Key Resources Table
| REAGENT OR RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| H3K4me1 | Active Motif | Cat#AM39297 |
| H3K4me3 | Active Motif | Cat#AM39155 |
| H3K27ac | Abcam | Cat#ab4729 |
| H3K27me3 | EMD Millipore | Cat#07–449 |
| H3K36me3 | Abcam | Cat#ab9050 |
| IKAROS | EMD Millipore | Cat#MABE912 |
| IKAROS | EMD Millipore | Cat#MABE913 |
| IKAROS | Abcam | Cat#ab191394 |
| CTCF | Abcam | Cat#ab188488 |
| NIPBL | Proteintech | Cat#18792–1-AP |
| SMC1a | Bethyl | Cat#A300–055A |
| GAPDH | Millipore | Cat#MAB374 |
| βTubulin | Santa Cruz Biotech | Cat#sc-9104 |
| FITC anti-mouse CD19 | Biolegend | Cat#152403 |
| Alexa Fluor 647 anti-mouse CD19 | Biolegend | Cat#115525 |
| APC anti-mouse CD43 | BD Biosciences | Cat#560663 |
| PE anti-mouse BP1 | Southern Biotech | Cat#1770–09L |
| APC anti-mouse B220 | Thermo Fisher Scientific | Cat#17–0452-81 |
| BV510 anti-mouse CD21 | BD Biosciences | Cat#563175 |
| PE anti-mouse CD23 | Thermo Fisher Scientific | Cat#12–0232-81 |
| BV421 anti-mouse CD5 | Biolegend | Cat#100629 |
| FITC-Ig-μ | BD Biosciences | Cat#553408 |
| FITC-Ig-κ | BD Biosciences | Cat#550003 |
| TER119 | BD Biosciences | Cat#553669 |
| Mac-1 (M1/70) | BD Biosciences | Cat#553307 |
| Gr-1 (RB6–8C5) | BD Biosciences | Cat#553123 |
| IgM (11/41) | BD Biosciences | Cat#562032 |
| CD3 (17A2) | BD Biosciences | Cat#557869 |
| CD8α (53–6.7) | BD Biosciences | Cat#553027 |
| TCRβ (H57–597) | BD Biosciences | Cat#553174 |
| CD49b (DX5) | BD Biosciences | Cat#553855 |
| Bacterial and virus strains | ||
| NEB® Stable Competent E. coli | New England Biolabs | C3040H |
| Chemicals, Peptides, and Recombinant Proteins | ||
| 4-Hydroxytamoxifen (4OHT) | Sigma | Cat#H7904 |
| Biotin-14-dATP | ThermoFisher Scientific | Cat#19524016 |
| Doxycycline (Dox) | ThermoFisher Scientific | Cat#BP26531 |
| Equisul-SDT | Aurora Pharmaceutical | Cat#28000 |
| Recombinant Human IL-7 | Biolegend | Cat#715302 |
| KAPA HiFi HotStart ReadyMix | Roche | Cat#KK2601 |
| Protease inhibitor cocktail | Roche | Cat#11873580001 |
| Critical commercial assays | ||
| Pan B cell isolation kit II (mouse) | Miltenyi Biotec | Cat#130-104-443 |
| CFSE Cell Division Tracker Kit | Biolegend | Cat#423801 |
| Pierce BCA Protein Assay Kit | ThermoFisher Scientific | Cat#23227 |
| ChIP DNA Clean and Concentrator | Zymo Research | Cat#D5205 |
| Quick-DNA Miniprep Plus kit | Zymo Research | Cat#D4068 |
| Direct-zol RNA Miniprep kit | Zymo Research | Cat#R2050 |
| Lenti-X Tet-On Advanced Inducible Expression System | Clontech | Cat# 630930 |
| TruSeq® Stranded mRNA Library Prep kit | Illumina | Cat#20020594 |
| Deposited Data | ||
| Raw and analyzed data | This study | GSE232490 |
| Western blot images | This study | https://doi.org/10.5281/zenodo.8339089 |
| Analyzed data | This study | https://doi.org/10.5281/zenodo.8339291 |
| RNAseq datasets for HSC, MPP, CLP,ILC2p and NKp cells | Shih et al, 201661 | GSE77695 |
| RNAseq datasets for pro-B, large pre-B and small pre-B cells | Kashiwagi et al, 202262 | GSE211079 |
