KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| BV510 or V450 rat anti-mouse CD45R/B220 (clone: RA3–6B2) | BD Biosciences | Cat#: 563103 Cat#: 560473 |
| PE mouse anti-rat CD90/mouse CD90.1 (clone: OX-7) | BD Biosciences | Cat#: 554898 |
| V500 rat anti-mouse I-A/I-E (clone: M5/114.15.2) | BD Biosciences | Cat#: 562366 |
| V450 rat anti-mouse CD45 (clone: 30-F11) | BD Biosciences | Cat#: 560501 |
| APC or BUV395 or biotin hamster anti-mouse CD11c (clone: HL3) | BD Biosciences | Cat#: 561119 Cat#: 744180 Cat#: 553800 |
| FITC, APC-Cy™ 7, Alexa Fluor® 700 or biotin rat anti-mouse Ly6C (clone: AL-21) | BD Biosciences | Cat#: 553104 Cat#: 560596 Cat#: 561237 Cat#: 557359 |
| PE-Cy™ 7 rat anti-mouse CD8a (clone: 53–6.7) | BD Biosciences | Cat#: 552877 |
| PE-Cy™ 7 or BUV 395 rat anti-mouse CD117 (clone: 2B8) | BD Biosciences | Cat#: 558163 Cat#: 564011 |
| PE-CF594 rat anti mouse-Flt3 (clone: A2F10.1) | BD Biosciences | Cat#: 562537 |
| BV510 rat anti-mouse CD16/32 (clone: 2.4G2) | BD Biosciences | Cat#: 740111 |
| Biotin rat anti-mouse CD19 (clone: 1D3) | BD Biosciences | Cat#: 553784 |
| Purified rat anti-mouse CD16/CD32 (clone: 2.4G2) | BD Biosciences | Cat#: 553142 |
| Brilliant Violet 510™ anti-mouse CD8a (clone: 53–6.7) | BioLegend | Cat#: 100752 |
| PerCP/Cyanine5.5 or Alexa Fluor® 700 anti-rat CD90/mouse CD90.1 (clone: OX-7) | BioLegend | Cat#: 202516 Cat#: 202527 |
| PE/Cyanine7 anti-mouse CD24 (clone: M1/69) | BioLegend | Cat#: 101822 |
| PE anti-mouse XCR1 (clone: ZET) | BioLegend | Cat#: 148204 |
| PE anti-mouse CD103 (clone: 2E7) | BioLegend | Cat#: 121406 |
| APC anti-mouse CD172a (clone: P84) | BioLegend | Cat#: 144014 |
| PE/Dazzle™ 594 anti-mouse/human CD45R/B220 (clone: RA3–6B2) | BioLegend | Cat#: 103258 |
| Brilliant Violet 605™ anti-mouse Ep-CAM (clone: G8.8) | BioLegend | Cat#: 118227 |
| Alexa Fluor® 488 or Brilliant Violet 711™ anti-mouse CD115 (clone: AFS98) | BioLegend | Cat#: 135512 Cat#: 135515 |
| Brilliant Violet 605™ anti-mouse CD64 (clone: X54–5/7.1) | BioLegend | Cat#: 139323 |
| Alexa Fluor® 647 anti-mouse CD11c (clone: N418) | BioLegend | Cat#: 117312 |
| Biotin anti-mouse CD3ε (clone: 145–2C11) | BioLegend | Cat#: 100304 |
| FITC or Biotin anti-mouse Ly6G (clone: 1A8) | BioLegend | Cat#: 127606 Cat#: 127604 |
| Biotin anti-mouse TER-119 (clone: TER-119) | BioLegend | Cat#: 116204 |
| Alexa Fluor® 488 anti-GFP (clone: 1GFP63) | BioLegend | Cat#: 338007 |
| APC or eFluor® 450 anti-mouse CD317 (clone: eBio927) | eBioscience | Cat#: 17–3172-82 Cat#: 48–3172-82 |
