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Ablation of cDC2 development by triple mutations within the Zeb2 enhancer

Abstract

The divergence of the common dendritic cell progenitor1,2,3 (CDP) into the conventional type 1 and type 2 dendritic cell (cDC1 and cDC2, respectively) lineages4,5 is poorly understood. Some transcription factors act in the commitment of already specified progenitors—such as BATF3, which stabilizes Irf8 autoactivation at the +32 kb Irf8 enhancer4,6—but the mechanisms controlling the initial divergence of CDPs remain unknown. Here we report the transcriptional basis of CDP divergence and describe the first requirements for pre-cDC2 specification. Genetic epistasis analysis7 suggested that Nfil3 acts upstream of Id2, Batf3 and Zeb2 in cDC1 development but did not reveal its mechanism or targets. Analysis of newly generated NFIL3 reporter mice showed extremely transient NFIL3 expression during cDC1 specification. CUT&RUN and chromatin immunoprecipitation followed by sequencing identified endogenous NFIL3 binding in the –165 kb Zeb2 enhancer8 at three sites that also bind the CCAAT-enhancer-binding proteins C/EBPα and C/EBPβ. In vivo mutational analysis using CRISPR–Cas9 targeting showed that these NFIL3–C/EBP sites are functionally redundant, with C/EBPs supporting and NFIL3 repressing Zeb2 expression at these sites. A triple mutation of all three NFIL3–C/EBP sites ablated Zeb2 expression in myeloid, but not lymphoid progenitors, causing the complete loss of pre-cDC2 specification and mature cDC2 development in vivo. These mice did not generate T helper 2 (TH2) cell responses against Heligmosomoides polygyrus infection, consistent with cDC2 supporting TH2 responses to helminths9,10,11. Thus, CDP divergence into cDC1 or cDC2 is controlled by competition between NFIL3 and C/EBPs at the –165 kb Zeb2 enhancer.

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Fig. 1: Transient NFIL3 expression drives cDC1 specification.
Fig. 2: Mutation of three NFIL3 binding sites in the –165 kb Zeb2 enhancer abrogates cDC2 and monocyte development.
Fig. 3: C/EBPs bind to the –165 kb Zeb2 enhancer to support cDC2 and monocyte development.
Fig. 4: Zeb2 is only required for the specification of cDC2, which support TH2 responses to H. polygyrus infection.

Data availability

The CUT&RUN, ChIP–seq and RNA-seq data generated in the current study are available in the Gene Expression Omnibus database with the accession number GSE188579. ChIP–seq datasets for NFIL3 in T cells were provided by V. K. Kuchroo28. ChIP–seq datasets for C/EBPβ in Ly-6Clow monocytes34 (GSE80031) and gene expression microarray datasets for Cebpa KO hematopoietic stem and progenitor cells22 (GSE146288) were downloaded and reanalyzed. Source data are provided with this paper.

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Acknowledgements

This work is supported by the US National Institutes of Health (R01AI150297, R01CA248919); D.-H.K. is supported by the National Research Foundation of Korea (NRF-2020R1A6A3A03037855); S.T.F. is a Cancer Research Institute Irvington Fellow supported by the Cancer Research Institute; R.W. is supported by the National Institutes of Health (5T32GM007200, F30CA247262); S.J.V.D. is supported by the National Institutes of Health (R01HL148033); M.S.D. is supported by NIH/NIDDK (R01DK122790-01A1); and M.K. is supported by AMED CREST (JP19gm1310002). We thank J. M. White at the Department of Pathology and Immunology Transgenic Mouse Core at Washington University in St Louis, and the Genetic Editing and iPS Cell (GEiC) centre at Washington University in St Louis for the generation of mouse models; the Genome Technology Access Center at the McDonnell Genome Institute at Washington University School of Medicine for help with genomic analysis; M. J. Murphy for advice on EMSA probe design; A. Look and T. Mak for providing Nfil3−/− mice; V. Durai for advice on embryonic stem cell targeting; H. W. Virgin for providing Hoxb8 construct; V. K. Kuchroo for providing NFIL3 ChIP–seq data in T cells; J. F. Urban Jr for providing H. polygyrus L3 larvae; and K. Saylor for technical assistance in breeding the Cebpbfl/fl mice. This research was supported in part by the Intramural Research Program of the NIH, National Cancer Institute, Center for Cancer Research. The content of this publication does not necessarily reflect the views or policies of the Department of Health and Human Services, nor does mention of trade names, commercial products or organizations imply endorsement by the US Government. This work benefitted from data assembled by the ImmGen consortium.

