May 18, 2024
Ablation of cDC2 development by triple mutations within the Zeb2 enhancer – Nature

Ablation of cDC2 development by triple mutations within the Zeb2 enhancer – Nature

  • Naik, S. H. et al. Development of plasmacytoid and conventional dendritic cell subtypes from single precursor cells derived in vitro and in vivo. Nat. Immunol. 8, 1217–1226 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Onai, N. et al. Identification of clonogenic common Flt3+ M-CSFR+ plasmacytoid and conventional dendritic cell progenitors in mouse bone marrow. Nat. Immunol. 8, 1207–1216 (2007).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Liu, K. et al. In vivo analysis of dendritic cell development and homeostasis. Science 324, 392–397 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Grajales-Reyes, G. E. et al. Batf3 maintains autoactivation of Irf8 for commitment of a CD8alpha(+) conventional DC clonogenic progenitor. Nat. Immunol. 16, 708–717 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Schlitzer, A. et al. Identification of cDC1- and cDC2-committed DC progenitors reveals early lineage priming at the common DC progenitor stage in the bone marrow. Nat. Immunol. 16, 718–728 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Durai, V. et al. Cryptic activation of an Irf8 enhancer governs cDC1 fate specification. Nat. Immunol. 20, 1161–1173 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Bagadia, P. et al. An Nfil3-Zeb2-Id2 pathway imposes Irf8 enhancer switching during cDC1 development. Nat. Immunol. 20, 1174–1185 (2019).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Huang, X. et al. Differential usage of transcriptional repressor Zeb2 enhancers distinguishes adult and embryonic hematopoiesis. Immunity 54, 1417–1432 (2021).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Kumamoto, Y. et al. CD301b+ dermal dendritic cells drive T helper 2 cell-mediated immunity. Immunity 39, 733–743 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Gao, Y. et al. Control of T helper 2 responses by transcription factor IRF4-dependent dendritic cells. Immunity 39, 722–732 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Tussiwand, R. et al. Klf4 expression in conventional dendritic cells is required for T helper 2 cell responses. Immunity 42, 916–928 (2015).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Murphy, T. L. et al. Transcriptional control of dendritic cell development. Annu. Rev. Immunol. 34, 93–119 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Cisse, B. et al. Transcription factor E2-2 is an essential and specific regulator of plasmacytoid dendritic cell development. Cell 135, 37–48 (2008).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Scott, C. L. et al. The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2. J. Exp. Med. 213, 897–911 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Wu, X. et al. Transcription factor Zeb2 regulates commitment to plasmacytoid dendritic cell and monocyte fate. Proc. Natl Acad. Sci. USA 113, 14775–14780 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Tamura, T. et al. IFN regulatory factor-4 and -8 govern dendritic cell subset development and their functional diversity. J. Immunol. 174, 2573–2581 (2005).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Bajana, S., Roach, K., Turner, S., Paul, J. & Kovats, S. IRF4 promotes cutaneous dendritic cell migration to lymph nodes during homeostasis and inflammation. J. Immunol. 189, 3368–3377 (2012).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Bajana, S., Turner, S., Paul, J., Ainsua-Enrich, E. & Kovats, S. IRF4 and IRF8 Act in CD11c+ cells to regulate terminal differentiation of lung tissue dendritic cells. J Immunol 196, 1666–1677 (2016).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Fogg, D. K. et al. A clonogenic bone marrow progenitor specific for macrophages and dendritic cells. Science 311, 83–87 (2006).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • Hettinger, J. et al. Origin of monocytes and macrophages in a committed progenitor. Nat. Immunol. 14, 821–830 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Welner, R. S. et al. C/EBPα is required for development of dendritic cell progenitors. Blood 121, 4073–4081 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Anirudh, S. et al. TNFα rescues dendritic cell development in hematopoietic stem and progenitor cells lacking C/EBPα. Cells 9, 1223 (2020).

    CAS 
    PubMed Central 
    Article 

    Google Scholar
     

  • Zhang, W. et al. Molecular cloning and characterization of NF-IL3A, a transcriptional activator of the human interleukin-3 promoter. Mol. Cell. Biol. 15, 6055–6063 (1995).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cowell, I. G., Skinner, A. & Hurst, H. C. Transcriptional repression by a novel member of the bZIP family of transcription factors. Mol. Cell. Biol. 12, 3070–3077 (1992).

    CAS 
    PubMed 
    PubMed Central 

    Google Scholar
     

  • Gilbert, L. A. et al. Genome-scale CRISPR-mediated control of gene repression and activation. Cell 159, 647–661 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cress, W. D. & Triezenberg, S. J. Critical structural elements of the VP16 transcriptional activation domain. Science 251, 87–90 (1991).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • Wang, G. G. et al. Quantitative production of macrophages or neutrophils ex vivo using conditional Hoxb8. Nat. Methods 3, 287–293 (2006).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Zhu, C. et al. An IL-27/NFIL3 signalling axis drives Tim-3 and IL-10 expression and T-cell dysfunction. Nat. Commun. 6, 6072 (2015).

