| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-RBP1 | Cell Signaling Technology | Cat#2629, RRID: AB_2167468 |
| Rabbit monoclonal anti-H3K27me3 | Cell Signaling Technology | Cat#9733, RRID: AB_2616029 |
| Rabbit monoclonal anti-H3K4me3 | Cell Signaling Technology | Cat#9751,RRID: AB_261602 |
| Rabbit polyclonal anti-Tri-Methyl-lysine | PTM BIO | Cat#PTM-601 |
| Rabbit monoclonal anti-β-catenin | Cell Signaling Technology | Cat#8480, RRID:AB_11127855 |
| Rabbit monoclonal anti-Vimentin | Cell Signaling Technology | Cat#5741, RRID:AB_10695459 |
| Rabbit monoclonal anti-total AKT | Cell Signaling Technology | Cat#4691, RRID:AB_91578 |
| Rabbit monoclonal anti-Phospho-AKT(Ser473) | Cell Signaling Technology | Cat#4060, RRID:AB_2315049 |
| Mouse monoclonal anti-TCF1 | Santa-Cruz Biotechnology | Cat#Sc-271453, RRID:AB_10649799 |
| Rabbit monoclonal anti-H3 | Cell Signaling Technology | Cat#4499, RRID:AB_10544537 |
| Rabbit monoclonal anti-GAPDH | Cell Signaling Technology | Cat#5174, RRID:AB_10622025 |
| Mouse Monoclonal anti-FLAG | Sigma-Aldrich | Cat#F3165, RRID:AB_259529 |
| Rabbit monoclonal anti-HA | Cell Signaling Technology | Cat#3724, RRID:AB_1549585 |
| Rabbit polyclonal anti-HA | EpiCypher | Cat#13-2010 |
| Rabbit monoclonal anti-TCF1 | Cell Signaling Technology | Cat#2203, RRID:AB_2199302 |
| Rabbit monoclonal anti- Phospho-Akt Substrate (RXXS∗/T∗) | Cell Signaling Technology | Cat#9614, RRID:AB_331810 |
| Rabbit monoclonal anti-EZH2 | Cell Signaling Technology | Cat# 5246, RRID:AB_10694683 |
| Bacterial and virus strains | ||
| MISSION shRNA Bacterial Stock, EZH2 | Sigma-Aldrich | Cat# SHCLNG-NM, TRCN0000010474 |
| MISSION shRNA Bacterial Stock, PTEN | Sigma-Aldrich | Cat# SHCLNG-NM, TRCN0000002748 |
| MISSION shRNA Bacterial Stock, TRC2 pLKO.5-puro Empty Vector | Sigma-Aldrich | Cat# SHC201 |
| Chemicals, peptides, and recombinant proteins | ||
| GSK690693 | Sigma-Aldrich | Cat#SML0428 |
| GSK503 | Sigma-Aldrich | Cat#SML2718 |
| Hydrogen Peroxide (30%) | Fisher-chemical | Cat#H325-500 |
| McCoy’s 5A | Corning | Cat#10-050-CV |
| DMEM | Corning | Cat#10-013-CV |
| RPMI 1640 | Corning | Cat#10-040-CV |
| Advanced DMEM/F12 | Gibco | Cat#12634-010 |
| N2 supplement | Fisher | Cat#17502048 |
| B27 supplement | Fisher | Cat#17504044 |
| EGF | R&D Systems | Cat#236-EG |
| Noggin | R&D Systems | Cat#6057-NG |
| Protease Inhibitor Tablets | Thermo Scientific | Cat#88266 |
| Phosphatase Inhibitor Cocktail 2 | Sigma-Aldrich | Cat#P5726 |
| N-ethylmaleimide | Acros Organics | Cat#128-53-0 |
| pAG-MNase | EpiCypher | Cat#15-1116 |
| Matrigel (Growth Factor Reduced) | Corning | Cat#354230 |
| Human FGF-basic (bFGF) | Invitrogen | Cat#13256-029 |
| Insulin | Sigma-Aldrich | Cat#19278 |
| 16% Formaldehyde solution (w/v), methanol free | Thermo Scientific | Cat#28908 |
| Fetal Bovine Serum | Corning | Cat#35-015-CV |
| Puromycin | Sigma-Aldrich | Cat# P8833 |
| Lipofectamine 3000 | Invitrogen | Cat#L3000015 |
| DMSO | VWR | Cat#97063-136 |