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Authors

Contributions

T.-T.L., T.L.M. and K.M.M. designed the study. T.-T.L., S.K., F.O. and T.L.M. performed experiments, with advice from X.H., S.T.F. and R.W. P.D. performed experiments related to helminths infection. D.-H.K. and S.J.V.D. performed experiments related to ILC2 and tuft cell analysis; P.F.J. provided Cebpbfl/fl mice and advice. M.K. provided Nfil3fl/fl mice and advice. T.E., M.S.D. and S.J.V.D. provided assistance with experimental design. T.-T.L., T.L.M. and K.M.M. wrote the manuscript with contributions from all authors.

Corresponding author

Correspondence to Kenneth M. Murphy.

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M.S.D. is a consultant for Inbios, Vir Biotechnology, Senda Biosciences, and Carnival Corporation, and on the Scientific Advisory Boards of Moderna and Immunome. The Diamond laboratory has received unrelated funding support in sponsored research agreements from Moderna, Vir Biotechnology, Kaleido, and Emergent BioSolutions. K.M.M. is on the Scientific Advisory Board for Harbour Biomed.

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Extended data figures and tables

Extended Data Fig. 1 Generation of Nfil3GFP reporter mice.

a, Schematic diagrams of mouse Nfil3 WT allele, targeting vector and targeted allele. Filled and open boxes denote coding and noncoding exons of Nfil3, respectively. N indicate NdeI site; Triangles indicate loxP sequences; TK, thymidine kinase promoter; DTA, diphtheria toxin A; pGK-Neo, neomycin selection cassette. b, Southern blot analysis of Nfil3+/+ and Nfil3GFP/+ mice. Genomic DNA was isolated from mouse liver, digested with NdeI, electrophoresed, and hybridized with Digoxigenin-labeled probes indicated in a. Southern blot with 5’ probe gave a 10.0 and a 5.0 kb band for WT and targeted allele. Southern blot with 3’ probe gave a 10.0 and a 7.7 kb band for WT and targeted allele, respectively. Progeny from ES cell clone 22 were bred to CMV-Cre mice to remove the neomycin selection cassette, and used in the following study. Data shown are one of two similar experiments. For gel source data, see Supplementary Figure 1. c, d, Frequency of cDC1 and representative flow plots showing pDCs and cDCs differentiated from WT CD117hi BM progenitors retrovirally expressing NFIL3 and GFP-NFIL3. Data are pooled from three independent experiments. e, f, Frequency of cDC1 and representative flow plots showing splenic pDCs and cDCs in WT and Nfil3GFP/GFP mice. Data are pooled from two independent experiments (n = 5 for each genotype). WT versus Nfil3GFP/GFP cDC1 P = 0.0952. g, PCA of the cDC1s and IL-4 + LPS stimulated B cells from WT, Nfil3GFP/GFP and Nfil3–/– mice by all expressed mRNAs. Mean ± s.d.; NS, not significant; f: unpaired, two-tailed Mann−Whitney test.

Source Data

Extended Data Fig. 2 Nfil3GFP reporter mice analysis.

a, Representative FACS histograms of GFP-NFIL3 expression of indicated splenic cell types from WT and Nfil3GFP/GFP mice. TCRβ+ T cells were directly analyzed or stimulated with plate-bound α-CD3 + α-CD28 (2 μg/mL) antibodies for 72 h. CD19+ B cells were directly analyzed or stimulated with IL-4 (20 ng/mL) + LPS (5 μg/mL) for 24 h. Data shown are one of three similar experiments. b, Nfil3 transcripts, measured by RT-qPCR, in cells sorted from a. Data shown are one of two similar experiments. c, d, Representative flow plots showing GFP-NFIL3 expression in indicated BM cell types from WT and Nfil3GFP/GFP mice. Data shown are one of three similar experiments. For sequential gating strategies, see Supplementary Figure 1.

