanisms for the regulation of IL-10
Zhang, H., & Kuchroo, V. K. (2019) · Seminars in Immunology · doi:10.1016/j.smim.2019.101324 · Cited by 65
Cieślak, A., Charbonnier, G., Tesio, M., Mathieu, È.-L., Belhocine, M., Touzart, A., Smith, C. L., Hypolite, G., Andrieu, G. P., Martens, J. H. A., et al. (2020) · The Journal of Experimental Medicine · doi:10.1084/jem.20192360 · Cited by 68
Miyazaki, K., Watanabe, H., Yoshikawa, G., Chen, K., Hidaka, R., Aitani, Y., Osawa, K., Takeda, R., Ochi, Y., Tani‐ichi, S., et al. (2020) · Science Immunology · doi:10.1126/sciimmunol.abb1455 · Cited by 62
Three-dimensional genome organization in immune cell fate and function
Cuartero, S., Stik, G., & Stadhouders, R. (2022) · Nature reviews. Immunology · doi:10.1038/s41577-022-00774-5 · Cited by 56
Yang, L., Chen, F., Zhu, H.-C., Chen, Y., Dong, B., Shi, M.-L., Wang, W., Jiang, Q., Zhang, L.-P., Huang, X., et al. (2021) · Nature Communications · doi:10.1038/s41467-021-24044-5 · Cited by 44
Shin, B., Hosokawa, H., Romero-Wolf, M., Zhou, W., Masuhara, K., Tobin, V. R., Levanon, D., Groner, Y., & Rothenberg, E. V. (2021) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2019655118 · Cited by 51
Self-citationMurphy, D., Salataj, E., Giammartino, D. C. D., Rodriguez-Hernaez, J., Kloetgen, A., Garg, V., Char, E., Uyehara, C. M., Ee, L.-S., Lee, U., et al. (2023) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01130-4 · Cited by 51
Fang, D., Cui, K., Cao, Y., Zheng, M., Kawabe, T., Hu, G., Khillan, J. S., Li, D., Zhong, C., Jankovic, D. L., et al. (2022) · Immunity · doi:10.1016/j.immuni.2022.03.005 · Cited by 50
Self-citationThe 3D enhancer network of the developing T cell genome is shaped by SATB1
Ζελένκα, Τ., Klonizakis, A., Tsoukatou, D., Papamatheakis, D.-A., Franzenburg, S., Tzerpos, P., Tzonevrakis, I.-R., Papadogkonas, G., Kapsetaki, M., Nikolaou, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-34345-y · Cited by 50
Chromatin Accessibility and Interactions in the Transcriptional Regulation of T Cells
Li, P., & Leonard, W. J. (2018) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02738 · Cited by 50
Taylor, T., Sikorska, N., Shchuka, V. M., Chahar, S., Ji, C., Macpherson, N. N., Moorthy, S. D., de Kort, M. A. C., Mullany, S., Khader, N., et al. (2022) · Genes & Development · doi:10.1101/gad.349489.122 · Cited by 45
Low RNA stability signifies increased post-transcriptional regulation of cell identity genes
Li, Y., Yang, Y., Lv, J., Gao, X., Yu, Y., Babu, S. S., Bruno, I., Zhao, D., Xia, B., Peng, W., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad300 · Cited by 43
Self-citationPikkupeura, L. M., Bressan, R. B., Guiu, J., Chen, Y., Maimets, M., Mayer, D., Schweiger, P. J., Hansen, S. L., Maciag, G. J., Larsen, H. L., et al. (2023) · Science Advances · doi:10.1126/sciadv.adf9460 · Cited by 45
Lineage-specific 3D genome organization is assembled at multiple scales by IKAROS
Hu, Y.-G., Figueroa, D. S., Zhang, Z., Veselits, M. L., Bhattacharyya, S., Kashiwagi, M., Clark, M. R., Morgan, B. A., Ay, F., & Georgopoulos, K. (2023) · Cell · doi:10.1016/j.cell.2023.10.023 · Cited by 36
Sanalkumar, R., Dong, R., Lee, L., Xing, Y., Iyer, S., Letovanec, I., Rosa, S. L., Finzi, G., Musolino, E., Papait, R., et al. (2023) · Science Advances · doi:10.1126/sciadv.abo3789 · Cited by 45
