Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| anti-mouse CD3ε | eBioscience | Cat# 16-0031-82, RRID: AB_468847 |
| anti-mouse CD28 | eBioscience | Cat# 14-0281-82, RRID: AB_467190 |
| anti-mouse IFNγ | Bio X Cell | Cat# BE0055, RRID: AB_1107694 |
| Anti-mouse IL-4 | Bio X Cell | Cat# BE0045, RRID: AB_1107707 |
| Anti-mouse IL-12 | eBioscience | Cat# 16-7123-81, RRID: AB_469232 |
| anti-H3K4me1 | Abcam | Cat# ab8895, RRID: AB_306847 |
| anti-H3K4me3 | Millipore | Cat# 17–614, RRID: AB_11212770 |
| anti-H3K27ac | Abcam | Cat# ab4729, RRID: AB_2118291 |
| anti-GATA3 | BD bioscience | Cat# 558686, RRID: AB_2108590 |
| Chemicals, peptides, and recombinant proteins | ||
| Recombinant Mouse IL-12 Protein | R&D SYSTEMS | Cat# 419-ML |
| Recombinant Mouse IL-4 Protein | R&D SYSTEMS | Cat# 404-ML |
| Recombinant Mouse IL-2 Protein | R&D SYSTEMS | Cat# 402-ML |
| Formaldehyde | Thermo Scientific | Cat# 28908 |
| Proteinase K | Roche | Cat# 03115828001 |
| T4 DNA polymerase | New England Biolabs | Cat# M0203L |
| CviQI | New England Biolabs | Cat# R0639L |
| CviAII | New England Biolabs | Cat# R0640L |
| BfaI | New England Biolabs | Cat# R0568L |
| MluCI | New England Biolabs | Cat# R0538L |
| NlaIII | New England Biolabs | Cat# R0125L |
| Klenow fragment (3’->5’ exo-) | New England Biolabs | Cat# M0212L |
| T4 DNA Ligase | New England Biolabs | Cat# M0202L |
| T7 DNA Ligase | New England Biolabs | Cat# M0318L |
| Dynabeads MyOne Streptavidin C1 beads | Invitrogen | Cat# 65001 |
| Dynabeads Protein A for Immunoprecipitation | Invitrogen | Cat# 10002D |
| QIAzol Lysis Reagent | Qiagen | Cat# 79306 |
| Critical commercial assays | ||
| EasySep™ Mouse Naive CD4+ T cell Isolation Kit | STEMCELL | Cat# 17965A |
| RNeasy Mini Kit | Qiagen | Cat# 74104 |
| End-It DNA-Repair kit | Epicentre | Cat# ER0720 |
| Deposited data | ||
| Mice Naive, Th1 (24h, 72h) and Th2 (24h, 72h) WT vs. Mll4 KO RNA-seq, ChIP-seq (H3K4me1, H3K4me3, H3K27ac) | This manuscript | GEO accession#: GSE23 7916 |
| Mice Th1 (24h, 72h) and Th2 (24h, 72h) WT vs. Mll4 KO Hi-TrAC | This manuscript | GEO accession#: GSE23 7916 |
| Mice Th2 (72h) WT vs. HSS3 deletion RNA-seq, ChIP-seq (H3K4me1, H3K4me3, H3K27ac) and Hi-TrAC | This manuscript | GEO accession#: GSE23 7916 |
| Mice Th2 (72h) WT vs. Gata3 KO Hi-C | This manuscript | GEO accession#: GSE23 7916 |
| Mice Naive and Th2 (72h) WT vs. Gata3 KO RNA-seq, ChIP-seq (H3K4me1, H3K4me3, H3K27ac) and Hi-TrAC | This manuscript | GEO accession#: GSE23 7916 |
| Mice IL-4/GFP positive vs. negative Th2 Hi-TrAC | This manuscript | GEO accession#: GSE23 7916 |
| ETS1 ChIP-seq from mice naive CD4+ cells | 110 | GEO accession#: GSM999187 |
| IRF4 ChIP-seq from mice Th1 CD4+ cells | 111 | GEO accession#: GSM5257931 |
| IRF4 ChIP-seq from mice Th2 CD4+ cells | 112 | GEO accession#: GSM2538525 |
| T-bet ChIP-seq from mice Th1 CD4+ cells | 61 | GEO accession#: GSM6202869 |
| GATA3 ChIP-seq from mice Th2 CD4+ cells | 113 | GEO accession#: GSM1829645 |
| GATA3 ChIP-seq from mice naive CD4+ cells | 61 | GEO accession#: GSM6202870 |
| STAT4 ChIP-seq from mice Th1 CD4+ cells | 29 | GEO accession#: GSM550303 |
| STAT6 ChIP-seq from mice Th2 CD4+ cells | 29 | GEO accession#: GSM550311 |
| Hi-TrAC data from mice WT vs. Mll4 KO naive CD4+ cells | 61 | GEO accessions#: GSM6946693 GSM6946694 GSM6946695 GSM6946696 GSM6946697 GSM6946698 GSM6946699 GSM6946700 GSM6946701 GSM6946702 GSM6946703 GSM6946704 |
| Hi-C data from mice naive CD4+ cells | 64 | GEO accession#: GSM1694157 GSM1694159 GSM1694160 |
| DNase-seq data from mice Th2 CD4+ cells | 114 | GEO accession#: GSM5253165 GSM5253166 |
| CTCF ChIP-seq from mice Th2 CD4+ cells | 115 | GEO accession#: GSM1620003 |
| CTCF ChIP-seq from mice naive CD4+ cells | 61 | GEO accessions#: GSM6202871 |
| Experimental models: Organisms/strains | ||
| Mouse: Mll4fl/flCD4Cre | 64 | N/A |
| Mouse: IL-4/GFP (G4) | 85 | N/A |
| Mouse: Gata3fl/fl | 35 | N/A |
| Mouse: hCD2Cre | JAX | Line 027406 |
| Mouse: CreERT2 | Taconic | Line 10471 |
| Mouse: HSS3Δ | This paper | N/A |
| Oligonucleotides | ||
| HSS3Δ sgRNA-1: GACTAGCTGTGGACCCCTAG | IDT | N/A |
| HSS3Δ sgRNA-2: GGCTCCTTTTGGAACTGGAC | IDT | N/A |
| Software and algorithms | ||
| Python (v3) | Python Community | https://www.python.org |
| seaborn (v0.11.0) | 116 | https://seaborn.pydata.org |
| SciPy (v1.2.1) | 117 | https://scipy.org |
| Bowtie2 (v.2.3.5) | 118 | https://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| STAR (v2.7.3a) | 119 | https://github.com/alexdobin/STAR |
| Cuffdiff (v2.2.1) | 120 | https://github.com/cole-trapnell-lab/cufflinks |
| deepTools2 (v3.3.0) | 121 | https://deeptools.readthedocs.io/en/develop/ |
| HiCUP (v0.7.2) | 122 | https://www.bioinformatics.babraham.ac.uk/proiects/hicup/ |
| cLoops2 (v0.0.5) | 123 | https://github.com/YaqiangCao/cLoops2 |
| HOMER (v4.10.4) | 124 | http://homer.ucsd.edu/homer/ |
| WashU Epigenome Browser | 125 | http://epigenomegateway.wustl.edu |
| GSEApy (v0.9.18) | 126 | https://github.com/zqfang/GSEApy |
| Bedtools (v2.27.1) | 127 | https://github.com/arq5x/bedtools2 |