Table 1.

Resources

Reagent or ResourceSourceIdentifier
Antibodies 
N-term CIZ1 Rabbit pAb Coverley et al. (2005)  1793 
C-term CIZ1 Mouse mAb Ex17 FDAB 87 Sofi et al. (2022)  
CIZ1 Rabbit pAb Ex17 Novus NB100-74624 
Rabbit H3K27me3 CST 9733S 
Rabbit H2AK119ub1 CST 8240 
Goat α Rabbit Alexa Fluor 568 (Red) Invitrogen A11011 
Goat α Mouse Alexa Fluor 488 (Green) Invitrogen A11001 
Goat α Rabbit Alexa Fluor 488 (Green) Invitrogen A11034 
Goat α Mouse Alexa Fluor 568 (Red) Invitrogen A11031 
Histone H3 Abcam ab1791 
β-Actin Abcam ab11003 
Peroxidase IgG α Rabbit Jackson 211-032-171 
Peroxidase IgG α Mouse Jackson 155-035-174 
Bacterial and virus strains 
Escherichia coli DH5α competent cells Invitrogen Cat#18265017 
Escherichia coli Stbl3 competent cells Invitrogen Cat#C737303 
Chemicals, peptides, and recombinant proteins 
MEBM basal medium Lonza Cat#CC-3150 
MEGM SingleQuots Lonza Cat#CC-4136 
HG DMEM Gibco Cat#31966-021 
Collagen Type I, Rat tail Thistle Scientific Cat#50201 
X2 Transfection reagent Mirus Cat#MIR 6003 
PR-619 Bio-Techne Cat#4482/10 
Nocodazole Sigma-Aldrich Cat#M1404 
Thymidine Sigma-Aldrich Cat#T1895 
PolyFect transfection reagent QIAGEN Cat#301105 
CloneAmp HiFi PCR premix Takara Cat#639298 
QIAprep Spin Miniprep Kit QIAGEN Cat#27104 
Protease inhibitor cocktail, EDTA-free BioVision Cat#K272-1 
PreScission protease GE Healthcare Cat#27084301 
Critical commercial assays 
TissueScan cancer and normal tissue cDNA arrays Origene https://www.origene.com/products/tissues/tissuescan 
Deposited data   
Murine cell transcriptomes BMK gene National Center for Biotechnology Information short Read archive project PRJNA1144651 
Experimental models: Cells   
Mouse: Female 3T3 fibroblast cell line Stewart et al. (2019)  D3T3 
Mouse: Primary embryonic fibroblasts (PEFs) Ridings-Figueroa et al. (2017) and this study Strain specific identifiers 
Human: Primary mammary epithelial cells Breast Cancer now HMEC 
Human: MCF-10A cell line ATCC CRL-10317 
Human: MCF7 cell line ECACC 86012803 
Human: BT-474 cell line TCBSR BT-474 
Human: SK-BR-3 cell line TCBSR SK-BR-3 
Human: MDA-MB-231 cell line ATCC HTB-26 
Human: Lenti-X 293T cell line Takara Cat#632180 
Experimental models: Organisms/strains 
Ciz1 null mice Ciz1Gt(IST13830B6)Tigm Ridings-Figueroa et al. (2017)  N/A 
Oligonucleotides 
qPCR primers   
5′-CAG​GGG​CAT​AAG​GAC​AAA​G-3′ CIZ1 13F P1 
5′-TCC​GAG​CCC​TTC​CAC​TCC​TCT​CTG​G-3′ CIZ1 15R P2 
5′-CGA​GGG​TGA​TGA​AGA​AGA​GGA-3′ CIZ1 14F P6 