| PE or APC-eFluor® 780 anti-mouse CD11c (clone: N418) | eBioscience | Cat#: 12–0114-83 Cat#: 47–0114-80 |
| V450 anti-mouse I-A/I-E (clone: M5/114.15.2) | eBioscience | Cat#: 48–5321-82 |
| PerCP-eFluor™ 710 anti-mouse CD172a (clone: P84) | eBioscience | Cat#: 46–1721-82 |
| APC-eFluor® 780 anti-mouse F4/80 (clone: BM8) | eBioscience | Cat#: 47–4801-82 |
| PerCP-Cyanine5.5 anti-mouse CD11b (clone: M1/70) | eBioscience | Cat#: 45–0112-82 |
| eFluor® 450 anti-mouse NK1.1 (clone: PK136) | eBioscience | Cat#: 48–5941-82 |
| APC-eFluor® 780 anti-mouse CD4 (clone: RM4–5) | eBioscience | Cat#: 47–0042-82 |
| PE-Cyanine7 anti-mouse Sca-1 (clone: D7) | eBioscience | Cat#: 25–5981-82 |
| PE-Cyanine7 anti-mouse CD45.1 (clone: A20) | eBioscience | Cat#: 25–0453-82 |
| eFluor450® anti-mouse CD45 (clone: 30-F11) | eBioscience | Cat#: 48–0451-82 |
| PE anti-mouse Vα2 TCR (clone: B20.1) | eBioscience | Cat#: 12–5812-82 |
| PerCP-eFluor™ 710 anti-mouse SiglecH (clone: eBio440c) | eBioscience | Cat#: 46–0333-82 |
| APC-eFluor® 780 anti-mouse CD44 (clone: IM7) | eBioscience | Cat#: 47–0441-82 |
| PE-anti-human/mouse IRF4 (clone: 3E4) | eBioscience | Cat#: 12–9858-82 |
| PerCP-eFluor™ 710-anti human/mouse-IRF8 (clone: V3GYWCH) | eBioscience | Cat#: 46–9852-82 |
| Biotin-anti-mouse CD105 (clone: MJ7/18) | eBioscience | Cat#: 13–1051-82 |
| PE-IL-12/IL-23 p40 monoclonal antibody (clone: C17.8) | eBioscience | Cat#: 12–7123-82 |
| PE anti-mouse CD115 (clone: AFS98) | TONBO biosciences | Cat#: 50–1152 |
| PE anti-mouse Ly6G (clone: 1A8) | TONBO biosciences | Cat#: 50–1276 |
| Rabbit IgG PE-conjugated antibody | R&D systems | Cat#: F0110 |
| Rabbit anti-BATF3 | Tussiwand 2012 | N/A |
| Bacterial and Virus Strains | ||
| Subcloning Efficiency™ DH5α™ competent cells | Invitrogen™ | Cat#: 18265017 |
| Chemicals, Peptides, and Recombinant Proteins | ||
| TransIT-LTI | MIRUS Bio | Cat#: MIR 2300 |
| Brefeldin A | Sigma-Aldrich | Cat#: B6542 |
| 20% Paraformaldehyde (formaldehyde) aqueous solution | Electron Microscopy Sciences | Cat#: 15713-S |
| Saponin | Sigma-Aldrich | Cat#: S7900 |
| Lipopolysaccharide from Escherichia coli (055:B5) | Sigma-Aldrich | Cat#: L2880 |
| Polyinosinic–polycytidylic acid sodium salt_Poly (I:C) | Sigma-Aldrich | Cat#: P1530 |
| Poly(deoxyinosinic-deoxycytidylic) acid sodium salt | Sigma-Aldrich | Cat#: P4929 |
| Doxycycline hyclate | Sigma-Aldrich | Cat#: D9891 |
| EasyTides® dCTP | PerkinElmer | Cat#: BLU513Z500UC |
| Bovine Serum Albumin Endotoxin-Free, BSA | Akron Biotech | Cat#: AK8917 |
| Iscove’s Modified Dulbecco’s Medium (IMDM) | Gibco | Cat#: 12440–046 |