Source Data

Extended Data Fig. 3 Nfil3 acts as a repressor to drive cDC1 specification.

a, Flow cytometric analysis of GFP-NFIL3+ BM cells from Nfil3GFP/GFP mice. Data shown are one of three similar experiments. b, c, Representative flow plots and frequencies of pDCs and cDCs differentiated from GFP-NFIL3 CDPs and GFP-NFIL3+ CDPs sorted from Nfil3GFP/GFP mice. Data are pooled from five independent experiments. d, Representative flow plots showing splenic cDC1s, cDC2s and pDCs from chimeras generated with equal mix of CD45.1+ WT BM and CD45.2+ Nfil3+/+ or Nfil3–/– BM. e, Chimerism ratio of indicated lineages in chimeras generated as in d, presented as the ratio of CD45.2+ to CD45.1+ cells normalized to the ratio of CD45.2+ to CD45.1+ LSK cells within the same mouse. Data are pooled from two independent experiments (n = 5 for Nfil3+/+ and n = 4 for Nfil3–/– mixed BM chimeras). f, g, Frequency of cDC1 and representative flow plots showing pDCs and cDCs differentiated from WT CD117hi BM progenitors retrovirally expressing NFIL3, NFIL3-KRAB or NFIL3-VP16. Data are pooled from three independent experiments. Schematic diagrams of NFIL3, NFIL3-KRAB and NFIL3-VP16 are depicted next to the plots. DBD denotes DNA-binding domain. Mean ± s.d.; e: unpaired, multiple t tests with Welch correction.

Source Data

Extended Data Fig. 4 NFIL3 binds to the –165 kb Zeb2 enhancer.

a, Representative flow plots showing DC potential of Hoxb8 cell line. The Hoxb8 cells were washed twice with cold PBS to remove residual β-estradiol and cytokines before standard Flt3L culture for 7 days. b, c, Frequency of cDC1 and representative flow plots showing cDCs differentiated from Hoxb8 cells retrovirally expressing NFIL3. Data are pooled from two independent experiments (n = 6 for each cell line). d, Nfil3 transcripts, measured by RT-qPCR, in GFP-NFIL3 CDP, GFP-NFIL3+ CDP, and Hoxb8 cell lines retrovirally expressing NFIL3 used for CUT&RUN and ChIP-seq experiments. Data are pooled from three independent experiments for GFP-NFIL3 CDP, GFP-NFIL3+ CDP, and two independent experiments for Hoxb8 cell lines. e, Rank of the NFIL3 CUT&RUN and ChIP-seq peaks at the –165 kb Zeb2 enhancer. f, Alignment of human, genome draft hg19, and mouse, genome draft mm10, for the –165 kb Zeb2 enhancer regions. Red boxes indicate NFIL3 binding sites. g, EMSA showing NFIL3 binding at –165 kb Zeb2 enhancer. A 37 bp 32P-labelled DNA probe encompassing the NFIL3 binding site 1 from the –165 kb Zeb2 enhancer was synthesized as site 1 probe. A 40 bp 32P-labelled DNA probe containing an optimized NFIL3 motif and flanking sequence of the NFIL3 binding site 3 from the –165 kb Zeb2 enhancer was synthesized as N > C probe. NFIL3 binding specificity was demonstrated by competition with non-radioactively labeled probes and supershift with anti-NFIL3 antibody. The competitor 1 indicates site 1, and the competitor 1mut has the same sequence as site 1 except that the NFIL3 binding site 1 was mutated. Data shown are one of two similar experiments. For gel source data, see Supplementary Figure 1. Mean ± s.d.

Source Data

Extended Data Fig. 5 Mutation of three NFIL3 binding sites in the –165 kb Zeb2 enhancer abrogates cDC2 development (Part I).

