Journal: The Journal of Experimental Medicine

Article Title: Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element

doi: 10.1084/jem.20141479

Figure Lengend Snippet: Impact of Eβ on topology, structural protein deposition, and transcription of Vβ segments. (A and B) Schematics and histograms of 3C data for the Trbv5 (A) and Trbv23 (B) viewpoints (anchors) in RAG-deficient DN thymocytes or pro-B cells (see for details). (C) Published ChIP-seq profile for CTCF in RAG-deficient DN thymocytes (top; ). (C and D) ChIP-qPCR for CTCF (C) and RAD21 (D) binding at the indicated sites in WT or mEβ thymocytes versus RAG-deficient pro-B cells. Data are presented as mean values for percent input signal from at least three independent experiments (±SEM). (E) Germline transcription of Trbv segments as monitored by RT-qPCR assays in the indicated cell types. Mean values from three independent experiments after normalization to signals for Actb are shown (±SEM). Thymocytes were pooled from 5–10 mice per experiment. Significant differences between WT and mEβ samples are denoted as *, P < 0.05 (Student’s t test).

Article Snippet: The following antibodies were used: CTCF (Rockland), Rad21 (Abcam), H3ac (EMD Millipore), H3K4me2 (Abcam), H3K4me3 (Abcam), H3K9me2 (Abcam), H3K27me3 (Abcam), and IgG (Santa Cruz Biotechnology, Inc.).

Techniques: ChIP-sequencing, ChIP-qPCR, Binding Assay, Quantitative RT-PCR

Journal: The Journal of Experimental Medicine

Article Title: Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element

doi: 10.1084/jem.20141479

Figure Lengend Snippet: Deletion of the 5′RC flank resolves two Trbv interaction domains. (A and B) 3C analysis of RAG-deficient thymocytes (WT, ΔPDβ1, or mEβ alleles) and pro-B cells using the Dβ2 (A, top), Trbv5 (A, bottom), and Eβ (B) viewpoints (anchors). Individual HindIII fragments are represented by alternating white and gray bars. Bold black bars indicate viewpoint locations. Schematics of Tcrb are shown on top and below primary 3C data, which are presented as mean values (±SEM) from at least three independent experiments. Thymocytes were pooled from 5–10 mice per 3C experiment. Significant differences between WT and ΔPDβ1 samples are denoted as *, P < 0.05 (Student’s t test). See for details of cartoon data summaries. Here, red shading indicates that Trbv -Dβ2 cross-linking in ΔPDb1 relative to WT alleles was unchanged (darkest red) or reduced to background levels in pro-B cells (white). (C and D) ChIP-qPCR assay for CTCF (C) and RAD21 (D) binding at sites near the indicated Trbv segments. Refer to for details. Data are presented as mean percent input (±SEM) with thymocytes pooled from at least 5–10 mice per experiment. (E) Trbv germline transcription was quantified relative to Actb by qRT-PCR from at least three independent experiments (involving one to three mice per experiment). Data are presented as mean relative expression (±SEM). Statistically significant differences are denoted as *, P < 0.05 (Student’s t test). (F) 3C assays were performed with the Trbv23 viewpoint (anchor). Schematic of Tcrb is shown on top. Data are presented as mean relative cross-linking (±SEM). Statistically significant differences between WT and ΔPDβ1 are denoted as *, P < 0.05 (Student’s t test).

Article Snippet: The following antibodies were used: CTCF (Rockland), Rad21 (Abcam), H3ac (EMD Millipore), H3K4me2 (Abcam), H3K4me3 (Abcam), H3K9me2 (Abcam), H3K27me3 (Abcam), and IgG (Santa Cruz Biotechnology, Inc.).