5′-CCC​CTG​AGT​TGC​TGT​GAT​A-3′ CIZ1 16R P7 
5′-CAC​AAC​TGG​CCA​CTC​CAA​AT-3′ CIZ1 5F P9 
5′-CCT​CTA​CCA​CCC​CCA​ATC​G-3′ CIZ1 5R P10 
5′-ACA​CAC​CAG​AAG​ACC​AAG​ATT​TAC​C-3′ CIZ1 6/7 junction F P13 
5′-TGC​TGG​AGT​GCG​TTT​TTC​CT-3′ CIZ1 7R P14 
5′-CAA​CCG​CGA​GAA​GAT​GAC​C-3′  Actin F 
5′-TCC​AGG​GCG​ACG​TAG​CAC​A-3′  Actin R 
qPCR probes   
5′-CGC​CAG​TCC​TTG​CTG​GGA​CC-3′ Ciz1 5 5 
5′-CCC​TGC​CCA​GAG​GAC​ATC​GCC-3′ Ciz1 7 7 
5′-TGG​TCC​TCA​TCT​TGG​CCA​GCA-3′ Ciz1 14 14 
5′-CAC​GGG​CAC​CAG​GAA​GTC​CA-3′ Ciz1 16 16 
5′-CCC​TGT​ACG​CCT​CTG​GCC​GT-3′  Actin 
Mutagenesis primers  Plasmid generated 
FP - 5′-GGA​GAG​ATT​GAG​GTG​AAG​CCG​AGA​GAA​ACA​TCC-3′  GFP-C181 Δ706–713 (CIZ1B) 
RP - 5′-GGA​TGT​TTC​TCT​CGG​CTT​CAC​CTC​AAT​CTC​TCC-3′   
FP - 5′-GGA​TTT​CCT​GGT​GCC​AGT​GAT​GAA​AGC​CAA​GAA​CCC​AAG​C  GFP-C181 Δ746–779 (ΔMH3) 
RP - 5′-GCT​TGG​GTT​CTT​GGC​TTT​CAT​CAC​TGG​CAC​CAG​GAA​ATC​C-3′   
FP - 5′-CCT​GAC​TGC​ACT​GTT​CTG​ATA​GAA​GCT​TCG​AAT​TCT​GC-3′  GFP-C181 Δ809–845 (Δ37) 
RP - 5′-GCA​GAA​TTC​GAA​GCT​TCT​ATC​AGA​ACA​GTG​CAG​TCA​GG-3′   
FP - 5′-GCC​CTC​CTC​CTA​CCA​GCC​ACC​AGC​CCA​GCC-3′  GFP-C181 Δ796–811 (ΔNALTAF) 
RP - 5′-GGC​TGG​GCT​GGT​GGC​TGG​TAG​GAG​GAG​GGC-3′   
FP - 5′-ATC​CCC​GAA​TTC​CCG​GGT​CGA​CAA​GGA​GAC​AGG​CAG​CCC  GST-C181 from GST-C275 
RP - 5′-GGG​CTG​CCT​GTC​TCC​TTG​TCG​ACC​CGG​GAA​TTC​GGG​GAT-3′   
FP- 5′-GCT​TTG​AGA​GTG​GTC​AAT​TCT​GCA​AGC​AGG​TGA​AGC-3′  GST-C181 Δ689–709 (ΔAcD) 
RP- 5′-GCT​TCA​CCT​GCT​TGC​AGA​ATT​GAC​CAC​TCT​CAA​AGC-3′   
FP - 5′-GGA​TTT​CCT​GGT​GCC​AGT​GAT​GAA​AGC​CAA​GAA​CCC​AAG​C-3′  GST- C181 Δ746–779 (ΔMH3) 
RP - 5′-GCT​TGG​GTT​CTT​GGC​TTT​CAT​CAC​TGG​CAC​CAG​GAA​ATC​C-3′   
FP - 5′-CCT​GAC​TGC​ACT​GTT​CTG​ATA​GAG​GGA​GC-3′  GST-C181 Δ809–845 (Δ37) 
RP - 5′-GCT​CCC​TCT​ATC​AGA​ACA​GTG​CAG​TCA​GG-3′   
5′-AGA​CAG​GCA​GCC​CAG​ATG​AGG-3′  Sequencing primer 
Recombinant plasmids 
Murine GFP-C275 Ainscough et al. (2007)  N/A 
Murine GFP-C181 This paper N/A 
Murine GFP-C181 CIZ1B This paper N/A 
Murine GFP-C181 ΔMH3 This paper N/A 
Murine GFP-C181 ΔNALTALF This paper N/A 
Murine GFP-C181 Δ37 This paper N/A 
Murine GFP-C181 Δ37, ΔMH3 This paper N/A 
Murine GFP-I122 Ainscough et al. (2007)  N/A 
psPAX2 Trono Lab unpublished Addgene plasmid #12260 
pMD2.G Trono Lab unpublished Addgene plasmid #12259 
pLVX-EF1α-IRES-ZsGreen1 Takara Cat#631982 
Software and algorithms 
Gene expression profiling Interactive analysis (GEPIA) Tang et al. (2017)  http://gepia.cancer-pku.cn/ 
The cancer genome atlas (TCGA)  https://portal.gdc.cancer.gov/ 
