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The genomic landscapes of inflammation
Open accessAbstract
Inflammation involves the activation of a highly coordinated gene expression program that is specific for the initial stimulus and occurs in a different manner in bystander parenchymal cells and professional immune system cells recruited to the inflamed site. Recent data demonstrate that developmental transcription factors like the macrophage fate-determining Pu.1 set the stage for the activity of ubiquitous transcription factors activated by inflammatory stimuli, like NF-kB, AP-1, and interferon regulatory factors (IRFs). The intersection of lineage-determining and stimulus-activated transcription factors at enhancers explains cell type specificity in inflammatory responses.
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“In myeloid, dendritic, and B lineage cells, PU.1 is a major contributor to the positive regulation of genes that establish lineage-specific identity (4, 17, 19).”
From Mechanisms of Action of Hematopoietic Transcription Factor PU.1 in Initiation of T-Cell Development (2019) · cites this paper as [17]
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Cites
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
Pattern Recognition Receptors and Inflammation
Takeuchi, O., & Akira, S. (2010) · Cell · doi:10.1016/j.cell.2010.01.022 · Cited by 8,895
Origin and physiological roles of inflammation
Medzhitov, R. (2008) · Nature · doi:10.1038/nature07201 · Cited by 6,618
Schroder, K., & Tschopp, J. (2010) · Cell · doi:10.1016/j.cell.2010.01.040 · Cited by 5,475
Histone modifications at human enhancers reflect global cell-type-specific gene expression
Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature · doi:10.1038/nature07829 · Cited by 2,533
Failure to Regulate TNF-Induced NF-κB and Cell Death Responses in A20-Deficient Mice
Lee, E. G., Boone, D. L., Chai, S., Libby, S. L., Chien, M., Lodolce, J. P., & Ma, A. (2000) · Science · doi:10.1126/science.289.5488.2350 · Cited by 1,409
In vivo enhancer analysis of human conserved non-coding sequences
Pennacchio, L. A., Ahituv, N., Moses, A. M., Prabhakar, S., Nobrega, M. A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K. D., et al. (2006) · Nature · doi:10.1038/nature05295 · Cited by 1,165
Liver X receptors as integrators of metabolic and inflammatory signaling
Zelcer, N. (2006) · Journal of Clinical Investigation · doi:10.1172/jci27883 · Cited by 978
Control of Inflammation, Cytokine Expression, and Germinal Center Formation by BCL-6
Dent, A. L., Shaffer, A. L., Yu, X., Allman, D., & Staudt, L. M. (1997) · Science · doi:10.1126/science.276.5312.589 · Cited by 950
A Large Fraction of Extragenic RNA Pol II Transcription Sites Overlap Enhancers
De Santa, F., Barozzi, I., Mietton, F., Ghisletti, S., Polletti, S., Tusi, B. K., Muller, H., Ragoussis, J., Wei, C.-L., & Natoli, G. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000384 · Cited by 934
Self-citationIRF3 Mediates a TLR3/TLR4-Specific Antiviral Gene Program
Doyle, S. E., Vaidya, S. A., O’Connell, R. M., Dadgostar, H., Dempsey, P. W., Wu, T., Rao, G., Sun, R., Haberland, M. E., Modlin, R. L., et al. (2002) · Immunity · doi:10.1016/s1074-7613(02)00390-4 · Cited by 847
The BCL-6 proto-oncogene controls germinal-centre formation and Th2-type inflammation
Ye, B. H., Cattoretti, G., Shen, Q. “., Zhang, J., Hawe, N., de Waard, R., Leung, C. C., Nouri-Shirazi, M. A., Orazi, A., Chaganti, R. S. K., et al. (1997) · Nature Genetics · doi:10.1038/ng0697-161 · Cited by 820
Regulation of B lymphocyte and macrophage development by graded expression of PU.1
DeKoter, R. P., & Singh, H. (2000) · Science · doi:10.1126/science.288.5470.1439 · Cited by 749
An atlas of combinatorial transcriptional regulation in mouse and man
Ravasi, T., Suzuki, H., Cannistraci, C. V., Katayama, S., Bajic, V. B., Tan, K., Akalin, A., Schmeier, S., Kanamori-Katayama, M., Bertin, N., et al. (2010) · Cell · doi:10.1016/j.cell.2010.01.044 · Cited by 715
Human macrophage activation programs induced by bacterial pathogens
Nau, G. J., Richmond, J. F. L., Schlesinger, A., Jennings, E. G., Lander, E. S., & Young, R. A. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.022649799 · Cited by 714
