Journal: Scientific reports

Article Title: Zinc finger protein 263 promotes colorectal cancer cell progression by activating STAT3 and enhancing chemoradiotherapy resistance.

doi: 10.1038/s41598-024-72636-0

Figure Lengend Snippet: Fig. 1. ZNF263 is upregulated in CRC tissues. (A) The expression levels of ZNF263 in CRC and adjacent non-tumor tissues (data from TCGA). (B) Representative images displaying ZNF263-targeted staining in CRC tissues alongside paired non-tumor tissues. (C) The relative protein expression levels of ZNF263 in eight pairs of CRC and corresponding adjacent tissues were determined by western blotting analysis (ZNF263, 77 kDa; GAPDH, 36 kDa). (D) The relative mRNA expression levels of ZNF263 in eight pairs of CRC and corresponding adjacent tissues were determined by reverse transcription-quantitative polymerase chain reaction. Analysis revealed the association between ZNF263 expression and (E) tumor grading, (F) lymph node metastasis and (G) distant metastasis in CRC (data from TCGA). Experiments were repeated at least three times and data are presented as the mean ± SD. *P < 0.05, **P < 0.01, ****P < 0.0001. ZNF263, zinc finger protein 263; CRC, colorectal cancer; TCGA, The Cancer Genome Atlas.

Article Snippet: Following fragmentation, 5–10 μg DNA was incubated overnight at 4 °C with 5 μg ZNF263 primary antibody (mouse; cat. no. sc-135612; Santa Cruz Biotechnology, Inc.) and normal rabbit IgG (from the Chromatin Immunoprecipitation Kit).

Techniques: Expressing, Staining, Western Blot, Reverse Transcription, Real-time Polymerase Chain Reaction

Journal: Scientific reports

Article Title: Zinc finger protein 263 promotes colorectal cancer cell progression by activating STAT3 and enhancing chemoradiotherapy resistance.

doi: 10.1038/s41598-024-72636-0

Figure Lengend Snippet: Fig. 2. ZNF263 significantly promotes the proliferation, invasion and migration of colorectal cancer cells. (A) ZNF263 protein expression in SW480 and HCT116 cells. The proliferation of SW480 and HCT116 cells was assessed using (B) Cell Counting Kit-8, (C) EdU and (D) colony formation assays. The (E) invasion and (F) migration abilities of SW480 and HCT116 cells were evaluated using Transwell assays. (G) The protein expression level of E-calmodulin, N-calmodulin, Vimentin and Snail in SW480 and HCT116 cells was determined by western blotting. Experiments were repeated at least three times and data are presented as the mean ± SD. **P < 0.01, ****P < 0.0001. ZNF263, zinc finger protein 263.

Article Snippet: Following fragmentation, 5–10 μg DNA was incubated overnight at 4 °C with 5 μg ZNF263 primary antibody (mouse; cat. no. sc-135612; Santa Cruz Biotechnology, Inc.) and normal rabbit IgG (from the Chromatin Immunoprecipitation Kit).

Techniques: Migration, Expressing, Cell Counting, Western Blot

Journal: Scientific reports

Article Title: Zinc finger protein 263 promotes colorectal cancer cell progression by activating STAT3 and enhancing chemoradiotherapy resistance.

doi: 10.1038/s41598-024-72636-0

Figure Lengend Snippet: Fig. 3. STAT3 is a target of ZNF263. (A) TIMER2.0 (http://timer.cistrome.org/) was used to analyze the correlation between ZNF263 and STAT3. Detection of STAT3 (B) mRNA and (C) protein expression. (D) The UCSC Genome Browser database (http://timer.cistrome.org/) was used to predict that ZNF263 binds to the promoter of STAT3. (E) The JASPAR database (https://jaspar.elixir.no/) was used to predict the binding site of the ZNF263 zinc finger structural domain. (F) The binding of ZNF263 to the STAT3 promoter region in CRC cells was verified by chromatin immunoprecipitation. (G) Luciferase activity driven by the STAT3 promoter was evaluated in CRC cells. Experiments were repeated at least three times and data are presented as the mean ± SD. **P < 0.01, ****P < 0.0001. ZNF263, zinc finger protein 263; CRC, colorectal cancer; STAT3, signal transducer and activator of transcription 3.

Article Snippet: Following fragmentation, 5–10 μg DNA was incubated overnight at 4 °C with 5 μg ZNF263 primary antibody (mouse; cat. no. sc-135612; Santa Cruz Biotechnology, Inc.) and normal rabbit IgG (from the Chromatin Immunoprecipitation Kit).