| Opti-MEM Reduced Serum Medium | Gibco | Cat#: 31985–070 |
| Hexadimethrine bromide (Polybrene) | Sigma-Aldrich | Cat#: H9268 |
| Fetal Bovine Serum (Characterized) | HyClone | Cat#: SH30071.03 |
| Sodium pyruvate | Corning | Cat#: 25–000-CI |
| L-Glutamine | Gibco | Cat#: 25030–164 |
| Pen Strep (Penicillin Streptomycin) | Gibco | Cat#: 15140–122 |
| 2-Mercaptoethanol | Sigma-Aldrich | Cat#: M3148 |
| MEM Non-essential Amino Acid Solution (100X) | Sigma-Aldrich | Cat#: M7145 |
| Dnase I | Sigma-Aldrich | Cat#: D4527 |
| Collagenase B | Sigma-Aldrich | Cat#: COLLB-RO |
| Collagenase D | Sigma-Aldrich | Cat#: COLLD-RO |
| Aprotinin bovine recombinant | Sigma-Aldrich | Cat#: A6103 |
| Leupeptin hydrochloride microbial, ≥90% (HPLC) | Sigma-Aldrich | Cat#: L9783 |
| HEPES | Sigma-Aldrich | Cat#: H3375 |
| Ethylenediaminetetraacetic acid (EDTA) | Sigma-Aldrich | Cat#: E9884 |
| Hanks’ Balanced Salt Solution (HBSS) 10X | Gibco | Cat#: 14185–052 |
| Percoll ® | Sigma-Aldrich | Cat#: P4937 |
| Normal rat serum | STEM CELL Technologies | Cat#: 13551 |
| CFSE [5-(and 6)-carboxyfluorescein diaetate succinimidyl ester] | eBiosciences | Cat#: 65–0850-84 |
| Recombinant murine IFN-gamma | PeproTech | Cat#: 315–05 |
| Recombinant murine GM-CSF | PeproTech | Cat#: 315–03 |
| Recombinant murine IL-4 | PeproTech | Cat#: 214–14 |
| Recombinant murine IL-3 | PeproTech | Cat#: 213–13 |
| Recombinant murine M-CSF | PeproTech | Cat#: 315–02 |
| Recombinant murine SCF | PeproTech | Cat#: 250–03 |
| Soluble Toxoplasma gondii antigen (STAg) | Tussiwand et al., 2012 | N/A |
| Resources and Reagents | ||
| MagniSort™ streptavidin negative selection beads | Invitrogen™ | Cat#: MSNB-6002 |
| CD11c MicroBeads UltraPure (mouse) | Miltenyi Biotec | Cat#: 130–108-338 |
| Qdot™ 605 Streptavidin conjugate | Invitrogen™ | Cat#: Q10101MP |
| Brilliant Violet 711™-Streptavidin | BioLegend | Cat#: 405241 |
| PE-Cy™7 Streptavidin | BD Biosciences | Cat#: 557598 |
| Critical Commercial Assays | ||
| NucleoSpin RNA XS Kit | Machery-Nagel | Cat#: 740902.50 |
| Foxp3 / Transcription Factor Staining Buffer Set | eBioscience | Cat#: 00–5523-00 |
| WT-Pico Kit | Applied Biosystems™ | Cat#: 902622 |
| Deposited Data | ||
| Microarray | This study |
GSE140451 GSE140452 |
| Microarray | Durai et al., 2017 | GSE110789 |
| Microarray | ImmGen |
GSE15079 GSE37448 |
| ATAC-seq | ImmGen | GSE100738 |
| ChIP-seq (IRF4, IRF8, BATF3, H3K4me1, H3K27ac) | Grajales-Reyes et al., 2015 | GSE66899 |
| ChIP-seq (PU.1) | Allhoff et al., 2014 | GSE57563 |
| Experimental Models: Cell Lines | ||
| Platinum-E retroviral packaging cell line | Morita et al., 2000 | N/A |