Notch2 complements Notch1 to mediate inductive signaling that initiates early T cell development
Romero-Wolf, M., Shin, B., Zhou, W., Koizumi, M., Rothenberg, E. V., & Hosokawa, H. (2020) · The Journal of Cell Biology · doi:10.1083/jcb.202005093 · Cited by 41
Self-citationFoxp3 orchestrates reorganization of chromatin architecture to establish regulatory T cell identity
Liu, Z., Lee, D.-S., Liang, Y., Zheng, Y., & Dixon, J. R. (2023) · Nature Communications · doi:10.1038/s41467-023-42647-y · Cited by 39
Feng, D., Chen, Y., Dai, R., Bian, S., Xue, W., Zhu, Y., Li, Z., Yang, Y., Zhang, Y., Zhang, J., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-33333-6 · Cited by 40
Lin, L., Hu, M., Li, Q., Du, L., Lin, L., Xue, Y., Zheng, F., Wang, F., Liu, K., Wang, Y., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01672-1 · Cited by 36
Self-citationSingle-cell insights into the hematopoietic generation of T-lymphocyte precursors in mouse and human
Rothenberg, E. V. (2021) · Experimental Hematology · doi:10.1016/j.exphem.2020.12.005 · Cited by 36
Self-citationOncogene-dependent function of BRG1 in hepatocarcinogenesis
Wang, P., Song, X., Cao, D., Cui, K., Wang, J., Utpatel, K., Shang, R., Wang, H., Che, L., Evert, M., et al. (2020) · Cell Death and Disease · doi:10.1038/s41419-020-2289-3 · Cited by 35
Self-citationRunx factors launch T cell and innate lymphoid programs via direct and gene network-based mechanisms
Shin, B., Zhou, W., Wang, J., Gao, F., & Rothenberg, E. V. (2023) · Nature Immunology · doi:10.1038/s41590-023-01585-z · Cited by 34
Self-citationChromosome compartmentalization: causes, changes, consequences, and conundrums
Li, H., Playter, C., Das, P., & McCord, R. P. (2024) · Trends in Cell Biology · doi:10.1016/j.tcb.2024.01.009 · Cited by 36
Li, C. C., Zhang, G., Du, J., Liu, D., Li, Z., Ni, Y., Zhou, J. R., Li, Y., Hou, S., Zheng, X., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28018-z · Cited by 34
Liu, S., Cao, Y., Cui, K., Ren, G., Zhao, T., Wang, X., Wei, D., Chen, Z., Gurram, R. K., Liu, C., et al. (2024) · Immunity · doi:10.1016/j.immuni.2024.03.018 · Cited by 34
Self-citationT Cell Development: Old Tales Retold By Single-Cell RNA Sequencing
Liu, C., Lan, Y., Liu, B., Zhang, H., & Hu, H. (2021) · Trends in Immunology · doi:10.1016/j.it.2020.12.004 · Cited by 33
Acute depletion of BRG1 reveals its primary function as an activator of transcription
Ren, G., Ku, W. L., Ge, G.-Z., Hoffman, J. A., Kang, J. Y., Tang, Q.-S., Cui, K.-R., He, Y., Guan, Y., Gao, B., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-48911-z · Cited by 32
Self-citationEpigenetic Dynamics in the Function of T-Lineage Regulatory Factor Bcl11b
Sidwell, T., & Rothenberg, E. V. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.669498 · Cited by 30
Self-citationPre-mitotic genome re-organisation bookends the B cell differentiation process
Chan, W. F., Coughlan, H. D., Zhou, J. H. S., Keenan, C. R., Bediaga, N. G., Hodgkin, P. D., Smyth, G. K., Johanson, T. M., & Allan, R. S. (2021) · Nature Communications · doi:10.1038/s41467-021-21536-2 · Cited by 31
The epigenetic landscape of fate decisions in T cells
Jay, A., Pondevida, C. M., & Vahedi, G. (2025) · Nature Immunology · doi:10.1038/s41590-025-02113-x · Cited by 32