UCSC genome browser Kent et al. (2002)  https://genome.ucsc.edu/ 
Catalogue of somatic Mutations In Cancer (COSMIC) Tate et al. (2019)  https://www.sanger.ac.uk/tool/cosmic/ 
Ensembl genome browser Cunningham et al. (2022)  https://www.ensembl.org/index.html 
Functional annotation of the mammalian genome (FANTOM5) Lizio et al. (2015)  https://fantom.gsc.riken.jp/5/ 
Cellosaurus Bairoch (2018)  https://www.cellosaurus.org/ 
GSEAPY Fang et al. (2023)  https://gseapy.readthedocs.io/en/latest/introduction.html 
FIJI Schindelin et al. (2012)  https://imagej.net/software/fiji/ 
IBM SPSS Statistics for Macintosh, version 28.0 IBM N/A 
nfcore/atacseq v2.1.2 workflow Zenodo https://doi.org/10.5281/zenodo.8222875 
LCsolution software Shimadzu N/A 
Astra V software Wyatt N/A 
PXi GenSys software Syngene N/A 
EVOS Xl digital inverted microscope software AMG (now Thermo Fisher Scientific) N/A 
Axiovision image acquisition software (SE64 release 4.9.1) Zeiss N/A 
CLASTR Bairoch (2018)  https://web.expasy.org/cellosaurus-str-search/ 
GSEA Broad Institute https://www.gsea-msigdb.org/gsea/index.jsp 
National center for biotechnology information genes and disease  https://www.ncbi.nlm.nih.gov/books/NBK22266/ 
Reagent or ResourceSourceIdentifier
Antibodies 
N-term CIZ1 Rabbit pAb Coverley et al. (2005)  1793 
C-term CIZ1 Mouse mAb Ex17 FDAB 87 Sofi et al. (2022)  
CIZ1 Rabbit pAb Ex17 Novus NB100-74624 
Rabbit H3K27me3 CST 9733S 
Rabbit H2AK119ub1 CST 8240 
Goat α Rabbit Alexa Fluor 568 (Red) Invitrogen A11011 
Goat α Mouse Alexa Fluor 488 (Green) Invitrogen A11001 
Goat α Rabbit Alexa Fluor 488 (Green) Invitrogen A11034 
Goat α Mouse Alexa Fluor 568 (Red) Invitrogen A11031 
Histone H3 Abcam ab1791 
β-Actin Abcam ab11003 
Peroxidase IgG α Rabbit Jackson 211-032-171 
Peroxidase IgG α Mouse Jackson 155-035-174 
Bacterial and virus strains 
Escherichia coli DH5α competent cells Invitrogen Cat#18265017 
Escherichia coli Stbl3 competent cells Invitrogen Cat#C737303 
Chemicals, peptides, and recombinant proteins 
MEBM basal medium Lonza Cat#CC-3150 
MEGM SingleQuots Lonza Cat#CC-4136 
HG DMEM Gibco Cat#31966-021 
Collagen Type I, Rat tail Thistle Scientific Cat#50201 
X2 Transfection reagent Mirus Cat#MIR 6003 
PR-619 Bio-Techne Cat#4482/10 
Nocodazole Sigma-Aldrich Cat#M1404 
Thymidine Sigma-Aldrich Cat#T1895 
PolyFect transfection reagent QIAGEN Cat#301105 
CloneAmp HiFi PCR premix Takara Cat#639298 
QIAprep Spin Miniprep Kit QIAGEN Cat#27104 