| HEK293FT cell line | Invitrogen™ | Cat#: R70007 |
| Experimental Models: Organisms/Strains | ||
| Mouse: C57BL/6 | Jackson Laboratory | JAX: 000664 |
| Mouse: 129S6/SvEv Tac | Taconic Biosciences | 129SVE-(F or M) |
| Mouse: B6.129S6(C)-Zbtb46tm1.1Kmm/J (Zbtb46GFP/GFP) | Jackson Laboratory | JAX: 027618 |
| Mouse: B6.129S6-Snx22tm1.1Kmm/J (Snx22GFP/GFP) | Jackson Laboratory | JAX: 031837 |
| Mouse: B6J.129(Cg)-Gt(ROSA)26Sortm1.1(CAG-cas9*,-EGFP)Fezh/J (Rosa26Cas9-GFP /Cas9-GFP) | Jackson Laboratory | JAX: 026179 |
| Mouse: B6(Cg)-Irf8tm1.1Hm/J | Jackson Laboratory | JAX: 014175 |
| Mouse: B6.C-Tg(CMV-cre)1Cgn/J | Jackson Laboratory | JAX: 006054 |
| Mouse: B6.129S1-Irf4tm1Rdf/J | Jackson Laboratory | JAX: 009380 |
| Mouse: B6.129S4-Gt(ROSA)26Sortm1(FLP1)Dym/JRainJ | Jackson Laboratory | JAX: 009086 |
| Mouse: C57BL/6J-Irf8em1Kmm/J (Irf8 +32 kb–/–) | Jackson Laboratory | JAX: 032744 |
| Mouse: C57BL/6-Tg(TcraTcrb)1100Mjb/J (OT-I) | Jackson Laboratory | JAX: 003831 |
| Mouse: 129S-Batftm1.1Kmm/J | Jackson Laboratory | JAX: 013757 |
| Mouse: 129S-Batf3tm1.1Kmm/J | Jackson Laboratory | JAX: 013596 |
| Oligonucleotides | ||
| Sequences of primers used for cloning Zbtb46 enhancer elements and mutants (5’ > 3’) | ||
| +23 kb (FW): CATGAAGCTTACAAACCCCTGACTGAAAAG | Sigma-Aldrich | N/A |
| +23 kb (RV): TCGAGGATCCAGAACTTTGCTTCCACTC | Sigma-Aldrich | N/A |
| +32 kb (FW): CATGAAGCTT ACAAGACCCAAGTTTGCTG | Sigma-Aldrich | N/A |
| +32 kb (RV): TCGAGGATCCTCAAATGGAAGAAATCACCT | Sigma-Aldrich | N/A |
| +48 kb (FW): CATGATCCATCCTTTGGTTTAAGCACCTC | Sigma-Aldrich | N/A |
| +48 kb (RV): TCGAGGATCCTAAATGTAGCATTCAACTC | Sigma-Aldrich | N/A |
| +23 kb ΔEICE_a (FW): CATAAGATAGTGAGCAACCAAAGT | Sigma-Aldrich | N/A |
| +23 kb ΔEICE_a (RV): ACTTTGGTTGCTCACTATCTTATG | Sigma-Aldrich | N/A |
| +23 kb ΔEICE_b (FW): GCCAGGCCGGTGCAGAGAAGGGTAGCACCGAGAG | Sigma-Aldrich | N/A |
| +23 kb ΔEICE_b (RV): TCTCGGTGCTACCCTTCTCTGCACCGGCCTGGC | Sigma-Aldrich | N/A |
| +23 kb ΔEICE_c (FW): GTAGCACCGAGAAGGGCAAGTGGT | Sigma-Aldrich | N/A |
| +23 kb ΔEICE_c (RV): ACCACTTGCCCTTCTCGGTGCTAC | Sigma-Aldrich | N/A |
| +23 kb ΔEICE_d (FW): AGTGGTGTATGGTGGGCAGGCATC | Sigma-Aldrich | N/A |
| +23 kb ΔEICE_d (RV): GATGCCTGCCCACCATACACCACT | Sigma-Aldrich | N/A |
| Sequences of primers used for cloning Snx22 enhancer elements and mutants (5’ > 3’) | ||
| –12 kb (FW): CATGAAGCTTAGCCAGCAGCTTATCTTCCA | Sigma-Aldrich | N/A |
| –12 kb (RV): TCGAGGATCCAGTGGCTATTGGGGACACAC | Sigma-Aldrich | N/A |
| –3 kb (FW): ATGAAGCTTTGTGAGAGAGAAGGAAACAGAGG | Sigma-Aldrich | N/A |
