Cell culture
MCF-7, T47D and HEK293 cells are got form American Type Culture Collection (ATCC). T47D cells are cultured with RPMI-1640 (42401, Life Technologies) supplemented with 2 mM L-glutamine (25030, Life Technologies) and 10% FBS. MCF-7 and HEK293 are culture with Dulbecco’s Modified Eagle’s Medium that contains 4,5 g/L glucose and 4 mM L-glutamine (DMEM, 41965, Life Technologies) supplemented with 10% Fetal Bovine Serum (FBS, 10270, Life Technologies). All cell lines are characterized by cell line authentication. The cell line authentication via Short Tandem Repeat (STR) is performed via PowerPlex 21 system. The STR data of MCF-7 and T47D cell lines are found consistent with STR data in ATCC.
Plasmids and siRNA
The Myc-ZNF231 plasmid is acquired from Origene Company (https://www.origene.com). The ZNF213 deletion constructs were sub-cloned from the full-length plasmid. The ER alpha full and deletion constructs were described in previous study. The HA-K48 and HA-Ub plasmids were used in previous study. The Estrogen-Response-Element (ERE)-TK reporter and renilla plasmids were used in previous study and are transfected with Lipofectamin 200 (1662298, Invitrogen). For siRNA transfection, the ZNF213 siRNA sequences are #1: 5- GGA UCU CUU CUG GGA CAU AdT dT-3’, 5- UAU GUC CCA GAA GAG AUC CdT dT-3; #2: 5- GGC AUU GGG AGA CAU CCC AdT dT-3, 5- UGG GAU GUC UCC CAA UGC CdT dT-3. The siControl sequences are 5-UUC UCC GAA CGU GUC ACG UTT-3, 5-ACG UGA CAC GUU CG GAGA ATT-3.
RNA extraction and qPCR analysis
RNeasy plus mini kits were used to extract total RNA (Qiagen) [18]. The RNA concentration was measured via Nanodrop. The RNA quality was pre-checked via 18S/28S ratio in 1% agarose gel. Real-time PCR was performed as previously described [19]. 36B4 was used as internal control. Primer sequences for qPCR are provided: GREB1 F: CGT GTG GTG ACT GGA GTA GC, R: ACC TCT TCA AAG CGT GTC GT; ER F: GCT ACG AAG TGG GAA TGA TGA AAG, R: TCT GGC GCT TGT GTT TCA AC; 36B4 F: GGC GAC CTG GAA GTC CA ACT, R: CCA TCA GCA CCA CAG CCT TC; PS2 (TFF1) F: TGG GCT TCA TGA GCT CCT TC, R:TTC ATA GTG AGA GAT GGC CGG.
Quantification of cell viability
MCF-7 and T47D cells were transfected with siZNF213 or siControl in 24-well plate. Twenty-Four hours after transfection, the cells number was countered and 4000 cells were seeded into 96-well plates. The relative cell viability was measured at indicated time points. Cell numbers were determined using the WST-1 cell proliferation reagent as previously described [20].
Western blotting
Cells were harvested and lysed with RIPA buffer. Proteins were separated by electrophoresis on SDS-polyacrylamide gel electrophoresis (PAGE) and electro-transferred to PVDF membrane. The antibodies used in this study were listed here: Anti-ZNF213 (HAP035000, Sigma); Anti-ER alpha (D8H8, 8644, Cell signaling Technology); Anti-HA (MMS-101R, COVANCE); Anti-myc (9E10, ab32, Abcam); Anti-myc (Ab9106, Abcam); Anti-Actin (A5441, Sigma); Anti-Flag (20543-1-AP, Proteintech); Anti-GFP (Ab290, Abcam). Membranes were then washed with PBS for three times and incubated with secondary antibodies Peroxidase-Conjugated AffiniPure Goat Anti-Mouse IgG or Goat Anti-Rabbit IgG. Fluorescent signals were visualized with ECL system. (amersham imager 600, USA).
Luciferase assay
The luciferase activity of estrogen signaling activity was performed using the Dual-Luciferase Reporter kit (Promega, Germany). The ERE luciferase reporter was transfected together with the Renilla plasmid into the cells. Luciferase activity was measured after 24 h.
Co-immunoprecipitation assay
Immunoprecipitation was performed as described in previous study [21]. The MCF-7 total cell lysls were pre-cleared with rabbit IgG for 2 h and subsequently immunoprecipitated with ER alpha antibody (SC8005, Santa Cruz) over night, while rabbit IgG (Santa Cruz) was used as the negative control. The bounded protein was analyzed by Anti-ZNF213 (HAP035000, Sigma). For the overexpression experiment, HEK293 cells were transfected with 5ug GFP-ZNF213 (Full length or deletion domains) and ER alpha plasmid (Full length or deletion domains) in 10 cm dish. Cell lysates were pre-cleared with IgG and subsequently incubate with GFP (Ab290, Abcam) antibody, while rabbit IgG was used as the negative control. The bound proteins were analyzed by western blotting.
Poly-ubiquitination detection assay
To directly detect the enriched overall ubiquitinated or K48-ubiqutinated ER alpha from the cell extracts, HEK293 cells were transfected with 4 ug Ub or 4 ug K48 Ubi plasmid, 2 ug ER alpha together with 0.5 ug Myc-ZNF213 or Myc-vector. After 48 h, total protein was extracted and pre-cleared with 20ul protein A (santa cruz, SC-2001) for 2 h. The supernatant was collected and immunoprecipitated by ER alpha antibody. Western blot with HA antibody was performed to detect total and K48 poly-ubiquitinated ER alpha.
Immunofluorescence assay
MCF-7 cells were fixed with 4% paraformaldehyde in PBS for 10 min, permeabilized with 0.2% Triton X-100 for 5 min, and blocked by 5% BSA in PBS for 1 h. A rabbit anti-ZNF213 (HAP035000, Sigma) and mouse anti-ERα monoclonal antibodies (SC-56833) were used, followed by Alexa Flour 647 (Invitrogen) anti-rabbit antibody and FITC-conjugated anti-mouse antibodies (Jackson ImmunoResearch, West Grove, PA). As negative controls, the samples were incubated with the secondary antibodies without primary antibodies. Images were acquired under conditions fulfilling the Nyquist criterion using Nikon A+ laser scanning confocal system with a 60X oil NA1.4 objective and pinhole size of 1.0 Airy Unit. The acquired pictures were further processed and assembled using ImageJ.
RNA sequence analysis
The global gene expression analysis (siControl and siZNF213) was based on RNA sequencing platform from BGI (Beijing Genomic Institute). The RNA sequence data are deposited in the Gene Expression Omnibus (GEO) database (Assessing number: GSE143948). Analysis was performed for differentially expressed genes (P < 0.01 and fold change > 2) by Ingenuity Pathway Analysis (IPA).
Statistics
Student's t-test, Pearson correlation coefficient, and Cox regression analysis were used for comparisons. A P-value of < 0.05 was considered to be significant.