| Antibodies |
| Rabbit monoclonal anti-PTEN |
Cell Signaling Technology |
Cat#9559; RRID: AB_390810 |
| Rabbit monoclonal anti c-Myc |
Abcam |
Cat#32072; RRID: AB_731658 |
| Rabbit polyclonal anti-FAH |
Yecuris |
Cat#20-0034 |
| Rat monoclonal anti-BrdU |
Abcam |
Cat#6326; RRID: AB_305426 |
| Mouse monoclonal anti-BrdU |
BD Biosciences |
Cat#555627; RRID: AB_10015222 |
| Rabbit polyclonal anti-Ki67 |
Abcam |
Cat#15580; RRID: AB_443209 |
| Rabbit monoclonal anti-E-cadherin |
Cell Signaling Technology |
Cat#3195; RRID: AB_2291471 |
| Rabbit polyclonal anti-H3K27ac |
Abcam |
Cat#4729; RRID: AB_2118291 |
| Rabbit polyclonal anti-H3K4me3 |
Abcam |
Cat#8580; RRID: AB_306649 |
| Rabbit polyclonal anti-H3K4me1 |
Abcam |
Cat#8895; RRID: AB_306847 |
| Mouse monoclonal anti-Flag |
Sigma Aldrich |
Cat#F1804; RRID: AB_262044 |
| Rabbit polyclonal anti-HNF4a |
Santa Cruz Biotechnology |
Cat#8987; RRID: AB_2116913 |
| Goat anti Rabbit IgG, Alexa Fluor 594 conjugated |
Invitrogen |
Cat#A-11012; RRID: AB_2534079 |
| Goat anti Rat IgG, Alexa Fluor 488 conjugated |
Invitrogen |
Cat#A-11006; RRID: AB_141373 |
| Goat anti Mouse IgG2a, Alexa Fluor 594 conjugated |
Invitrogen |
Cat#A-21135; RRID: AB_2535774 |
| Bacterial and virus strains |
| Biological samples |
| Chemicals, peptides, and recombinant proteins |
| CuRx Nitisinone (NTBC) |
Yecuris |
Cat #20-0027 |
| 5-ethynyl-2’-deoxyuridine (EdU) |
Abcam |
Cat #146186 |
| 5-Bromo-2'-deoxyuridine (BrdU) |
Sigma Aldrich |
Cat #B5002 |
| Carbon tetrachloride (CCl4) |
Sigma Aldrich |
Cat #289116 |
| Saponin |
Sigma Aldrich |
Cat #47036 |
| GSK8583 |
WuXi AppTec |
N/A |
| GSK2801 |
WuXi AppTec |
N/A |
| BAZ2-ICR |
Sigma Aldrich |
Cat #SML1276 |
| Dextran sulfate sodium (DSS) |
TdB Consultancy |
Cat #DB001 |
| O-Propargyl-Puromycin (OP-Puro) |
Cayman Chemical |
Cat #15134 |
| Rapamycin |
Selleck Chemicals |
Cat #S1039 |
| Acetaminophen |
Sigma Aldrich |
Cat #A7085 |
| DAPI Solution |
Thermo Scientific |
Cat #62248 |
| UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) |
Invitrogen |
Cat #15593031 |
| TRIzol Reagent |
Invitrogen |
Cat #15596018 |
| 4% Paraformaldehyde Solution in PBS |
Alfa Aesar |
Cat #J19943K2 |
| Formaldehyde solution |
Sigma Aldrich |
Cat #F8775 |
| Hematoxylin QS |
Vector Laboratories |
Cat #NC9788954 |
| Fetal Bovine Serum |
Sigma Aldrich |
Cat #F4135 |
| Dulbecco’s High Glucose Modified Eagles Medium |
Cytiva Hyclone |
Cat #SH30022.FS |
| Dexamethasone |
Sigma Aldrich |
Cat #4902 |
| Penicillin Streptomycin 100X solution |
Cytiva Hyclone |
Cat #SV30010 |
| Critical commercial assays |
| VECTASTAIN Elite ABC-HRP Kit (Rabbit IgG) |
Vector Laboratories |
Cat #PK-6101 |
| VECTASTAIN Elite ABC-HRP kit (Rat IgG) |
Vector Laboratories |
Cat #PK-6104 |
| M.O.M Elite Immunodetection Kit |
Vector Laboratories |
Cat #PK-2200 |
| Q5 High-Fidelity DNA Polymerase |
New England BioLabs |
Cat #M0515 |
| Click-iT Edu Alexa Fluor 488 Flow Cytometry Kit |
Invitrogen |
Cat #C10425
|
| Alexa Fluor 555 Antibody Labeling Kit |
Invitrogen |
Cat #A20187 |
| Click-iT Cell Reaction Buffer Kit |
Invitrogen |
Cat #C10269
|
| Alexa Fluor 555 Azide |
Invitrogen |
Cat #A20012 |
| Liver Perfusion Medium |
Gibco |
Cat #17701038 |
| Liver Digest Medium |
Gibco |
Cat #17703034 |
| Hepatocyte Wash Medium |
Gibco |
Cat #17704024 |
| AST Activity Assay Kit |
Sigma Aldrich |
Cat #MAK055 |
| ALT Activity Assay Kit |
Sigma Aldrich |
Cat #MAK052 |
| iScript Reverse Transcription Supermix |
Bio-Rad Laboratories |
Cat #1708840 |
| iTaq Universal SYBR Green Supermix |
Bio-Rad Laboratories |
Cat #1725124 |
| ColoScreen ES Lab Pack |
Helena Laboratories |
Cat #5086 |
| Ovation Mouse RNA-Seq System |
Nugen |
Cat #0348-32 |
| RNeasy Mini Kit |
Qiagen |
Cat #74104 |
| QIAquick PCR Purification Kit |
Qiagen |
Cat #28104 |
| NEBNext Ultra II DNA Library Prep Kit |