Techniques: ChIP-qPCR, Binding Assay, Quantitative RT-PCR, Expressing

Journal: The Journal of Experimental Medicine

Article Title: Lineage-specific compaction of Tcrb requires a chromatin barrier to protect the function of a long-range tethering element

doi: 10.1084/jem.20141479

Figure Lengend Snippet: Identification of a Trbv tethering point in the RC flank. (A–E) 3C data for Trbv5 (A; the bottom shows ChIP-seq track for CTCF in DN thymocytes as well as locations of repetitive elements), 5′PC (B; schematic shown on top for 5′PC viewpoint; see ), Trbv3 (C), Trbv12-2 (D), and Trbv23 (E) viewpoints (anchors) in RAG-deficient DN thymocytes (WT, ΔPDβ1, or ΔminPDβ1 mice) or pro-B cells (see for details). (F) ChIP-qPCR for CTCF and RAD21 at 5′PC in the indicated cell types. All data are represented as means (±SEM) of three independent experiments. Thymocytes were pooled from 5–10 mice for each 3C or ChIP assay. Significant differences are denoted as *, P ≤ 0.05 (Student’s t test between WT and ΔPDβ1 genotypes).

Article Snippet: The following antibodies were used: CTCF (Rockland), Rad21 (Abcam), H3ac (EMD Millipore), H3K4me2 (Abcam), H3K4me3 (Abcam), H3K9me2 (Abcam), H3K27me3 (Abcam), and IgG (Santa Cruz Biotechnology, Inc.).

Techniques: ChIP-sequencing, ChIP-qPCR

Journal: Molecular cell

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.

doi: 10.1016/j.molcel.2024.11.031

Figure Lengend Snippet: Figure 1. ZFP143 can be homozygously tagged and stably binds to chromatin (A) Overview of genome-engineered cell lines. (B) Depletion western blots. On the left, ZFP143 (top) or CTCF (bottom) time courses for clones A and B. On the right, clones D and 3041 at the 3 h time point. TATA- binding protein (TBP) was used as a loading control. Black borders indicate cropping of whitespace or superfluous lanes. (C) Live-cell imaging of a clone A mESC colony showing nuclear localization of both CTCF and ZFP143. (D) Growth curve showing live-cell counts in clone D with (blue) and without (gray) constitutive ZFP143 depletion for 6 days. On day 3, cells were reseeded at a density of 250,000 live cells per well. Error bars indicate 95% confidence interval (CI) (n = 6). (E) Example FRAP images in the H2B-Halo, Halo-CTCF, and ZFP143-Halo conditions at 10 s before bleaching, on the bleach frame, 20 s after, and 600 s after bleaching. (F) FRAP curves showing normalized intensity of ZFP143 recovery (left) for clones A (magenta) and B (blue) and CTCF recovery (right) for clones A (magenta), B (blue), and D (orange) as well as the C87 Halo-CTCF line14 (red). Halo-NLS and H2B-Halo controls shown in gray. Error bars indicate 95% CI. (G) Example images of particles from SPT. (H) Jump displacement histograms for CTCF (clone D, left) and ZFP143 (clones A and B, right) for seven time lags. (I) Cumulative distribution functions (CDFs) comparing jump lengths between clones A and B (left) and clone D and C87 (right). (J) Summary of key measurements ±1 SD from SPT, FRAP, and absolute abundance quantification. See also Figure S1.

Article Snippet: Due to the findings by Magnitov and Maresca et al. in their 6 Molecular Cell 85, 1–15, January 2, 2025 companion paper that a commonly used ZFP143 antibody from Proteintech cross-reacts with CTCF, we used an antibody from Novus Biologicals, which does not show cross-reactivity.95 Using this antibody, we found that for all clones, >90% of ZFP143 peaks responded to the depletion, indicating no cross-reactivity (Figure S4E).

Techniques: Stable Transfection, Western Blot, Clone Assay, Binding Assay, Control, Live Cell Imaging

Journal: Molecular cell

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.

doi: 10.1016/j.molcel.2024.11.031

Figure Lengend Snippet: Figure 2. Loops are unaffected by ZFP143 depletion in mESCs (A and B) Two representative loci averaging clones A/B. From top to bottom are Micro-C maps at 2,000 bp resolution comparing untreated to DZFP143 (3 h), DCTCF (3 h) to DZFP143/DCTCF (3 h), ZFP143 ChIP-seq tracks (cyan), CTCF ChIP-seq tracks (red), and PRO-seq showing plus strand (blue) and minus strand (magenta) for all conditions. Below are zoom-ins on ZFP143-regulated genes showing reduction in PRO-seq signal upon ZFP143 depletion. (A) The Timm13/ Lmnb2 locus. (B) The Rpp30 locus. (C) Aggregate peak analysis (APA)/loop pileup analysis for all loops, cohesin-bound loops, E-P loops, and P-P loops from Hsieh et al.74 and ZFP143-bound loops for untreated, DZFP143 (3 h), DCTCF (3 h), and DZFP143/DCTCF (3 h) conditions in log10 scale with average dot strength (upper left). (D) Scatterplots of loop strengths calculated as in (C) for cohesin loops (red), E-P loops (orange), P-P loops (teal), and ZFP143 loops (cyan) comparing DZFP143 (3 h), DCTCF (3 h), or DZFP143/DCTCF (3 h) to untreated.