Protease inhibitor cocktail, EDTA-free BioVision Cat#K272-1 
PreScission protease GE Healthcare Cat#27084301 
Critical commercial assays 
TissueScan cancer and normal tissue cDNA arrays Origene https://www.origene.com/products/tissues/tissuescan 
Deposited data   
Murine cell transcriptomes BMK gene National Center for Biotechnology Information short Read archive project PRJNA1144651 
Experimental models: Cells   
Mouse: Female 3T3 fibroblast cell line Stewart et al. (2019)  D3T3 
Mouse: Primary embryonic fibroblasts (PEFs) Ridings-Figueroa et al. (2017) and this study Strain specific identifiers 
Human: Primary mammary epithelial cells Breast Cancer now HMEC 
Human: MCF-10A cell line ATCC CRL-10317 
Human: MCF7 cell line ECACC 86012803 
Human: BT-474 cell line TCBSR BT-474 
Human: SK-BR-3 cell line TCBSR SK-BR-3 
Human: MDA-MB-231 cell line ATCC HTB-26 
Human: Lenti-X 293T cell line Takara Cat#632180 
Experimental models: Organisms/strains 
Ciz1 null mice Ciz1Gt(IST13830B6)Tigm Ridings-Figueroa et al. (2017)  N/A 
Oligonucleotides 
qPCR primers   
5′-CAG​GGG​CAT​AAG​GAC​AAA​G-3′ CIZ1 13F P1 
5′-TCC​GAG​CCC​TTC​CAC​TCC​TCT​CTG​G-3′ CIZ1 15R P2 
5′-CGA​GGG​TGA​TGA​AGA​AGA​GGA-3′ CIZ1 14F P6 
5′-CCC​CTG​AGT​TGC​TGT​GAT​A-3′ CIZ1 16R P7 
5′-CAC​AAC​TGG​CCA​CTC​CAA​AT-3′ CIZ1 5F P9 
5′-CCT​CTA​CCA​CCC​CCA​ATC​G-3′ CIZ1 5R P10 
5′-ACA​CAC​CAG​AAG​ACC​AAG​ATT​TAC​C-3′ CIZ1 6/7 junction F P13 
5′-TGC​TGG​AGT​GCG​TTT​TTC​CT-3′ CIZ1 7R P14 
5′-CAA​CCG​CGA​GAA​GAT​GAC​C-3′  Actin F 
5′-TCC​AGG​GCG​ACG​TAG​CAC​A-3′  Actin R 
qPCR probes   
5′-CGC​CAG​TCC​TTG​CTG​GGA​CC-3′ Ciz1 5 5 
5′-CCC​TGC​CCA​GAG​GAC​ATC​GCC-3′ Ciz1 7 7 
5′-TGG​TCC​TCA​TCT​TGG​CCA​GCA-3′ Ciz1 14 14 
5′-CAC​GGG​CAC​CAG​GAA​GTC​CA-3′ Ciz1 16 16 
5′-CCC​TGT​ACG​CCT​CTG​GCC​GT-3′  Actin 
Mutagenesis primers  Plasmid generated 
FP - 5′-GGA​GAG​ATT​GAG​GTG​AAG​CCG​AGA​GAA​ACA​TCC-3′  GFP-C181 Δ706–713 (CIZ1B) 
RP - 5′-GGA​TGT​TTC​TCT​CGG​CTT​CAC​CTC​AAT​CTC​TCC-3′   
FP - 5′-GGA​TTT​CCT​GGT​GCC​AGT​GAT​GAA​AGC​CAA​GAA​CCC​AAG​C  GFP-C181 Δ746–779 (ΔMH3) 
RP - 5′-GCT​TGG​GTT​CTT​GGC​TTT​CAT​CAC​TGG​CAC​CAG​GAA​ATC​C-3′   
FP - 5′-CCT​GAC​TGC​ACT​GTT​CTG​ATA​GAA​GCT​TCG​AAT​TCT​GC-3′  GFP-C181 Δ809–845 (Δ37) 
RP - 5′-GCA​GAA​TTC​GAA​GCT​TCT​ATC​AGA​ACA​GTG​CAG​TCA​GG-3′   
FP - 5′-GCC​CTC​CTC​CTA​CCA​GCC​ACC​AGC​CCA​GCC-3′  GFP-C181 Δ796–811 (ΔNALTAF) 
RP - 5′-GGC​TGG​GCT​GGT​GGC​TGG​TAG​GAG​GAG​GGC-3′   
FP - 5′-ATC​CCC​GAA​TTC​CCG​GGT​CGA​CAA​GGA​GAC​AGG​CAG​CCC  GST-C181 from GST-C275 