The evolution and genetics of innate immunity
Kimbrell, D., & Beutler, B. (2001) · Nature reviews genetics · doi:10.1038/35066006 · Cited by 679
Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation
Hargreaves, D. C., Horng, T., & Medzhitov, R. M. (2009) · Journal of End-to-End-testing · doi:10.1016/j.cell.2009.05.047 · Cited by 676
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
Self-citationRamirez-Carrozzi, V. R., Braas, D., Bhatt, D. M., Cheng, C. S., Hong, C., Doty, K. R., Black, J. C., Hoffmann, A., Carey, M., & Smale, S. T. (2009) · Journal of End-to-End-testing · doi:10.1016/j.cell.2009.04.020 · Cited by 595
Genome-wide analysis of ETS-family DNA-binding in vitro and in vivo
Wei, G., Badis, G., Berger, M. F., Kivioja, T., Palin, K., Enge, M., Bonke, M., Jolma, A., Varjosalo, M., Gehrke, A. R., et al. (2010) · The EMBO Journal · doi:10.1038/emboj.2010.106 · Cited by 568
Unbiased Reconstruction of a Mammalian Transcriptional Network Mediating Pathogen Responses
Amit, I., Garber, M., Chevrier, N., Leite, A. P., Donner, Y., Eisenhaure, T., Guttman, M., Grenier, J. K., Li, W., Zuk, O., et al. (2009) · Science · doi:10.1126/science.1179050 · Cited by 488
Beg, A. A., Sha, W. C., Bronson, R. T., & Baltimore, D. (1995) · Genes & Development · doi:10.1101/gad.9.22.2736 · Cited by 466
PU.1 induces myeloid lineage commitment in multipotent hematopoietic progenitors
Nerlov, C., & Graf, T. (1998) · Genes & Development · doi:10.1101/gad.12.15.2403 · Cited by 449 · cited 1×
“Although Bcl-6 is considered mainly a developmental regulator, it is responsive to extracellular cues (Bereshchenko et al. 2002; Pantano et al. 2006).”
BackgroundRamirez-Carrozzi, V. R., Nazarian, A. A., Li, C. C., Gore, S. L., Sridharan, R., Imbalzano, A. N., & Smale, S. T. (2006) · Genes & Development · doi:10.1101/gad.1383206 · Cited by 422
Two Waves of Nuclear Factor κb Recruitment to Target Promoters
Saccani, S., Pantano, S., & Natoli, G. (2001) · The Journal of Experimental Medicine · doi:10.1084/jem.193.12.1351 · Cited by 398
Self-citationAcetylation inactivates the transcriptional repressor BCL6
Bereshchenko, O., Gu, W. J., & Dalla‐Favera, R. (2002) · Nature Genetics · doi:10.1038/ng1018 · Cited by 394
Selective Transcription in Response to an Inflammatory Stimulus
Smale, S. T. (2010) · Cell · doi:10.1016/j.cell.2010.01.037 · Cited by 327
Basso, K., & Dalla‐Favera, R. (2010) · Advances in immunology · doi:10.1016/s0065-2776(10)05007-8 · Cited by 303
Bcl-6 and NF-κB cistromes mediate opposing regulation of the innate immune responsePreprint
Barish, G. D., Yu, R. T., Karunasiri, M. S., Ocampo, C. B., Dixon, J. R., Benner, C. W., Dent, A. L., Tangirala, R. K., & Evans, R. M. (2010) · Genes & Development · doi:10.1101/gad.1998010 · Cited by 258
Maintaining Cell Identity through Global Control of Genomic Organization
Natoli, G. (2010) · Immunity · doi:10.1016/j.immuni.2010.07.006 · Cited by 208
Self-citationBCL-6 regulates chemokine gene transcription in macrophages
Toney, L. M., Cattoretti, G., Graf, J. A., Merghoub, T., Pandolfi, P. P., Dalla‐Favera, R., Ye, B. H., & Dent, A. L. (2000) · Nature Immunology · doi:10.1038/79749 · Cited by 171
Sensors of the innate immune system: their mode of action
Baccalà, R., González‐Quintial, R., Lawson, B. R., Stern, M. E., Kono, D. H., Beutler, B., & Theofilopoulos, A. N. (2009) · Nature Reviews Rheumatology · doi:10.1038/nrrheum.2009.136 · Cited by 145
The functional repertoires of metazoan genomes
Ponting, C. P. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2413 · Cited by 110
Class-specific Regulation of Pro-inflammatory Genes by MyD88 Pathways and IκBζ
Kayama, H., Ramirez-Carrozzi, V. R., Yamamoto, M., Mizutani, T., Kuwata, H., Iba, H., Matsumoto, M., Honda, K., Smale, S. T., & Takeda, K. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m709965200 · Cited by 105
Control of NF- B-dependent Transcriptional Responses by Chromatin OrganizationPreprint
Natoli, G. (2009) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000224 · Cited by 96
Self-citationClass-specific regulation of pro-inflammatory genes by MyD88 pathways and IκBζ.