Astori, A., Tingvall-Gustafsson, J., Kuruvilla, J., Coyaud, É., Laurent, E. M. N., Sunnerhagen, M., Åhsberg, J., Ungerbäck, J., Strid, T., Sigvardsson, M., et al. (2020) · The Journal of Immunology · doi:10.4049/jimmunol.1900959 · Cited by 30
Miyazaki, K., & Miyazaki, M. (2021) · Frontiers in Immunology · doi:10.3389/fimmu.2021.659761 · Cited by 31
Multiscale 3D genome organization underlies ILC2 ontogenesis and allergic airway inflammation
Michieletto, M. F., Tello-Cajiao, J. J., Mowel, W. K., Chandra, A., Yoon, S.-Y., Joannas, L., Clark, M., Jimenez, M. T., Wright, J. M., Lundgren, P., et al. (2022) · Nature Immunology · doi:10.1038/s41590-022-01295-y · Cited by 29
Tunable, division-independent control of gene activation timing by a polycomb switch
Pease, N. A., Nguyen, P. H., Woodworth, M. A., Ng, K. K. H., Irwin, B., Vaughan, J. C., & Kueh, H. Y. (2021) · Cell Reports · doi:10.1016/j.celrep.2021.108888 · Cited by 26
Philips, R. L., Lee, J., Gaonkar, K. S., Chanana, P., Chung, J. Y., Arocha, S. R. R., Schwab, A. D., Ördög, T., & Shapiro, V. S. (2019) · eLife · doi:10.7554/elife.43821 · Cited by 28
Integration site–dependent HIV-1 promoter activity shapes host chromatin conformationPreprint
Collora, J. A., & Ho, Y. (2023) · Genome Research · doi:10.1101/gr.277698.123 · Cited by 26
Transcriptional network dynamics in early T cell development
Shin, B., Chang, S. J., MacNabb, B. W., & Rothenberg, E. V. (2024) · The Journal of Experimental Medicine · doi:10.1084/jem.20230893 · Cited by 29
Self-citationGenome organization in immune cells: unique challenges
Johanson, T. M., Chan, W. F., Keenan, C. R., & Allan, R. S. (2019) · Nature reviews. Immunology · doi:10.1038/s41577-019-0155-2 · Cited by 28
Epigenetic regulation of hematopoietic stem cell homeostasis
Jiang, P., Wang, H., Zheng, J., Han, Y., Huang, H., & Qian, P. (2019) · Blood Science · doi:10.1097/bs9.0000000000000018 · Cited by 29
SATB1-mediated chromatin landscape in T cells
Ζελένκα, Τ., & Spilianakis, C. G. (2020) · Nucleus · doi:10.1080/19491034.2020.1775037 · Cited by 30
Kurotaki, D., Kikuchi, K., Cui, K., Kawase, W., Saeki, K., Fukumoto, J., Nishiyama, A., Nagamune, K., Zhao, K., Ozato, K., et al. (2022) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2207009119 · Cited by 27
Self-citationChIATAC is an efficient strategy for multi-omics mapping of 3D epigenomes from low-cell inputs
Chai, H.-X., Tjong, H., Li, P., Liao, W., Wang, P., Wong, C.-H., Ngan, C., Leonard, W., Wei, C.-L., & Ruan, Y. (2023) · Nature Communications · doi:10.1038/s41467-023-35879-5 · Cited by 23
Liu, J., Zhu, S., Hu, W., Zhao, X., Shan, Q., Peng, W., & Xue, H. (2023) · The Journal of Experimental Medicine · doi:10.1084/jem.20221288 · Cited by 26
Diploid genome architecture revealed by multi-omic data of hybrid micePreprint
Han, Z., Cui, K., Placek, K., Hong, N., Lin, C., Chen, W., Zhao, K., & Jin, W. (2020) · Genome Research · doi:10.1101/gr.257568.119 · Cited by 26
Self-citation3D Chromosomal Landscapes in Hematopoiesis and Immunity
Kloetgen, A., Thandapani, P., Tsirigos, A., & Aifantis, I. (2019) · Trends in Immunology · doi:10.1016/j.it.2019.07.003 · Cited by 25
3D Genome Organization as an Epigenetic Determinant of Transcription Regulation in T Cells
Papadogkonas, G., Papamatheakis, D.-A., & Spilianakis, C. G. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.921375 · Cited by 25
Postmitotic differentiation of human monocytes requires cohesin-structured chromatin