Techniques: Expressing, Binding Assay, Chromatin Immunoprecipitation, Luciferase, Activity Assay

Journal: Scientific reports

Article Title: Zinc finger protein 263 promotes colorectal cancer cell progression by activating STAT3 and enhancing chemoradiotherapy resistance.

doi: 10.1038/s41598-024-72636-0

Figure Lengend Snippet: Fig. 4. ZNF263 promotes CRC cell proliferation and migration by upregulating STAT3. (A) The expression of STAT3 protein in SW480 and HCT116 cells. The proliferation of SW480 and HCT116 cells was assessed using (B) Cell Counting Kit-8, (C) EdU and (D) colony formation assays. The (E) invasion and (F) migration abilities of SW480 and HCT116 cells was analyzed using Transwell assays. (G) Western blotting was used to analyze the effect of STAT3 on the protein expression level of E-calmodulin, N-calmodulin, Vimentin and Snail in SW480 and HCT116 cells. Experiments were repeated at least three times and data are presented as the mean ± SD. **P < 0.01, ***P < 0.001, ****P < 0.0001. ZNF263, zinc finger protein 263; STAT3, signal transducer and activator of transcription 3.

Article Snippet: Following fragmentation, 5–10 μg DNA was incubated overnight at 4 °C with 5 μg ZNF263 primary antibody (mouse; cat. no. sc-135612; Santa Cruz Biotechnology, Inc.) and normal rabbit IgG (from the Chromatin Immunoprecipitation Kit).

Techniques: Migration, Expressing, Cell Counting, Western Blot

Journal: Scientific reports

Article Title: Zinc finger protein 263 promotes colorectal cancer cell progression by activating STAT3 and enhancing chemoradiotherapy resistance.

doi: 10.1038/s41598-024-72636-0

Figure Lengend Snippet: Fig. 5. ZNF263 increases the resistance of colorectal cancer cells to chemoradiotherapy. (A) The proliferative capacity of irradiated SW480 and HCT116 cells was assessed using the CCK-8 assay. (B) Representative images and quantification of the colony formation of SW480 and HCT116 cells exposed to varying doses of X-ray radiation. (C) The survival of SW480 and HCT116 cells treated with different concentrations of cisplatin was evaluated using the CCK-8 assay. (D) Representative images and quantification of the colony formation of SW480 and HCT116 cells treated with varying doses of cisplatin. Experiments were repeated at least three times and data are presented as the mean ± SD. *P < 0.05, **P < 0.01, ****P < 0.0001. ZNF263, zinc finger protein 263; CCK-8, Cell Counting Kit-8.

Article Snippet: Following fragmentation, 5–10 μg DNA was incubated overnight at 4 °C with 5 μg ZNF263 primary antibody (mouse; cat. no. sc-135612; Santa Cruz Biotechnology, Inc.) and normal rabbit IgG (from the Chromatin Immunoprecipitation Kit).

Techniques: Irradiation, CCK-8 Assay, Cell Counting

Journal: Molecular cell

Article Title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries

doi: 10.1016/j.molcel.2024.08.007

Figure Lengend Snippet: (A) Venn diagram showing RAD21, CTCF, and PATZ1 binding in HEK293 cells. (B) Heat maps of RAD21, CTCF, PATZ1, MAZ, and other zinc finger proteins, ZNF263, ZNF341 and ZNF467 in HEK293 cells. ChIP-seq read density was grouped as Cluster 1, Cluster 2, and Cluster 3 based on the indicated overlaps with RAD21 signal within a 4 kb window. (C) Western blot analysis of RAD21, FLAG, and CTCF upon FLAG-PATZ1 immunoprecipitation from mESCs (n=2, see for biological replicate). (D) Visualization of Hi-C contact matrices for a zoomed-in region around the TBC1D1 locus in HepG2 cells. Shown below are loops with PATZ1 at both anchors in HepG2 cells, ChIP-seq read densities for RAD21, CTCF, PATZ1, and MAZ, and gene annotations. ChIP-seq data in HepG2 cells is from two combined biological replicates. (E) Percentage of Hi-C loops in HepG2 cells overlapping with RAD21, CTCF, and PATZ1 ChIP-seq peaks. (F) Heat maps of RAD21, PATZ1, ZNF263, ZNF341, and ZNF467 in HEK293 cells. ChIP-seq read density was grouped as Cluster 1, Cluster 2, Cluster 3, and Cluster 4 based on the combinatorial overlaps of zinc finger proteins with RAD21 within a 4 kb window in HEK293 cells. The model on the right side indicates combinatorial binding of the indicated factors in each cluster (see ). ChIP-seq data in HEK293 cells is from one replicate for RAD21 and one representative of two biological replicates for others (see for datasets).

Article Snippet: The mouse Znf263 coding sequence (NM_148924.3) with an HA-tag sequence fused to its 5’ end was cloned into a PiggyBac vector (pPB-CAG-FLAG-HA, a modified version of pPB-CAG-3xFLAG-empty-pgk-hph from Addgene, #48754) to create pPB-CAG-FLAG-HA-ZNF263 plasmid via Gibson assembly (NEB, #E2611).