Kayama, H., Ramirez-Carrozzi, V. R., Yamamoto, M., Mizutani, T., Kuwata, H., Iba, H., Matsumoto, M., Honda, K., Smale, S. T., & Takeda, K. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.a114.709965 · Cited by 30
Pantano, S., Jarrossay, D., Saccani, S., Bosisio, D., & Natoli, G. (2006) · Experimental Cell Research · doi:10.1016/j.yexcr.2005.12.020 · Cited by 11
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Flagged first, then by citations
Research works printed but not linked: 1
- 1887, Sur la lutte des cellules de l'organisme contre l'invasion des microbes, Annales de l'Institut Pasteur, 1, 321
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Ivashkiv, L. B., & Donlin, L. T. (2013) · Nature reviews. Immunology · doi:10.1038/nri3581 · Cited by 3,442
Diversity, Mechanisms, and Significance of Macrophage Plasticity
Locati, M., Curtale, G., & Mantovani, A. (2020) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-012418-012718 · Cited by 2,199
Microglial brain region-dependent diversity and selective regional sensitivities to aging
Grabert, K., Michoel, T., Karavolos, M. H., Clohisey, S., Baillie, J. K., Stevens, M. P., Freeman, T. C., Summers, K. M., & McColl, B. W. (2016) · Nature Neuroscience · doi:10.1038/nn.4222 · Cited by 1,151
Latent Enhancers Activated by Stimulation in Differentiated Cells
Ostuni, R., Piccolo, V., Barozzi, I., Polletti, S., Termanini, A., Bonifacio, S., Curina, A., Prosperini, E., Ghisletti, S., & Natoli, G. (2013) · Cell · doi:10.1016/j.cell.2012.12.018 · Cited by 867
Self-citationMacrophage-Mediated Inflammation in Normal and Diabetic Wound Healing
Boniakowski, A. E., Kimball, A., Jacobs, B. N., Kunkel, S. L., & Gallagher, K. A. (2017) · The Journal of Immunology · doi:10.4049/jimmunol.1700223 · Cited by 564
Metadata
- Authors
- Natoli, G., Ghisletti, S., & Barozzi, I.
- Affiliations
- European Institute of Oncology (IT)
- Venue
- Genes & Development
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2011-01-15
- Volume
- 25
- Issue
- 2
- Pages
- 101-106
- ISSN
- 0890-9369 (ISSN-L)
- 1549-5477
- PMC
- PMC3022255
- OpenAlex
- W2005656449
- Cited by
- 152
- References
- 37
- Citations by year
- 2025: 6 · 2024: 3 · 2023: 11 · 2022: 7 · 2021: 10 · 2020: 8 · 2019: 7 · 2018: 11 · 2017: 10 · 2016: 9 · 2015: 14 · 2014: 19 · 2013: 15 · 2012: 10
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genes & Development (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- Funders
- Associazione Italiana per la Ricerca sul Cancro
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › NF-κB Signaling Pathways
- Life Sciences › Immunology and Microbiology › Immunology › Immune Response and Inflammation
- Keywords
- inflammation, transcriptional programs, transcription factors, enhancers, PU.1, macrophage differentiation, NF-kB, AP-1, interferon regulatory factors, cell type specificity
- MeSH terms
- Animals, Gene Expression Regulation, Humans, Inflammation, Macrophages, Transcription Factors, Genome
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