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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 19, 2022 |
| Title |
Ablation of cDC2 specification by triple mutations in the Zeb2 enhancer [CUT&RUN] |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
The divergence of the common dendritic cell progenitor (CDP) into specified progenitors for the cDC1 and cDC2 dendritic cells subsets is poorly understood. Some transcription factors (TFs) act in commitment of already specified progenitors, such as Batf3 which stabilizes Irf8 autoactivation at the +32 kb Irf8 enhancer, but the mechanism of CDP divergence remains unknown. Here, we report the transcriptional basis of CDP divergence and describe the first requirements for pre-cDC2 specification. Genetic epistasis analysis suggested that Nfil3 acts upstream of Id2, Batf3, and Zeb2 in cDC1 development but has not revealed its mechanism or targets. Analysis of newly generated NFIL3 reporter mice showed extremely transient NFIL3 expression during cDC1 specification. CUT&RUN and ChIP-seq analysis identified endogenous NFIL3 binding in the –165 kb Zeb2 enhancer at three sites that also bind CCAAT-enhancer-binding proteins C/EBPa and C/EBPb. 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, respectively. Mutation of all three NFIL3/C/EBP sites ablated Zeb2 expression in myeloid, but not lymphoid progenitors, causing complete loss of pre-cDC2 specification and mature cDC2 development in vivo. These mice failed to generate TH2 responses against H. polygyrus infection, consistent with cDC2 supporting TH2 responses to helminths. Thus, CDP divergence is controlled by competition between NFIL3 and C/EBPs at the –165 kb Zeb2 enhancer.
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| Overall design |
Examination of endogenous NFIL3 binding in the primary BM cells; NFIL3, C/EBPa and C/EBPb binding in the Hoxb8 cell lines by CUT&RUN.
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| Contributor(s) |
Liu T, Kim S, Murphy KM |
| Citation(s) |
35732734 |
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| Submission date |
Nov 09, 2021 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Tiantian Liu |
| E-mail(s) |
ltt0321@gmail.com
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| Organization name |
Washington University in St. Louis
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| Department |
Pathology and Immunology
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| Lab |
Dr. Kenneth Murphy
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| Street address |
660 S. Euclid Ave.
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| City |
Saint Louis |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (9)
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| This SubSeries is part of SuperSeries: |
| GSE188579 |
Ablation of cDC2 development by triple mutations within the Zeb2 enhancer |
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| Relations |
| BioProject |
PRJNA779044 |
| SRA |
SRP345273 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE188482_RAW.tar |
201.0 Mb |
(http)(custom) |
TAR (of BED, BEDGRAPH, TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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