a, Targeting strategy of NFIL3 binding site mutant mice. gRNA-1 and donor-1 were introduced into WT zygotes to mutate NFIL3 binding site 1. Δ1 mice were generated from the first round of targeting. gRNA-2, gRNA-3 and donor-2 were introduced into Δ1 homozygous zygotes to mutant NFIL3 binding site 2 and 3. Δ1+2 and Δ1+3 mice were generated from the second round of targeting. gRNA-4 and donor-3 were introduced into Δ1+2 heterozygous zygotes to mutate NFIL3 binding site 3. Δ1+2+3 mice were generated from the third round of targeting. b, Representative flow plots showing splenic cDCs and pDCs in WT, Δ1, Δ1+2, Δ1+3 and Δ1+2+3 mice. c, Number of splenic cDC1 and cDC2 in WT, Δ1, Δ1+2, Δ1+3 and Δ1+2+3 mice. Data are pooled from five independent experiments (n = 12 for WT, n = 11 for Δ1, Δ1+2, Δ1+3, and n = 8 for Δ1+2+3 mice). WT versus Δ1+2 cDC1 P = 0.2447, WT versus Δ1 cDC2 P = 0.9885, WT versus Δ1+2 cDC2 P > 0.9999. NS, not significant; c: Brown−Forsythe and Welch ANOVA with Dunnett’s T3 multiple comparisons test.

Source Data

Extended Data Fig. 6 Mutation of three NFIL3 binding sites in the –165 kb Zeb2 enhancer abrogates cDC2 development (Part II).

a, Representative flow plots showing migratory and resident cDCs in mesenteric lymph nodes (MLNs) from WT and Δ1+2+3 naïve mice or mice infected with H. polygyrus (H.p.) for 14 days. b, Frequency of migratory CD24 CD172a+ cDC2 and resident CD172a+ cDC2 in MLNs from WT and Δ1+2+3 naïve mice or mice infected with H.p. for 14 days. Data are pooled from seven independent experiments (n = 9 for naïve mice and n = 5 for H.p. infected mice). c, Frequency of migratory CD103 CD11b+ cDC2 and resident CD172a+ cDC2 in SLNs from WT and Δ1+2+3 mice. Data are pooled from three independent experiments (n = 3 for each genotype). d, Frequency of CD103 CD11b+ cDC2 in small intestine lamina propria from WT and Δ1+2+3 mice. Data are pooled from four independent experiments (n = 4 for each genotype). e, Representative flow plots showing small intestine lamina propria cDCs in WT and Δ1+2+3 mice. f, Frequency and number of splenic pDC in WT, Δ1, Δ1+2, Δ1+3 and Δ1+2+3 mice. Data are pooled from five independent experiments (n = 12 for WT, n = 11 for Δ1, Δ1+2, Δ1+3, and n = 8 for Δ1+2+3 mice). g, Frequency of BM pDC in WT and Δ1+2+3 mice. Data are pooled from three independent experiments (n = 7 for each genotype). h, IFN-α, measured from splenic pDCs stimulated for 16 h with CpG-A 2216, or left unstimulated. Data are pooled from two independent experiments (n = 4 for each genotype). Mean ± s.d.; b, c, h: unpaired, multiple t tests with Welch correction; d, g: unpaired, two-tailed Mann−Whitney test; f: Brown−Forsythe and Welch ANOVA with Dunnett’s T3 multiple comparisons test.

Source Data

Extended Data Fig. 7 Mutation of three NFIL3 binding sites in the –165 kb Zeb2 enhancer abrogates monocyte development.

a, Representative flow plots showing monocytes among CD45+ peripheral blood cells from WT, Δ1, Δ1+2, Δ1+3 and Δ1+2+3 mice. b, Representative flow plots showing cMoPs and monocytes (Mo) in BM of WT and Δ1+2+3 mice. Data shown are one of five similar experiments. c, Frequency of peripheral blood monocytes, splenic monocytes, and number of splenic monocytes in WT, Δ1, Δ1+2, Δ1+3 and Δ1+2+3 mice. Data are pooled from two independent experiments for peripheral blood monocytes and five independent experiments for splenic monocytes (peripheral blood monocytes: n = 13 for WT, n = 10 for Δ1, n = 8 for Δ1+2, n = 9 for Δ1+3 and n = 7 for Δ1+2+3 mice; splenic monocytes: n = 11 for WT, n = 7 for Δ1, n = 4 for Δ1+2, n = 7 for Δ1+3 and n = 8 for Δ1+2+3 mice). d, Representative flow plots showing splenic B cells and T cells in WT and Δ1+2+3 mice. e, Frequency of splenic B cells and T cells in WT, Δ1, Δ1+2, Δ1+3 and Δ1+2+3 mice. Data are pooled from three independent experiments (n = 9 for WT, n = 7 for Δ1, Δ1+2, Δ1+3, and n = 5 for Δ1+2+3 mice). WT versus Δ1+2+3 B cell P = 0.9238, WT versus Δ1+2+3 T cell P = 0.6980. f, Representative flow plots showing monocytes and macrophages in small intestine lamina propria from WT and Δ1+2+3 mice. g, Frequency of small intestine lamina propria monocytes and macrophages in WT and Δ1+2+3 mice. Data are pooled from four independent experiments (n = 4 for each genotype). Mean ± s.d.; NS, not significant; c, e: Brown−Forsythe and Welch ANOVA with Dunnett’s T3 multiple comparisons test; g: unpaired, two-tailed Mann−Whitney test.