Article Snippet: Due to the findings by Magnitov and Maresca et al. in their 6 Molecular Cell 85, 1–15, January 2, 2025 companion paper that a commonly used ZFP143 antibody from Proteintech cross-reacts with CTCF, we used an antibody from Novus Biologicals, which does not show cross-reactivity.95 Using this antibody, we found that for all clones, >90% of ZFP143 peaks responded to the depletion, indicating no cross-reactivity (Figure S4E).

Techniques: Clone Assay, ChIP-sequencing

Journal: Molecular cell

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.

doi: 10.1016/j.molcel.2024.11.031

Figure Lengend Snippet: Figure 3. Loops are unaffected at longer ZFP143 depletion timescales in mESCs (A and B) Two representative loci (as in Figures 2A and 2B) in clone D time course. From top to bottom are Micro-C maps at 2,000 bp resolution comparing untreated to DZFP143 (6 h), DZFP143 (12 h), and DZFP143 (24 h); ZFP143 untreated ChIP-seq tracks (cyan); and CTCF untreated ChIP-seq tracks (red). (C) APA/loop pileup analysis for all loops, E-P loops, P-P loops, and ZFP143-bound loops for untreated and DZFP143 (6 h), DZFP143 (12 h), and DZFP143 (24 h) conditions in log10 scale with average dot strength (upper left). (D) Scatterplots of boundary strengths calculated as in (C) for E-P loops (orange), P-P loops (teal), and ZFP143 loops (cyan) comparing DZFP143 (6 h), DZFP143 (12 h), and DZFP143 (24 h) to untreated. (E) Boxplots of the log2 loop strengths plotted in (D) relative to the untreated condition versus ZFP143 depletion time for cohesin (red), E-P (orange), P-P (teal), and ZFP143-bound (cyan) loops. See also Figure S3.

Article Snippet: Due to the findings by Magnitov and Maresca et al. in their 6 Molecular Cell 85, 1–15, January 2, 2025 companion paper that a commonly used ZFP143 antibody from Proteintech cross-reacts with CTCF, we used an antibody from Novus Biologicals, which does not show cross-reactivity.95 Using this antibody, we found that for all clones, >90% of ZFP143 peaks responded to the depletion, indicating no cross-reactivity (Figure S4E).

Techniques: ChIP-sequencing

Journal: Molecular cell

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.

doi: 10.1016/j.molcel.2024.11.031

Figure Lengend Snippet: Figure 4. Loops are unaffected by ZFP143 depletion in HEK293T cells (A and B) Two representative loci in HEK293T clone 30. From top to bottom are Micro-C maps at 2,000 bp resolution comparing untreated to DZFP143 (3 h), ZFP143 ChIP-seq tracks (cyan), CTCF ChIP-seq tracks (red), and PRO-seq41 with plus strand (blue) and minus strand (magenta) for untreated and DZFP143 (3 h). Below are zoom-ins on ZFP143-bound genes for the ABL1 locus (A) and the CSRNP2 locus (B). (C) APA/loop pileup analysis for all called loops, E-P loops, P-P loops, and ZFP143-bound loops across untreated and DZFP143 (3 h) conditions in log10 scale with average dot strength (upper left). (D) Scatterplots of boundary strengths calculated as in (C) for E-P loops (orange), P-P loops (teal), and ZFP143 loops (cyan) comparing DZFP143 (3 h) to un- treated. (E) Metaplots over insulation score tracks called at 50 kb resolution comparing untreated (gray) and DZFP143 (3 h) (cyan). (F) Venn diagrams of overlap in genes with ZFP143- or CTCF-bound promoters between mESC and HEK293T. (G) Diagram of mouse and human ZFP143 showing the location of the seven C2H2 zinc-finger domains. Below, identical (teal), similar (cyan), and dissimilar (red) amino acids between species. See also Figure S3.