Minderjahn, J., Fischer, A. H., Maier, K., Mendes, K., Nuetzel, M., Raithel, J., Stanewsky, H., Ackermann, U., Månsson, R., Gebhard, C., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-31892-2 · Cited by 24
Bortnick, A., He, Z., Aubrey, M., Chandra, V., Denholtz, M., Chen, K., Lin, Y. C., & Murre, C. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107876 · Cited by 24
Bcl11b/Ctip2 in Skin, Tooth, and Craniofacial System
Daher, M., Bausero, P., Agbulut, O., Li, Z., & Parlakian, A. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.581674 · Cited by 22
NuRD complex recruitment to Thpok mediates CD4 + T cell lineage differentiation
Gao, Y., Zamisch, M., Vacchio, M. S., Chopp, L. B., Ciucci, T., Paine, E. L., Lyons, G. C., Nie, J., Xiao, Q., Zvezdova, E., et al. (2022) · Science Immunology · doi:10.1126/sciimmunol.abn5917 · Cited by 25
Liao, R. J., Wu, Y., Qin, L., Jiang, Z., Gou, S., Zhou, L., Hong, Q., Li, Y., Shi, J., Yao, Y., et al. (2023) · The EMBO Journal · doi:10.15252/embj.2023113448 · Cited by 25
Self-citationStage-specific action of Runx1 and GATA3 controls silencing of PU.1 expression in mouse pro–T cells
Hosokawa, H., Koizumi, M., Masuhara, K., Romero-Wolf, M., Tanaka, T., Nakayama, T., & Rothenberg, E. V. (2021) · The Journal of Experimental Medicine · doi:10.1084/jem.20202648 · Cited by 23
Self-citationGoldman, N., Chandra, A., Johnson, I., Sullivan, M. A., Patil, A. R., Vanderbeck, A., Jay, A., Zhou, Y., Ferrari, E. K., Mayne, L. C., et al. (2023) · Nature Immunology · doi:10.1038/s41590-023-01599-7 · Cited by 24
Causal Gene Regulatory Network Modeling and Genomics: Second-Generation Challenges
Rothenberg, E. V. (2019) · Journal of Computational Biology · doi:10.1089/cmb.2019.0098 · Cited by 20
Self-citation3D genome organization during lymphocyte development and activation
Schoonhoven, A. O.-V., Huylebroeck, D., Hendriks, R. W., & Stadhouders, R. (2019) · Briefings in Functional Genomics · doi:10.1093/bfgp/elz030 · Cited by 24
Mapping the regulatory landscape of auditory hair cells from single-cell multi-omics dataPreprint
Wang, S., Lee, M. P., Jones, S., Liu, J., & Waldhaus, J. (2021) · Genome Research · doi:10.1101/gr.271080.120 · Cited by 21
Human induced-T-to-natural killer cells have potent anti-tumour activities
Jiang, Z., Qin, L., Tang, Y., Liao, R. J., Shi, J., He, B., Li, S., Zheng, D., Cui, Y., Wu, Q., et al. (2022) · Biomarker Research · doi:10.1186/s40364-022-00358-4 · Cited by 20
Self-citationNoncoding RNA transcription at enhancers and genome folding in cancer
Isoda, T., Morio, T., & Takagi, M. (2019) · Cancer Science · doi:10.1111/cas.14107 · Cited by 19
Bortnick, A., He, Z., Aubrey, M., Chandra, V. K., Denholtz, M., Chen, K., Lin, Y. C., & Murre, C. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.03.034 · Cited by 20
Logic and lineage impacts on functional transcription factor deployment for T-cell fate commitment
Rothenberg, E. V. (2021) · Biophysical Journal · doi:10.1016/j.bpj.2021.04.002 · Cited by 17
Self-citationTranscription induces context-dependent remodeling of chromatin architecture during differentiation
Chahar, S., Zouari, Y. B., Salari, H., Molitor, A. M., Kobi, D., Maroquenne, M., Erb, C., Mossler, A., Karasu, N., Jost, D., et al. (2023) · PLoS Biology · doi:10.1371/journal.pbio.3002424 · Cited by 19
Tsagaratou, A. (2021) · Immunological Reviews · doi:10.1111/imr.12940 · Cited by 16