    CAS 
    PubMed 
    Article 
    ADS 

    Google Scholar
     

  • Grant, C. E., Bailey, T. L. & Noble, W. S. FIMO: scanning for occurrences of a given motif. Bioinformatics 27, 1017–1018 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Haas, N. B., Cantwell, C. A., Johnson, P. F. & Burch, J. B. DNA-binding specificity of the PAR basic leucine zipper protein VBP partially overlaps those of the C/EBP and CREB/ATF families and is influenced by domains that flank the core basic region. Mol. Cell. Biol. 15, 1923–1932 (1995).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Ozkurt, I. C. & Tetradis, S. Parathyroid hormone-induced E4BP4/NFIL3 down-regulates transcription in osteoblasts. J. Biol. Chem. 278, 26803–26809 (2003).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Li, F., Liu, J., Jo, M. & Curry, T. E. Jr. A role for nuclear factor interleukin-3 (NFIL3), a critical transcriptional repressor, in down-regulation of periovulatory gene expression. Mol. Endocrinol. 25, 445–459 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Tamura, A. et al. C/EBPβ is required for survival of Ly6C monocytes. Blood 130, 1809–1818 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Thomas, G. D. et al. Deleting an Nr4a1 super-enhancer subdomain ablates Ly6Clow monocytes while preserving macrophage gene function. Immunity 45, 975–987 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Heng, T. S. et al. The Immunological Genome Project: networks of gene expression in immune cells. Nat. Immunol. 9, 1091–1094 (2008).

  • Sathe, P., Vremec, D., Wu, L., Corcoran, L. & Shortman, K. Convergent differentiation: myeloid and lymphoid pathways to murine plasmacytoid dendritic cells. Blood 121, 11–19 (2013).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Rodrigues, P. F. et al. Distinct progenitor lineages contribute to the heterogeneity of plasmacytoid dendritic cells. Nat. Immunol. 19, 711–722 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Dress, R. J. et al. Plasmacytoid dendritic cells develop from Ly6D+ lymphoid progenitors distinct from the myeloid lineage. Nat. Immunol. 20, 852–864 (2019).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Satpathy, A. T. et al. Notch2-dependent classical dendritic cells orchestrate intestinal immunity to attaching-and-effacing bacterial pathogens. Nat. Immunol. 14, 937–948 (2013).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Anderson, D. A. III, Dutertre, C. A., Ginhoux, F. & Murphy, K. M. Genetic models of human and mouse dendritic cell development and function. Nat. Rev. Immunol. 21, 101–115 (2020).

    PubMed 
    Article 
    CAS 

    Google Scholar
     

  • Durai, V. & Murphy, K. M. Functions of murine dendritic cells. Immunity 45, 719–736 (2016).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Cervantes-Barragan, L. et al. Plasmacytoid dendritic cells control T-cell response to chronic viral infection. Proc. Natl Acad. Sci. USA 109, 3012–3017 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Hildner, K. et al. Batf3 deficiency reveals a critical role for CD8α+ dendritic cells in cytotoxic T cell immunity. Science 322, 1097–1100 (2008).

    CAS 
    PubMed 
    PubMed Central 
    Article 
    ADS 

    Google Scholar
     

  • Shortman, K. How does batf3 determine dendritic cell development? Immunol Cell Biol 93, 681–682 (2015).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Satpathy, A. T. et al. Zbtb46 expression distinguishes classical dendritic cells and their committed progenitors from other immune lineages. J. Exp. Med. 209, 1135–1152 (2012).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Motomura, Y. et al. The transcription factor E4BP4 regulates the production of IL-10 and IL-13 in CD4+ T cells. Nat. Immunol. 12, 450–459 (2011).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Sterneck, E., Zhu, S., Ramirez, A., Jorcano, J. L. & Smart, R. C. Conditional ablation of C/EBPβ demonstrates its keratinocyte-specific requirement for cell survival and mouse skin tumorigenesis. Oncogene 25, 1272–1276 (2006).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Kamizono, S. et al. Nfil3/E4bp4 is required for the development and maturation of NK cells in vivo. J. Exp. Med. 206, 2977–2986 (2009).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Camberis, M., Le Gros, G. & Urban, J.Jr Animal model of Nippostrongylus brasiliensis and Heligmosomoides polygyrus. Curr. Protoc. Immunol. 19, 12 (2003).

    PubMed 

    Google Scholar
     

  • Kim, S. et al. High amount of transcription factor IRF8 engages AP1–IRF composite elements in enhancers to direct type 1 conventional dendritic cell identity. Immunity 53, 759–774.e9 (2020).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Skene, P. J., Henikoff, J. G. & Henikoff, S. Targeted in situ genome-wide profiling with high efficiency for low cell numbers. Nat. Protoc. 13, 1006–1019 (2018).

    CAS 
    PubMed 
    Article 

    Google Scholar
     

  • Zhu, Q., Liu, N., Orkin, S. H. & Yuan, G. C. CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis. Genome Biol. 20, 192 (2019).

    PubMed 
    PubMed Central 
    Article 
    CAS 

    Google Scholar
     

  • Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 2114–2120 (2014).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Iwata, A. et al. Quality of TCR signaling determined by differential affinities of enhancers for the composite BATF–IRF4 transcription factor complex. Nat. Immunol. 18, 563–572 (2017).

    CAS 
    PubMed 
    PubMed Central 
    Article 

    Google Scholar
     

  • Source link