Article Snippet: Due to the findings by Magnitov and Maresca et al. in their 6 Molecular Cell 85, 1–15, January 2, 2025 companion paper that a commonly used ZFP143 antibody from Proteintech cross-reacts with CTCF, we used an antibody from Novus Biologicals, which does not show cross-reactivity.95 Using this antibody, we found that for all clones, >90% of ZFP143 peaks responded to the depletion, indicating no cross-reactivity (Figure S4E).

Techniques: ChIP-sequencing, Insulation

Journal: Molecular cell

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.

doi: 10.1016/j.molcel.2024.11.031

Figure Lengend Snippet: Figure 5. ZFP143 largely binds independently to CTCF (A) Venn diagrams of overlap in CTCF and ZFP143 binding between HEK293T and mESC ChIP-seq. (B) The percentage of ZFP143 and CTCF ChIP-seq peaks overlapping TSS (teal), enhancer (orange), intragenic (red), or intergenic (gray) regions. (C) Scatterplots showing the log2 fold-change of read counts at ChIP-seq peaks between either DCTCF (3 h) and untreated ZFP143 ChIP-seq (left) or DZFP143 (3 h) and untreated CTCF ChIP-seq (right) versus peak size. The number of significantly increased or decreased peaks (red) from DESeq2 (padj % 0.05, fold change R 1.5) is at the top. On the right is a histogram of point density. (D) Metaplots over ChIP-seq peaks for untreated or DCTCF (3 h) ZFP143 ChIP-seq (left) or untreated or DZFP143 (3 h) CTCF ChIP-seq (right). In the left plot, peaks overlapping a CTCF peak (magenta, top) and those not overlapping a CTCF peak (blue, bottom) are shown. (E and F) FRAP curves show normalized intensity over time. Halo-NLS and H2B-Halo controls are gray. Error bars indicate 95% CI. (E) ZFP143 in the untreated (blue) condition versus DCTCF (2–4 h, magenta) averaging clones A/B. (F) CTCF in the untreated (blue) condition versus DZFP143 (2–4 h, magenta). (G and H) Jump displacement CDFs from SPT for an 18 ms time-lag. (G) SPT of ZFP143 comparing DCTCF (2–4 h, magenta) with untreated (blue). (H) SPT of CTCF comparing DZFP143 (2–4 h, magenta) with untreated (blue). (I) State-array SPT (saSPT) showing the posterior distribution versus diffusion coefficient in mm2 s–1 for ZFP143 SPT (left) and CTCF SPT (right). Curves give the mean across traces. The shaded area gives the 95% CI across all movies. Heatmaps show individual traces. Either DCTCF (2–4 h) or DZFP143 (2–4 h) is magenta, and untreated is blue. See also Figures S4 and S5.

Article Snippet: Due to the findings by Magnitov and Maresca et al. in their 6 Molecular Cell 85, 1–15, January 2, 2025 companion paper that a commonly used ZFP143 antibody from Proteintech cross-reacts with CTCF, we used an antibody from Novus Biologicals, which does not show cross-reactivity.95 Using this antibody, we found that for all clones, >90% of ZFP143 peaks responded to the depletion, indicating no cross-reactivity (Figure S4E).

Techniques: Binding Assay, ChIP-sequencing, Clone Assay, Diffusion-based Assay

Journal: Molecular cell

Article Title: ZNF143 is a transcriptional regulator of nuclear-encoded mitochondrial genes that acts independently of looping and CTCF.