Chromatin Network Analyses: Towards Structure-Function Relationships in Epigenomics
Pancaldi, V. (2021) · Frontiers in Bioinformatics · doi:10.3389/fbinf.2021.742216 · Cited by 17
Kashiwagi, M., Figueroa, D. S., Ay, F., Morgan, B. A., & Georgopoulos, K. (2022) · Nature Immunology · doi:10.1038/s41590-022-01322-y · Cited by 16
Mahmood, S. R., Said, N. H. E., Gunsalus, K. C., & Percipalle, P. (2023) · Genome biology · doi:10.1186/s13059-023-02853-9 · Cited by 16
Short tandem repeats are important contributors to silencer elements in T cells
Hussain, S., Sadouni, N., van Essen, D., Dao, L. T. M., Ferré, Q., Charbonnier, G., Torres, M., Gallardo, F., Lecellier, C., Sexton, T., et al. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad187 · Cited by 14
Chromatin-Modifying Enzymes in T Cell Development
Shapiro, M. J., & Shapiro, V. S. (2020) · Annual Review of Immunology · doi:10.1146/annurev-immunol-092719-082622 · Cited by 17
Speed and navigation control of thymocyte development by the fetal T‐cell gene regulatory network
MacNabb, B. W., & Rothenberg, E. V. (2023) · Immunological Reviews · doi:10.1111/imr.13190 · Cited by 16
Self-citationDynamic control of the T-cell specification gene regulatory network
Rothenberg, E. V. (2019) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2019.10.012 · Cited by 17
Self-citationOlariu, V., Yui, M. A., Krupinski, P., Zhou, W., Deichmann, J., Andersson, E., Rothenberg, E. V., & Peterson, C. (2021) · Cell Reports · doi:10.1016/j.celrep.2020.108622 · Cited by 15
Self-citationReorganization of 3D chromatin architecture in doxorubicin-resistant breast cancer cells
Wang, X., Yan, J., Ye, Z., Zhang, Z., Wang, S., Hao, S., Shen, B., & Wei, G. (2022) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2022.974750 · Cited by 15
Self-citation
Metadata
- Authors
- Hu, G., Cui, K., Fang, D., Hirose, S., Wang, X., Wangsa, D., Jin, W., Ried, T., Liu, P., Zhu, J., Rothenberg, E. V., & Zhao, K.
- Affiliations
- National Institutes of Health (US)
- California Institute of Technology (US)
- Wellcome Sanger Institute (GB)
- Corresponding author
- Hu, Gangqing
- Rothenberg, Ellen V.
- Zhao, Keji
- ORCID
- Venue
- Immunity
- Publisher
- Elsevier BV
- Published
- 2018-02
- Volume
- 48
- Issue
- 2
- Pages
- 227-242.e8
- ISSN
- 1074-7613 (ISSN-L)
- PMC
- PMC5847274
- OpenAlex
- W2788037203
- Cited by
- 199
- References
- 70
- Citations by year
- 2026: 5 · 2025: 11 · 2024: 15 · 2023: 40 · 2022: 33 · 2021: 34 · 2020: 24 · 2019: 27 · 2018: 10
- FWCI
- 8.45
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- Locations
- Immunity (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- Division of Intramural Research of the National Cancer Institute
- National Institute of Allergy and Infectious Diseases
- NHLBI
- NIH (R01 AI083514)
- 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
- T cell lineage commitment, chromatin accessibility, 3D genome organization, topologically associating domains, A/B compartments, hematopoietic stem and progenitor cells, double-negative T cells, BCL11B, chromatin interactions, cell fate determination, T cell differentiation
- MeSH terms
- Animals, Cell Differentiation, Cell Nucleus, Chromatin, Humans, Repressor Proteins, T-Lymphocytes, Cell Lineage, Tumor Suppressor Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
