Appendix 1—key resources table.
| Reagent type (species) or resource |
Designation | Source or reference | Identifiers | Additional information |
|---|---|---|---|---|
| Other | MNase | Sigma-Aldrich | Cat#:N3755-200U | |
| Other | Protein-G Magnetic beads | Thermo Fisher Scientific | Cat#:1004D | |
| Other | FLAG M2 antibody-conjugated beads | Sigma-Aldrich | Cat#:M8823 RRID:AB_2637089 |
|
| Other | c-Kit magnetic beads | Miltenyi Biotec | Cat#:130-091-224 RRID:AB_2753213 |
|
| Other | MI-2–2 | Calbiochem | Cat#:444825 | |
| Other | WM1119 | Enamine | Cat#:EN300-1719156 | |
| Antibody | MLL(N) | Cell Signaling Technology | Cat#:14689 RRID:AB_2688009 |
WB(1000:1) |
| ChIP(1 μL/400 μL) | ||||
| Antibody | MLL(N) | Generated in-house Yokoyama et al., 2002 | rpN1 | ChIP(1 μg/400 μL) |
| Antibody | MOZ | Active motif | Cat#:39868 | ChIP(1 μg/400 μL) |
| Antibody | AF4 | Santa Cruz Biotechnology | Cat#:sc-49350 RRID:AB_2226113 |
ChIP(1 μg/400 μL) |
| Antibody | TAF1C | Bethyl Laboratories | Cat#:A303-698A RRID:AB_11203194 |
ChIP(1 μg/400 μL) |
| Antibody | AF17 | Bethyl Laboratories | Cat#:A302-198A RRID:AB_1659777 |
ChIP(1 μg/400 μL) |
| Antibody | DOT1L | Bethyl Laboratories | Cat#:A300-953A RRID:AB_805775 |
ChIP(1 μg/400 μL) |
| Antibody | CyclinT1 | Santa Cruz Biotechnology | Cat#:sc-8127 RRID:AB_2073892 |
ChIP(1 μg/400 μL) |
| Antibody | ENL | Cell Signaling Technology | Cat#:14893S | WB(1000:1) |
| ChIP(5 μL/400 μL) | ||||
| Antibody | Histone H3K4me3 | Active motif | Cat#:39159 RRID:AB_2615077 |
ChIP(1 μg/400 μL) |
| Antibody | Histone H3K18ac | Abcam | Cat#:ab1191 RRID:AB_298692 |
ChIP(1 μg/400 μL) |
| Antibody | RNAP2 non-P | Abcam | 8WG16/Cat#:ab817 RRID:AB_306327 |
ChIP(1 μg/400 μL) |
| Antibody | RNAP2 Ser5-P | Millipore | Cat#:05–623 AB_309852 |
ChIP(1 μg/400 μL) |
| Antibody | FLAG | Sigma-Aldrich | Cat#:F3165 RRID:AB_259529 |
ChIP(1 μg/400 μL) |
| Antibody | FLAG | Sigma-Aldrich | Cat#:F7425 RRID:AB_439687 |
WB(1000:1) |
| Antibody | HA | Roche | 3F10/Cat#:11867423001 RRID:AB_390918 |
WB(1000:1) |
| ChIP(0.2 μg/400 μL) | ||||
| Antibody | Xpress | Santa Cruz Biotechnology | Cat#:sc-7270 RRID:AB_675763 |
WB(1000:1) |
| ChIP(1 μg/400 μL) | ||||
| Antibody | ELL | Cell Signaling Technology | Cat#:14468S RRID:AB_2798489 |
WB(1000:1) |
| Antibody | HBO1 | Abcam | Cat#:70183 RRID:AB_1269226 |
WB(1000:1) |
| ChIP(1 μg/400 μL) | ||||
| Antibody | PHF16 | Abcam | Cat#:129495 RRID:AB_11157084 |
WB(1000:1) |
| ChIP(1 μg/400 μL) | ||||
| Antibody | MEAF6 | STJ | Cat#:116836 | WB(1000:1) |
| ChIP(1 μg/400 μL) | ||||
| Antibody | ING4 | Abcam | Cat#:108621 RRID:AB_10860023 |
WB(1000:1) |
| ChIP(1 μg/400 μL) | ||||
| Antibody | MLL(C) | Cell Signaling Technology | Cat#:14197S RRID:AB_2688010 |
WB(1000:1) |
| Antibody | AF4 | Bethyl Laboratories | Cat#:A302-344A RRID:AB_1850255 |
WB(1000:1) |
| Antibody | AF5Q31 | Bethyl Laboratories | Cat#:A302-538A RRID:AB_1998985 |
WB(1000:1) |
| Antibody | P53 | Santa Cruz Biotechnology | Cat#:sc-126 RRID:AB_628082 |
WB(1000:1) |
| Sequence-based reagent | GAPDH | Thermo Fisher Scientific | Hs02786624_g1 | |