doi: 10.1016/j.molcel.2024.11.031

Figure Lengend Snippet: Figure 6. ZFP143 is a transcriptional regulator of ribosomal and mitochondrial genes (A) Histogram of the distribution of the distance of ZFP143 motifs in ChIP-seq peaks overlapping ±1 kb to a TSS showing a median of 38 bp. (B) Metaplots over PRO-seq signal centered on ZFP143 motifs for the same strand as the ZFP143 motif (blue), and the opposite strand as the ZFP143 motif (magenta). (C) Orientations of motifs in (A) relative to their nearest TSS. (D and E) Volcano plots showing –log10 of the padj value versus the log2 fold-change of read counts of PRO-seq signal at genes. Genes with a fold-change greater than two are green, genes with a padj value less than 0.001 are blue, and genes significant in both are red. The number of significantly changed genes evaluated by DESeq2 is above. (D) DZFP143 (3 h). (E) DCTCF (3 h). (F) Metaplots over gene bodies showing average PRO-seq signal in the untreated (left) versus DZFP143 (3 h, right) conditions. Genes with ZFP143-bound promoters (magenta, upper). Non-ZFP143-bound genes (blue, bottom). (G) The percentage of significantly changing expression genes bound by either ZFP143 (cyan), CTCF (red), both (teal), or neither (gray) in PRO-seq evaluated by DESeq2. (H) Venn diagrams of overlaps in genes significantly changing in the DZFP143 (3 h, cyan), DCTCF (3 h, red), or DZFP143/DCTCF (3 h, teal) conditions. (I) Significant gene sets versus normalized enrichment score for GO-term enrichment analysis of significantly changed genes in the DZFP143 (3 h) condition. The size of the circle corresponds to the set size, and points are colored by log10 padj value. See also Figure S6.

Article Snippet: Due to the findings by Magnitov and Maresca et al. in their 6 Molecular Cell 85, 1–15, January 2, 2025 companion paper that a commonly used ZFP143 antibody from Proteintech cross-reacts with CTCF, we used an antibody from Novus Biologicals, which does not show cross-reactivity.95 Using this antibody, we found that for all clones, >90% of ZFP143 peaks responded to the depletion, indicating no cross-reactivity (Figure S4E).

Techniques: ChIP-sequencing, Expressing

Journal: International Journal of Biological Sciences

Article Title: Maternal EHMT2 is essential for homologous chromosome segregation by regulating Cyclin B3 transcription in oocyte meiosis

doi: 10.7150/ijbs.75298

Figure Lengend Snippet: EHMT2 regulates ccnb3 transcriptions by regulating CTCF binding near ccnb3 gene body in genome in oocytes. (A) The genome browser view by IGV showing few H3K9me2 enrichment near Ccnb3 in mouse oocytes (a published dataset and this study using CUT&RUN). (B) Upper is the diagram showing the approximate position of the CpG island near Ccnb3 gene promoter; Lower is the methylation degree of CpG island of the indicated genotype. (C) The genome browser view by IGV showing decreased CTCF enrichment near Ccnb3 in mouse oocytes (this study using STAR-seq). (D) Scheme showing the early secondary follicles microinjected with Ctcf siRNA. (E) Relative expression of Ctcf after Ctcf siRNA treatment in oocytes. Error bars, S.D. ***P < 0.001 by two-tailed Student's t tests. (F) Relative expression of Ccnb3 after Ctcf siRNA treatment in follicles.

Article Snippet: The following primary antibodies were used, respectively: mouse anti-EHMT1 antibody (for IF, Abcam, ab41969), rabbit anti-EHMT2 antibody (for IF, Cell Signaling, 3306S), rabbit anti-H3K9me2 (for IF, Millipore, 07-212), rabbit anti-CCNB3 (for IHC, Bioss, bs-7884R), rabbit anti-H3K9me1 (for IF, Abcam, ab9045), mouse anti-HA-tag (for Co-IP, Abclonal, AE008), mouse anti-Myc-Tag (for Co-IP, Abclonal, AE010), rabbit anti-CTCF antibody (for STAR-seq, Active Motif, 61311), mouse anti- H3K9me2 antibody (for CUT&RUN, abcam ab1220), mouse anti-β-actin (for WB, Zhongshan Golden Bridge Biotechnology, TA-09).