Source Data

Extended Data Fig. 8 C/EBP factors bind to the –165 kb Zeb2 enhancer to support cDC2 and monocyte development.

a, Rank of the C/EBPα and C/EBPβ CUT&RUN peaks at the –165 kb Zeb2 enhancer. b, Representative flow plots showing GFP-reporter activity in monocytes transduced with empty retrovirus (minimal CMV promoter only) or retroviruses expressing the –165 kb Zeb2 enhancer or mutants of the indicated NFIL3/C/EBP binding sites. Data shown are one of three similar experiments. A bar graph on the right shows mean values of MFI ± s.d. c, Representative flow plots showing cDCs differentiated from WT CDPs retrovirally expressing C/EBPγ or C/EBPδ. Data shown are one of two similar experiments. d, Representative flow plots showing monocytes differentiated from WT CDPs retrovirally expressing C/EBPα or C/EBPβ (LAP isoform) (pre-gate: CD317 B220 cells). cDCs expressing empty-retroviral vectors are shown as controls (dashed black lines) for Ly-6C and CD115 expression in MHCII CD11c cells. Data shown are one of two similar experiments. e, Frequency of cDC1s, cDC2s and monocytes in all infected cells (left panel) or infected cDCs (right panel) differentiated from WT or Δ1+2+3 CDPs retrovirally expressing C/EBPα or C/EBPβ (LAP isoform). Data are pooled from four independent experiments. f, Single-cell RNA transcriptome analysis of CDPs showing Cebpa, Cebpb and Cebpe expression visualized with Loupe Browser. g, h, Frequency of cDC2 and representative flow plots showing in vivo developmental potential of Cebpbfl/fl CD117hi BM progenitors transduced with empty retrovirus or retrovirus expressing Cre recombinase. Recipient spleens were analyzed for the presence of retroviral transduced and donor-derived cDCs. Data are pooled from two independent experiments (n = 4 for each retrovirus). i, Gene expression microarray analysis of hematopoietic stem and progenitor cells from WT or Cebpa knockout mice. The cells were left un-treated or treated with Flt3L for 4 h. Shown are averages of quadruplicate gene expression values of the indicated genes. Mean ± s.d.; h: unpaired, two-tailed Mann−Whitney test.

Source Data

Extended Data Fig. 9 Myeloid and lymphoid pathways of pDC development are distinguished by different requirements in the –165 kb Zeb2 enhancer.

a, Representative flow plots showing pDCs and cDCs differentiated from sort purified CDPs and MDPs of WT and Δ1+2+3 mice, assessed after 5 days of culture with Flt3L. Data shown are one of three similar experiments. b, Representative flow plots showing in vivo developmental potential of CDPs and MDPs from WT and Δ1+2+3 mice. Recipient spleens were analyzed for the presence of CD45.2+ donor-derived pDCs and cDCs. Data shown are one of two (CDP) or three (MDP) similar experiments. c, Representative flow plots showing pDCs differentiated from sort purified CMPs and CLPs of WT and Δ1+2+3 mice, assessed after 7 (CMPs) or 5 (CLPs) days of culture with Flt3L. Data shown are one of two (CMP) or three (CLP) similar experiments. d, Representative flow plots showing CDPs (CD115+ CD127), IL-7R+ LPs (CD115 CD127+) and IL-7R CSF1R NPs (CD115 CD127) in the BM of WT and Δ1+2+3 mice (pre-gate: lineage CD16/CD32 CD135+ CD117int-neg cells). Data shown are one of three similar experiments. e, Representative flow plots showing pDCs differentiated from sort purified CDPs, IL-7R+ LPs and IL-7RCSF1R NPs (as in d) of WT and Δ1+2+3 mice, assessed after 4 days of culture with Flt3L. Data shown are one of three similar experiments.