RP - 5′-GGG​CTG​CCT​GTC​TCC​TTG​TCG​ACC​CGG​GAA​TTC​GGG​GAT-3′   
FP- 5′-GCT​TTG​AGA​GTG​GTC​AAT​TCT​GCA​AGC​AGG​TGA​AGC-3′  GST-C181 Δ689–709 (ΔAcD) 
RP- 5′-GCT​TCA​CCT​GCT​TGC​AGA​ATT​GAC​CAC​TCT​CAA​AGC-3′   
FP - 5′-GGA​TTT​CCT​GGT​GCC​AGT​GAT​GAA​AGC​CAA​GAA​CCC​AAG​C-3′  GST- C181 Δ746–779 (ΔMH3) 
RP - 5′-GCT​TGG​GTT​CTT​GGC​TTT​CAT​CAC​TGG​CAC​CAG​GAA​ATC​C-3′   
FP - 5′-CCT​GAC​TGC​ACT​GTT​CTG​ATA​GAG​GGA​GC-3′  GST-C181 Δ809–845 (Δ37) 
RP - 5′-GCT​CCC​TCT​ATC​AGA​ACA​GTG​CAG​TCA​GG-3′   
5′-AGA​CAG​GCA​GCC​CAG​ATG​AGG-3′  Sequencing primer 
Recombinant plasmids 
Murine GFP-C275 Ainscough et al. (2007)  N/A 
Murine GFP-C181 This paper N/A 
Murine GFP-C181 CIZ1B This paper N/A 
Murine GFP-C181 ΔMH3 This paper N/A 
Murine GFP-C181 ΔNALTALF This paper N/A 
Murine GFP-C181 Δ37 This paper N/A 
Murine GFP-C181 Δ37, ΔMH3 This paper N/A 
Murine GFP-I122 Ainscough et al. (2007)  N/A 
psPAX2 Trono Lab unpublished Addgene plasmid #12260 
pMD2.G Trono Lab unpublished Addgene plasmid #12259 
pLVX-EF1α-IRES-ZsGreen1 Takara Cat#631982 
Software and algorithms 
Gene expression profiling Interactive analysis (GEPIA) Tang et al. (2017)  http://gepia.cancer-pku.cn/ 
The cancer genome atlas (TCGA)  https://portal.gdc.cancer.gov/ 
UCSC genome browser Kent et al. (2002)  https://genome.ucsc.edu/ 
Catalogue of somatic Mutations In Cancer (COSMIC) Tate et al. (2019)  https://www.sanger.ac.uk/tool/cosmic/ 
Ensembl genome browser Cunningham et al. (2022)  https://www.ensembl.org/index.html 
Functional annotation of the mammalian genome (FANTOM5) Lizio et al. (2015)  https://fantom.gsc.riken.jp/5/ 
Cellosaurus Bairoch (2018)  https://www.cellosaurus.org/ 
GSEAPY Fang et al. (2023)  https://gseapy.readthedocs.io/en/latest/introduction.html 
FIJI Schindelin et al. (2012)  https://imagej.net/software/fiji/ 
IBM SPSS Statistics for Macintosh, version 28.0 IBM N/A 
nfcore/atacseq v2.1.2 workflow Zenodo https://doi.org/10.5281/zenodo.8222875 
LCsolution software Shimadzu N/A 
Astra V software Wyatt N/A 
PXi GenSys software Syngene N/A 
EVOS Xl digital inverted microscope software AMG (now Thermo Fisher Scientific) N/A 
Axiovision image acquisition software (SE64 release 4.9.1) Zeiss N/A 
CLASTR Bairoch (2018)  https://web.expasy.org/cellosaurus-str-search/ 
GSEA Broad Institute https://www.gsea-msigdb.org/gsea/index.jsp 
National center for biotechnology information genes and disease  https://www.ncbi.nlm.nih.gov/books/NBK22266/ 
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