Techniques: Binding Assay, Methylation, Expressing, Two Tailed Test

Journal: International Journal of Biological Sciences

Article Title: Maternal EHMT2 is essential for homologous chromosome segregation by regulating Cyclin B3 transcription in oocyte meiosis

doi: 10.7150/ijbs.75298

Figure Lengend Snippet: Schematic figure showing possible regulatory mechanisms of EHMT2 on homologous chromosome separation in mouse oocytes. We propose that EHMT2 but not EHMT1 was involved in regulating the methylation establishment of H3K9me2 in mouse oocytes, which is consistent with our previous report that WIZ protein was not present in mouse oocytes. In Ehmt2 GKO oocytes, unknown protein can be used to modify H3K9me2 in an abnormal form to establish compensatory establishment. At the same time, we proved that the deletion of maternal EHMT2 indirectly led to a decrease of Ccnb3 mRNA, which in turn reduced the protein level of CCNB3, and ultimately led to the failure of homologous chromosome separation. Furthermore, maternal EHMT2 regulates the binding of CTCF to Ccnb3 gene body nearby in oocytes using STAR-seq.

Article Snippet: The following primary antibodies were used, respectively: mouse anti-EHMT1 antibody (for IF, Abcam, ab41969), rabbit anti-EHMT2 antibody (for IF, Cell Signaling, 3306S), rabbit anti-H3K9me2 (for IF, Millipore, 07-212), rabbit anti-CCNB3 (for IHC, Bioss, bs-7884R), rabbit anti-H3K9me1 (for IF, Abcam, ab9045), mouse anti-HA-tag (for Co-IP, Abclonal, AE008), mouse anti-Myc-Tag (for Co-IP, Abclonal, AE010), rabbit anti-CTCF antibody (for STAR-seq, Active Motif, 61311), mouse anti- H3K9me2 antibody (for CUT&RUN, abcam ab1220), mouse anti-β-actin (for WB, Zhongshan Golden Bridge Biotechnology, TA-09).

Techniques: Methylation, Binding Assay

Journal: PLoS ONE

Article Title: Construction of ceRNA network to identify the lncRNA and mRNA related to non-small cell lung cancer

doi: 10.1371/journal.pone.0259091

Figure Lengend Snippet: The primers used in this study.

Article Snippet: The membranes were incubated with the primary antibody CTCFL (60079-1-Ig, 1: 1000, proteintech), KRT5 (66727-1-Ig, 1: 10000, proteintech), LY6D (17361-1-AP, 1: 300, proteintech), TMEM (20995-1-AP, 1: 500, proteintech), GBP6 (23001-1-AP, 1: 1000, proteintech), TMEM179 (24799-1-AP, 1: 600, proteintech), β-actin (60008-1-Ig, 1: 5000, proteintech) overnight at 4°C.

Techniques:

Journal: PLoS ONE

Article Title: Construction of ceRNA network to identify the lncRNA and mRNA related to non-small cell lung cancer

doi: 10.1371/journal.pone.0259091

Figure Lengend Snippet: A. Survival curve of CTCFL. B. Survival curve of GBP6. C. Survival curve of KRT5. D. Survival curve of LY6D. E. Survival curve of TMEM. F. Survival curve of TMEM179. The abscissa represented survival time (days), and the ordinate represented survival rate. The blue line represented the low risk curve and the red line represents the high risk curve, p<0.05.

Article Snippet: The membranes were incubated with the primary antibody CTCFL (60079-1-Ig, 1: 1000, proteintech), KRT5 (66727-1-Ig, 1: 10000, proteintech), LY6D (17361-1-AP, 1: 300, proteintech), TMEM (20995-1-AP, 1: 500, proteintech), GBP6 (23001-1-AP, 1: 1000, proteintech), TMEM179 (24799-1-AP, 1: 600, proteintech), β-actin (60008-1-Ig, 1: 5000, proteintech) overnight at 4°C.

Techniques:

Journal: PLoS ONE

Article Title: Construction of ceRNA network to identify the lncRNA and mRNA related to non-small cell lung cancer

doi: 10.1371/journal.pone.0259091

Figure Lengend Snippet: qRT-PCR (A) and WB (B) were used to detect the expression levels of CTCFL, KRT5, LY6D, TMEM, GBP6, TMEM179. (C) Pearson analysis was used to detect the correlation between LINC00968 and CTCFL, GBP6, KRT5.