| Critical commercial assays | ||
| Diagenode iDeal ChIP-seq Kit for transcription factor | Diagenode | Cat#C01010055 |
| RNeasy Mini Kit | Qiagen | Cat#74104 |
| ALDEFLUOR assay | Stem Cell Technologies | Cat#01700 |
| CUTANA™ DNA Purification Kit | EpiCypher | Cat#14-0050 |
| NEBNext Ultra II DNA Library Prep kit | New England BioLabs | Cat#E7645 |
| Maxima first strand cDNA synthesis kit | Thermo Fisher Scientific | Cat#K1642 |
| Deposited data | ||
| Raw and analyzed data | This paper | GEO: GSE226589 |
| Experimental models: Cell lines | ||
| Human: SW480 | ATCC | Cat#CCL-228, RRID:CVCL_0546 |
| Human: RKO | ATCC | Cat#CRL-2577, RRID:CVCL_0504 |
| Human: Lovo | ATCC | Cat#CCL-229, RRID:CVCL_0399 |
| Human: LS174T | ATCC | Cat#CL-188, RRID:CVCL_1384 |
| Human: HEK293T | ATCC | Cat#CRL-3216, RRID:CVCL_0063 |
| Human: Caco2 | ATCC | Cat#HTB-37, RRID:CVCL_0025 |
| 519 human colorectal cancer organoids | Miller et al.48 | N/A |
| SW480 PIK3CA E453K and E453K mutant cells | This paper | N/A |
| Oligonucleotides | ||
| Primers and oligos for RT-qPCR, plasmid construction and base editing, see Table S1 | This paper | N/A |
| Recombinant DNA | ||
| pCMV-HA-EZH2 | Addgene | RRID:Addgene_24230 |
| FLAG- β-catenin WT | Addgene | RRID:Addgene_16828 |
| FLAG- β-catenin K49R | Addgene | RRID:Addgene_44750 |
| pLenti-U6-tdTomato-P2A-BlasR (LRT2B) | Addgene | RRID:Addgene_110854 |
| pLenti-FNLS-P2A-Puro | Addgene | RRID:Addgene_110841 |
| pCMV-HA-EZH2 S21A | This paper | N/A |
| pCMV-HA-EZH2 S21D | This paper | N/A |
| Software and algorithms | ||
| FastQC (v0.11.9) | Simon Andrews | https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ |
| STAR (v2.7.10a) | Alex Dobin, dobin@cshl.eu | https://github.com/alexdobin/STAR |
| clusterProfiler (v1.38.3) | Yu et al.49 | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| EnhancedVolcano | Blighe, Rana, and Lewis50 | https://bioconductor.org/packages/devel/bioc/vignettes/EnhancedVolcano/inst/doc/EnhancedVolcano.html |
| Bowtie2 | Langmead et al.51 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| MACS (v2.2.7.1) | Zhang et al.52 | https://github.com/macs3-project/MACS |
| Bedtools (v2.26.0) | Quinlan & Hall53 | https://bedtools.readthedocs.io/en/latest/ |
| deeptools | Ramírez et al.54 | https://deeptools.readthedocs.io/en/latest/ |
| GVIS (v3.5.1) | Hahne & Ivanek55 | https://bioconductor.org/packages/release/bioc/html/Gviz.html |
| Deseq2 | Love et al.56 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| Metascape pathway analysis | Zhou et al.57 | https://metascape.org/gp/index.html#/main/step1 |
| UCSC xenabrowser | Goldman et al.58 | https://xenabrowser.net/ |
| RStudio (V 4.2.2) | R | https://posit.co/download/rstudio-desktop/ |
Official websites use .gov
A
.gov website belongs to an official
government organization in the United States.
Secure .gov websites use HTTPS
A lock (
) or https:// means you've safely
connected to the .gov website. Share sensitive
information only on official, secure websites.