| –3 kb (RV): TCGAGGATCCGGCAGAGGACATCCTTACCA | Sigma-Aldrich | N/A |
| –12 kb ΔAICE_a (FW): ACCCACAGAAAAACCCAGGACCTTTCCCTA | Sigma-Aldrich | N/A |
| –12 kb ΔAICE_a (FW): TAGGGAAAGGTCCTGGGTTTTTCTGTGGGT | Sigma-Aldrich | N/A |
| –12 kb ΔAICE_b (FW): GAGATCCGACAACTGTTCCCCCTGTCAGCT | Sigma-Aldrich | N/A |
| –12 kb ΔAICE_b (FW): AGCTGACAGGGGGAACAGTTGTCGGATCTC | Sigma-Aldrich | N/A |
| –3 kb ΔEICE_c (FW): ACATCCCAAAGACCCCAGCACTTC | Sigma-Aldrich | N/A |
| –3 kb ΔEICE_c (FW): GAAGTGCTGGGGTCTTTGGGATGT | Sigma-Aldrich | N/A |
| –3 kb ΔEICE_d (FW): TGGTAGGGGTCAAGAGACCACACC | Sigma-Aldrich | N/A |
| –3 kb ΔAICE_d (FW): GGTGTGGTCTCTTGACCCCTACCA | Sigma-Aldrich | N/A |
| Sequences of sgRNA for targeting Zbtb46 enhancer (+23 kb EICE_b) (5’ > 3’) | ||
| sgRNA1 (FW): CACCGGGTGCAGAGGGAACTGAGAA | Sigma-Aldrich | N/A |
| sgRNA1 (RW): AAACTTCTCAGTTCCCTCTGCACCC | Sigma-Aldrich | N/A |
| sgRNA2 (FW): CACCGAGAAGCCAGGCCGGTGCAGA | Sigma-Aldrich | N/A |
| sgRNA2 (RW): AAACTCTGCACCGGCCTGGCTTCTC | Sigma-Aldrich | N/A |
| Sequences of sgRNA for targeting Snx22 enhancers (–12 kb AICE) (5’ > 3’) | ||
| sgRNA1 (FW): CACCGAGTCATTTGGAAACAGTTGT | Sigma-Aldrich | N/A |
| sgRNA1 (RW): AAACACAACTGTTTCCAAATGACTC | Sigma-Aldrich | N/A |
| sgRNA2 (FW): CACCGGACAGGGGGAAATAGTCATT | Sigma-Aldrich | N/A |
| sgRNA2 (RW): AAACAATGACTATTTCCCCCTGTCC | Sigma-Aldrich | N/A |
| Sequences of sgRNA for targeting Snx22 enhancers (–3 kb EICE) (5’ > 3’) | ||
| sgRNA3 (FW): CACCGCCAGCACTTCTCCTTGGTAG | Sigma-Aldrich | N/A |
| sgRNA3 (RW): AAACCTACCAAGGAGAAGTGCTGGC | Sigma-Aldrich | N/A |
| sgRNA4 (FW): CACCGAAGGGAAATGACCCCTACCA | Sigma-Aldrich | N/A |
| sgRNA4 (RW): AAACTGGTAGGGGTCATTTCCCTTC | Sigma-Aldrich | N/A |
| Sequences of EMSA probes (5’ > 3’) | ||
| Snx22 –12 kb AICE (FW): CAGGGGGAAATAGTCATTTGGAAACAGTTGT | Sigma-Aldrich | N/A |
| Snx22 –12 kb AICE (RV): CCGACAACTGTTTCCAAATGACTATTTCC | Sigma-Aldrich | N/A |
| Snx22 –3 kb EICE (FW): GTGCTGGGGTTTCATTTCCTCTTTGGGAT | Sigma-Aldrich | N/A |
| Snx22 –12 kb EICE (RV): GATCCCAAAGAGGAAATGAAACCCCAG | Sigma-Aldrich | N/A |
| Software and Algorithms | ||
| GraphPad Prism 7.0 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| FlowJo v10 | Tree Star | https://www.flowjo.com/solutions/flowjo |
| FACSDiva | BD Biosciences | https://www.bdbiosciences.com/en-us/instruments/research-instruments/research-software/flow-cytometry-acquisition/facsdiva-software |
| ArrayStar 15 | DNASTAR | https://www.dnastar.com/ |
| Metascape | Tripathi et al., 2015 | https://metascape.org/gp/index.html#/main/step1 |
| Morpheus | Broad Institute |
https://software.broadinstitute.org/morpheus/ |