| Sequence-based reagent | HOXA9 | Thermo Fisher Scientific | Hs00365956_m1 | |
| Sequence-based reagent | MYC | Thermo Fisher Scientific | Hs01570247_m1 | |
| Sequence-based reagent | RPL13A | Thermo Fisher Scientific | Hs04194366_g1 | |
| Sequence-based reagent | CDKN2C | Thermo Fisher Scientific | Hs00176227_m1 | |
| Sequence-based reagent | Gapdh | Thermo Fisher Scientific | Mm99999915_g1 | |
| Sequence-based reagent | Hoxa9 | Thermo Fisher Scientific | Mm00439364_m1 | |
| Sequence-based reagent | Mllt1 | Thermo Fisher Scientific | Mm00452080_m1 | |
| Sequence-based reagent | sgRNAs | This study | See Supplementary file 1 | |
| Sequence-based reagent | Custom made qPCR primers | Thermo Fisher Scientific | See Supplementary file 1 | |
| Recombinant DNA reagent | pMSCV-neo | Clontech | Cat#:634401 | |
| Recombinant DNA reagent | pLKO5.EFS.GFP | Addgene (gift from Benjamin Ebert) Heckl et al., 2014 | Addgene #57822 RRID:Addgene_57822 |
|
| Recombinant DNA reagent | pKLV2-Cas9.bsd | Addgene (gift from Kosuke Yusa) Tzelepis et al., 2016 | Addgene #68343 RRID:Addgene_68343 |
|
| Recombinant DNA reagent | pMDLg/pRRE | Addgene (gift from Didier Trono) Dull et al., 1998 | Addgene #12251 RRID:Addgene_12251 |
|
| Recombinant DNA reagent | pRSV-rev | Addgene (gift from Didier Trono) Dull et al., 1998 | Addgene #12253 RRID:Addgene_12253 |
|
| Recombinant DNA reagent | pMD2.G | Addgene (gift from Didier Trono) Dull et al., 1998 | Addgene #12259 RRID:Addgene_12259 |
|
| Recombinant DNA reagent | pLKO.1-puro | Addgene (gift from Bob Weinberg) Stewart et al., 2003 | Addgene #8453 RRID:Addgene_84530 |
|
| Recombinant DNA reagent | pLKO.1-sh-Mllt1-puro | GE Healthcare | TRCN0000084405 | |
| Software, algorithm | GraphPad Prism7 | GraphPad Software Inc | RRID:SCR_002798 | |
| Software, algorithm | Integrative Genomics Viewer | Thorvaldsdóttir et al., 2013 | RRID:SCR_011793 | |
| Software, algorithm | Cutadapt | Martin, 2011 | RRID:SCR_011841 | |
| Software, algorithm | BWA | Li and Durbin, 2009 | RRID:SCR_010910 | |
| Cell line (Homo sapiens) | Human: HEK293T | Gift from Michael Cleary | Authenticated by JCRB Cell Bank in 2019 | |
| Cell line (Homo sapiens) | Human: HB1119 | Gift from Michael Cleary Tkachuk et al., 1992 | The cell line was verified by the expression of MLL-ENL | |
| Cell line (Homo sapiens) | Human: REH | Gift from Michael Cleary Yokoyama et al., 2004 | RRID:CVCL_1650 | Authenticated by JCRB Cell Bank in 2021 |
| Cell line (Homo sapiens) | Human: PLAT-E | Gift from Toshio Kitamura Morita et al., 2000 | RRID:CVCL_B488 | |
| Cell line (Homo sapiens) | Human: HEK293TN | System Bioscience | Cat#:LV900A-1 | |
| RRID:CVCL_UL49 | ||||
| Cell line (Homo sapiens) | Human: HEK293T dMLLc3 | Generated in-house Miyamoto et al., 2020 | ||
| Cell line (Homo sapiens) | Human: HEK293T dMLLc7 | Generated in-house Miyamoto et al., 2020 | ||
| Cell line (Homo sapiens) | Human: HEK293TL | Generated in-house Okuda et al., 2015 | ||
| Strain, strain background (Mus musculus) | Mouse: C57BL/6J | CLEA Japan |