Article Snippet: The membranes were incubated with the primary antibody CTCFL (60079-1-Ig, 1: 1000, proteintech), KRT5 (66727-1-Ig, 1: 10000, proteintech), LY6D (17361-1-AP, 1: 300, proteintech), TMEM (20995-1-AP, 1: 500, proteintech), GBP6 (23001-1-AP, 1: 1000, proteintech), TMEM179 (24799-1-AP, 1: 600, proteintech), β-actin (60008-1-Ig, 1: 5000, proteintech) overnight at 4°C.

Techniques: Quantitative RT-PCR, Expressing

Journal: PLoS ONE

Article Title: Construction of ceRNA network to identify the lncRNA and mRNA related to non-small cell lung cancer

doi: 10.1371/journal.pone.0259091

Figure Lengend Snippet: (A) qRT-PCR was explored to examine whether knockdown of LINC00968 is successful. (B) CCK8 was performed to measure cell proliferation. qRT-PCR (C) and WB (D) were used to detect the expression of CTCFL, GBP6, KRT5. (E) Flow cytometry was utilized to detect cell apoptosis. (F) Tunel was explored to determined cell apoptosis.

Article Snippet: The membranes were incubated with the primary antibody CTCFL (60079-1-Ig, 1: 1000, proteintech), KRT5 (66727-1-Ig, 1: 10000, proteintech), LY6D (17361-1-AP, 1: 300, proteintech), TMEM (20995-1-AP, 1: 500, proteintech), GBP6 (23001-1-AP, 1: 1000, proteintech), TMEM179 (24799-1-AP, 1: 600, proteintech), β-actin (60008-1-Ig, 1: 5000, proteintech) overnight at 4°C.

Techniques: Quantitative RT-PCR, Knockdown, Expressing, Flow Cytometry, TUNEL Assay

Journal: PLoS Genetics

Article Title: Two cis -regulatory SNPs upstream of ABCG2 synergistically cause the blue eggshell phenotype in the duck

doi: 10.1371/journal.pgen.1009119

Figure Lengend Snippet: (A) Supershift EMSA was performed using CTCF antibody. CTCF antibody (1 μg) was incubated with 0.5 μg recombinant human CTCF protein prior to the addition of the binding buffer and probe. G and A represent labelled probes containing the white eggshell and blue eggshell allele, respectively, and G cold and A cold represent cold probes containing the white eggshell and blue eggshell allele, respectively. (B) ChIP-qPCR analysis of CTCF binding on variation M5 in uteruses from blue-eggshelled and white-eggshelled ducks. Chromatin extracts from four individuals of each genotype were immunoprecipitated with CTCF antibody. ChIP-enriched DNA was quantified by qPCR with primers specific for variation M5. Rabbit IgG was used as a negative control. Values of immunoprecipitated samples were normalized to that of the input DNA. Data are presented as mean±SD from four independent individuals.

Article Snippet: CTCF antibody (1μg) was incubated with 0.5 μg recombinant human CTCF protein (Novus biologicals, Littleton, USA) prior to addition of the binding buffer and probe.

Techniques: Incubation, Recombinant, Binding Assay, ChIP-qPCR, Immunoprecipitation, Negative Control

Journal: eLife

Article Title: Translation in amino-acid-poor environments is limited by tRNA Gln charging

doi: 10.7554/eLife.62307

Figure Lengend Snippet:

Article Snippet: The following primary antibodies were used: phospho-Thr899 GCN2 (ab75836, Abcam), total GCN2 (3302, Cell Signaling), phospho-Thr-389-S6K1 (9234, Cell Signaling), S6K1 (2708, Cell Signaling), vinculin (V9131, Sigma-Aldrich), ATF4 (sc-200, Santa Cruz), MED12 (A300-774A, Bethyl), TBP (A301-229A, Bethyl), CBP (A300-362A, Bethyl), CBFα1 (12556, Cell Signaling), BRD4 (ab128874, Abcam), CTCF (A700-041-T, Bethyl), RNA pol II (39497, Active Motif), Histone H3 (3638, Cell Signaling), α-Tubulin (T9026, Sigma-Aldrich), β-Actin (A5441, Sigma-Aldrich), HA tag (2367, Cell Signaling), puromycin (MABE343, EMD Millipore), and GLS (ab156876, Abcam).

Techniques: Recombinant, Control, shRNA, Luciferase, Plasmid Preparation, Expressing, Virus, Sequencing