New England BioLabs |
Cat #7645 |
| NEBNext High-Fidelity 2X PCR Master Mix |
New England BioLabs |
Cat #M0544 |
| Illumina Tagment DNA Enzyme and Buffer |
Illumina |
Cat #20034197 |
| Qubit dsDNA BR Assay Kit |
Invitrogen |
Cat #Q32850
|
| BAZ2B inhibitor AlphaScreen Kit |
BPS Bioscience |
Cat #32600 |
| NEBNext Multiplex Oligos for Illumina (Set 1) |
New England BioLabs |
Cat #7335 |
| NEBNext Multiplex Oligos for Illumina (Set 2) |
New England BioLabs |
Cat #7500 |
| NEBNext Multiplex Oligos for Illumina (Set 3) |
New England BioLabs |
Cat #7710 |
| NEBNext Multiplex Oligos for Illumina (Set 4) |
New England BioLabs |
Cat #7730 |
| Deposited data |
| Raw and analyzed RNA-seq and ChIP-seq data |
This paper |
GEO: GSE183502
|
| Experimental models: Cell lines |
|
|
| Mouse: H2.35 cells |
ATCC |
CRL-1995 |
| Experimental models: Organisms/strains |
|
|
| Mouse: C57BL/6J |
The Jackson Laboratories |
JAX: 000664 |
| Mouse: CD1 IGS |
Charles River Laboratories |
N/A |
| Mouse: Rpl24Bst/+ on C57BL/6J |
Oliver et al., 2004
|
RRID:MGI:5295283 |
| Mouse: Fah KO on C57BL/6J |
This paper |
N/A |
| Mouse: Rag1 KO; Fah KO; Il2rg KO on C57BI/6 |
Yecuris |
Cat #10-0001 |
| Mouse: Baz2b KO on 129/C57BL/6J mixed background |
This paper |
N/A |
| Oligonucleotides |
|
|
| Primers for qRT-PCR: listed in Table S4
|
This paper; Feng et al., 2012
|
Table S4
|
| Primer for ATAC-seq library prep: listed in Table S4
|
This paper |
Table S4
|
| sgRNA sequences for screening validation: listed in Table S4
|
Shi et al., 2015
|
Table S4
|
| CRISPR sgRNA sequence against mouse Pten
|
Xue et al., 2014
|
Table S4
|
| CRISPRa sgRNA sequence against mouse c-Myc
|
Wangensteen et al., 2018
|
Table S4
|
| In vivo siRNAs for mouse Baz2a
|
Life Technologies |
Cat #s100272 |
| In vivo siRNAs for mouse Baz2b
|
Life Technologies |
Cat #s129008 |
| Primers for screening library: listed in Table S4
|
This paper |
Table S4
|
|
|
|
| Recombinant DNA |
|
|
|
Fah-Cas9
|
This paper |
N/A |
|
Fah-dCas9-VP64
|
This paper |
N/A |
|
Fah-Cas9-sgBaz2a
|
This paper |
N/A |
|
Fah-Cas9-sgBaz2b
|
This paper |
N/A |
|
Fah-BAZ2A
|
This paper |
N/A |
|
Fah-BAZ2B
|
This paper |
N/A |
|
Fah-Cas9-sgPten
|
This paper |
N/A |
|
Fah-GFP
|
This paper |
N/A |
|
Fah-dCas9-VP64-sgMyc
|
This paper |
N/A |
|
pCMV(CAT)T7-SB100
|
Mátés et al., 2009
|
pCMV(CAT)T7-SB100 Addgene Cat #34879 |
|
FAHIG
|
Wuestefeld et al., 2013
|
N/A |
| Software and algorithms |
|
|
| HISAT |
Kim et al., 2015
|
http://www.ccb.jhu.edu/software/hisat/index.shtml
|
| HTSeq |
Anders et al., 2015
|
https://htseq.readthedocs.io/en/master/
|
| DESeq2 |
Love et al., 2014
|
https://bioconductor.org/packages/release/bioc/html/DESeq2.html
|
| BWA aligner |
Li and Durbin. 2009
|
http://bio-bwa.sourceforge.net/
|
| MACS |
Zhang et al. 2008
|
https://orionedocumentation.readthedocs.io/en/latest/chip_seq/ngs_peak_calling/macs14.html
|
| DiffBind |
Stark and Brown, 2011 Ross-Innes et al., 2012
|
http://bioconductor.org/packages/release/bioc/vignettes/DiffBind/inst/doc/DiffBind.pdf
|
| HOMER |
Heinz et al., 2010
|
http://homer.ucsd.edu/homer/
|
| deepTools |
Ramirez et al., 2016
|
https://deeptools.readthedocs.io/en/develop/
|
| UCSC |
Kuhn et al., 2013
|
https://genome.ucsc.edu/util.html
|
| Gene Set Enrichment Analysis |
Subramanian et al., 2005
Mootha et al., 2003
|
https://www.gseamsigdb.org/gsea/index.jsp
|
| clusterProfiler |
Yu et al., 2012 Wu et al., 2021
|
https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html
|
| Other |
|
|
| Agencourt Ampure XP Beads |
Beckman Coulter |
Cat #A63881 |
| Pierce Protein A/G Magnetic Beads |
Thermo Scientific |
Cat #26162 |
| BD FACSAria Fusion Flow Cytometer |
BD Biosciences |
N/A |
| Nickel Chelate AlphaLISA Acceptor Beads |
Perkin Elmer |
Cat #AL108C |
| Streptavidin-conjugated donor beads |
Perkin Elmer |
Cat #6760002 |