Extended Data Fig. 10 Zeb2 is not required for the maintenance of cDC2, which support TH2 responses to H. polygyrus infection.

a, Diagrams showing DC development in WT, Δ1+2+3, Irf8 +32–/– and Δ1+2+3 × Irf8 +32–/– mice. b, Representative flow plots showing monocytes among CD45+ peripheral blood cells from WT, Δ1+2+3, Irf8 +32–/– and Δ1+2+3 × Irf8 +32–/– mice. c, Frequency of peripheral blood monocytes in WT, Δ1+2+3, Irf8 +32–/– and Δ1+2+3 × Irf8 +32–/– mice. Data are pooled from two independent experiments (n = 6 for WT, Δ1+2+3, n = 7 for Irf8 +32–/– and n = 6 for Δ1+2+3 × Irf8 +32–/– mice). d, Frequency of IL-4, IL-5, IL-13 or IFN-γ expressing CD4+ T cells in MLNs from WT, Δ1+2+3, Irf8 +32–/– and Δ1+2+3 × Irf8 +32–/– naïve mice or mice infected with H.p. for 14 days (pre-gate: TCRβ+ CD4+ cells). Data are pooled from two independent experiments (n = 3 for naïve mice, n = 6 for H.p. infected WT, Δ1+2+3, Irf8 +32–/– mice and n = 5 for H.p. infected Δ1+2+3 × Irf8 +32–/– mice). WT versus Δ1+2+3 × Irf8 +32–/– IL-4 expressing CD4+ T cells in H.p. infected mice P = 0.1044, WT versus Δ1+2+3 × Irf8 +32–/– IL-13 expressing CD4+ T cells in H.p. infected mice P = 0.8243. e, f, Frequency of IgG1+ class-switched B cells (e) or FAS+ GL7+ germinal center B cells (f) of total CD19+ B cells in MLNs from WT or Δ1+2+3 naïve mice or mice infected with H.p. for 14 days (n = 3 for WT or Δ1+2+3 naïve mice, n = 5 for H.p. infected WT mice and n = 4 for H.p. infected Δ1+2+3 mice). WT versus Δ1+2+3 IgG1+ class-switched B cells in H.p. infected mice P = 0.2145. g, Total serum IgE and IgG1 in naïve WT, Δ1+2+3 mice or mice infected with H.p. for 14 days. Data are pooled from two independent experiments (n = 4 for naïve mice and n = 9 for H.p. infected mice). h, Frequency of peripheral blood eosinophils and neutrophils in WT and Δ1+2+3 mice (n = 8 for each genotype). i, Number of ILC2s per cm small intestine and frequency of ILC2s in small intestine lamina propria CD45+ cells of WT and Δ1+2+3 mice (n = 3 for each genotype). WT versus Δ1+2+3 ILC2 number P > 0.9999, frequency P = 0.4000. j, Number of tuft cells per cm small intestine and frequency of tuft cells in small intestine epithelium CD45 cells of WT and Δ1+2+3 mice (n = 3 for each genotype). WT versus Δ1+2+3 tuft cell number P = 0.7000, frequency P = 0.7000. Mean ± s.d.; NS, not significant; c: Brown−Forsythe and Welch ANOVA with Dunnett’s T3 multiple comparisons test; d: ordinary two-way ANOVA with Dunnett’s multiple comparisons test; eg: unpaired, multiple t tests with Welch correction; hj: unpaired, two-tailed Mann−Whitney test.

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Supplementary information

Supplementary Figure 1

FACS sequential gating/sorting strategies and gel source data.

Reporting Summary

Peer Review File

Supplementary Table 1

List of oligonucleotide primers.

Supplementary Table 2

gRNA and ssODN donor sequences for generating Δ1, Δ1+2, Δ1+3, Δ1+2+3 mice, and genomic DNA sequences of the –165 kb Zeb2 enhancer in the new mouse models.

Supplementary Table 3

List of antibodies used for flow cytometry.

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Liu, TT., Kim, S., Desai, P. et al. Ablation of cDC2 development by triple mutations within the Zeb2 enhancer. Nature 607, 142–148 (2022). https://doi.org/10.1038/s41586-022-04866-z

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