Techniques: Binding Assay, ChIP-sequencing, Western Blot, Immunoprecipitation, Hi-C

Journal: Molecular cell

Article Title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries

doi: 10.1016/j.molcel.2024.08.007

Figure Lengend Snippet: (A) Normalized ChIP-seq densities for RAD21, CTCF, and PATZ1, and ZNF263 in WT, Patz1 KO, and Znf263 KO mESCs at the indicated regions in the HoxA cluster. ChIP-seq data represents one representative replicate of two biological replicates for RAD21, CTCF, and one replicate for FH-PATZ1 and FH-ZNF263. (B-D) RT-qPCR analysis for the indicated Hox genes in (B) the HoxA , (C) the HoxC , and (D) the HoxD clusters in WT and Patz1 KO cervical MNs. RT-qPCR signal was normalized to Atp5f1 and ActB levels. The fold-change in expression was calculated relative to WT MNs. All RT-qPCR results are represented as mean values and error bars indicating log 2 (SE) across three biological replicates (two-sided Student’s t -test without multiple testing correction; *** P ≤ 0.001, ** P ≤ 0.01, * P < 0.05). (E) Differentially expressed genes by RNA-seq upon Patz1 KO in MNs from two biological replicates (see all in ). (F) GO analysis showing the top biological processes enriched in the differentially expressed genes in Patz1 KO versus WT MNs. PANTHER overrepresentation test tools were used for GO analysis and top 15 categories having a fold enrichment > 2.5 were plotted (see all in ). (G-I) RT-qPCR analysis for the indicated Hox genes in (G) the HoxA , (H) the HoxC , and (I) the HoxD clusters in WT and Znf263 KO cervical MNs. RT-qPCR signal was normalized to Atp5f1 and Gapdh levels. The fold-change in expression was calculated relative to WT MNs. All RT-qPCR results are represented as mean values and error bars indicating log 2 (SE) across three technical replicates. Two independent Znf263 KO clones are shown (see ).

Article Snippet: The mouse Znf263 coding sequence (NM_148924.3) with an HA-tag sequence fused to its 5’ end was cloned into a PiggyBac vector (pPB-CAG-FLAG-HA, a modified version of pPB-CAG-3xFLAG-empty-pgk-hph from Addgene, #48754) to create pPB-CAG-FLAG-HA-ZNF263 plasmid via Gibson assembly (NEB, #E2611).

Techniques: ChIP-sequencing, Quantitative RT-PCR, Expressing, RNA Sequencing, Clone Assay

Journal: Molecular cell

Article Title: Members of an array of zinc finger proteins specify distinct Hox chromatin boundaries

doi: 10.1016/j.molcel.2024.08.007

Figure Lengend Snippet: Key Resources Table

Article Snippet: The mouse Znf263 coding sequence (NM_148924.3) with an HA-tag sequence fused to its 5’ end was cloned into a PiggyBac vector (pPB-CAG-FLAG-HA, a modified version of pPB-CAG-3xFLAG-empty-pgk-hph from Addgene, #48754) to create pPB-CAG-FLAG-HA-ZNF263 plasmid via Gibson assembly (NEB, #E2611).

Techniques: Virus, Recombinant, Magnetic Beads, SYBR Green Assay, Western Blot, Cloning, Plasmid Preparation, Software, Injection

Journal: ERJ Open Research

Article Title: COL4A3 expression in asthmatic epithelium depends on intronic methylation and ZNF263 binding

doi: 10.1183/23120541.00802-2020

Figure Lengend Snippet: ZNF263 binding is interrupted in asthmatic patients due to increased methylation at site cg11797365 leading to a reduced COL4A3 expression. a) Detection hits of chromatin-immunoprecipitation sequencing (ChIP-seq) data of ZNF263 in COL4A3 region. Large peak corresponds to region of first exon and start of first intron. cg11797365 is indicated by the red arrow and corresponds with previous report on ZNF263 binding (ENCODE track). The methylation site cg11797365 is close to the consensus binding site (green highlight in ENCODE track) of ZNF263. Custom track from ChIP-seq data from normal human bronchial epithelial cells (NHBE) is shown as indicated. b) Quantitative ChIP-seq analysis of ZNF263 binding to genomic region COL4A3 (1. intron) of cg11797365 in human bronchial epithelial cells (BEAS-2B) and NHBEs. Normalised binding events (per 1000 cells), n=4 per cell line (BEAS-2B and NHBE; Lonza). c) Quantitative (q)PCR to quantify ZNF263 expression levels in HeLA cells transfected with small interfering (si)RNA against ZNF263 in comparison to cells transfected with a nontarget control. d) Expression of COL4A3 in HeLA cells transfected with siRNA against ZNF263 compared to cells transfected with a nontarget control. Δct values are normalised to GAPDH . *: p<0.05, **: p<0.01, ***: p<0.001, ****: p<0.0001, Mann–Whitney U-test.

Article Snippet: Concisely, the zinc finger protein 263 (ZNF263) ChIP-quantitative (q)PCR assay was performed using 30 μg BEAS-2B and NHBE chromatin and 5 μL antibody against ZNF263 (Novus Biologicals, Germany).

Techniques: Binding Assay, Methylation, Expressing, ChIP-sequencing, Transfection, Comparison, Control, MANN-WHITNEY