| ChIP-seq datasets for B cell and extra-lineage transcription factors | Hu et al, 201642 | GSE86897 |
| Experimental Models: Cell lines | ||
| Human: HEK 293T/17 cells | ATCC | Cat#CRL-11268 |
| Human: HaCaT cells | J.M. Park | N/A |
| Mouse: OP9 bone marrow stromal cells | ATCC | Cat#CRL-2749 |
| Mouse: Passage 4 IkE5fl/fl hCD2-Cre (+/−) large pre-B cells |
This study |
N/A |
| Mouse: Passage 2 IkE5fl/fl Rosa26-Cre-ERT2 large pre-B cells | This study | N/A |
| Experimental Models: Organisms/Strains | ||
| IkE5fl/fl hCD2-Cre (+/−) | Joshi et al, 201441 | N/A |
| IkE5fl/fl Rosa26-Cre-ERT2 | Hu et al, 201642 | N/A |
| Oligonnucleotides | ||
| Igk forward primer (Vκ) | Intergrated DNA Technologies (IDT) | GGCTGCAGSTTCAGTGGCAGTGGRTCWGGRAC |
| Igk reverse primer (Jκ5) | IDT | ATGCGACGTCAACTGATAATGAGCCCTCTCC |
| Igk probe (upstream of Jκ5) | IDT | ACCAAGCTGGAGCTGAAACGTAAGTACAC |
| Dntt forward primer | IDT | CCCAAGTTCACTGTTCTTTCTGTC |
| Dntt reverse primer | IDT | CTCACCAGCAAACCCATAGGTA |
| Recombinant DNA | ||
| pLVX-Tight-Puro (TetOn) | Clontech | Cat# 630930 |
| pTRE-Tight-Luc control vector | Clontech | Cat# 630930 |
| pLVX-Tet-On Advanced | Clontech | Cat# 630930 |
| pLVX-Tight-FH-IKZF1 | This study | N/A |
| Software and Algorithms | ||
| Code for data analysis | This study | https://github.com/ay-lab/3D-IKAROS |
| FlowJo v10.9 | BD Biosciences | https://www.flowjo.com |
| bedGraphToBigWig v4 | Kent et al., 201096 | https://github.com/ENCODE-DCC/kentUtils |
| CALDER v1.0 | Liu et al., 2021107 | https://github.com/CSOgroup/CALDER |
| dcHiC v2.1 | Chakraborty et al., 2022106 | https://github.com/ay-lab/dcHiC |
| DEseq2 | Love et al., 201499 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| FitHiC v.2.0.7 | Kaul et al., 2020104 | https://github.com/ay-lab/fithic |
| FitHiChIP v9.1 | Bhattacharyya et al., 2019105 | https://ay-lab.github.io/FitHiChIP/html/index.html |
| GENOVA v1.0.0.9 | van der Weide et al., 2021109 | https://github.com/robinweide/GENOVA |
| GenomicRanges v1.42.0 | Lawrence et al., 201398 | https://bioconductor.org/packages/release/bioc/html/GenomicRanges.html |
| Gene Ontology (GO) analysis | Zhou et al., 2019101 | https://metascape.org |
| HiCExplorer v3.5.1 | Wolff et al., 2020108 | https://hicexplorer.readthedocs.io/en/latest/index.html |
| HiC-Pro 2.8.0 | Servant et al., 2015102 | https://github.com/nservant/HiC-Pro |
| hicreppy v0.0.6 | Yang et al., 2017112 | https://github.com/cmdoret/hicreppy |
| Homer v4.11 | Heinz et al., 2010100 | http://homer.ucsd.edu/homer/ |
| Juicebox v1.11.08 | Durand et al., 2016103 | https://github.com/aidenlab/Juicebox |
| Liftover v2 | Hinrichs et al., 2006111 | https://genome.ucsc.edu/cgi-bin/hgLiftOver |
| MACS2 v2.11 | Zhang et al., 200895 | https://github.com/macs3-project/MACS |
| ngs.plot v2.63 | Shen et al., 201497 | https://github.com/shenlab-sinai/ngsplot |
| STAR v5.02 | Dobin et al., 201394 | https://github.com/alexdobin/STAR |
| TCseq v1.14 | Wu & Gu, 2022110 | https://doi.org/10.18129/B9.bioc.TCseq |