Journal: bioRxiv

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

doi: 10.1101/2024.03.08.583864

Figure Lengend Snippet: (A) Relative contact probability plot (top panel) and its derivative (bottom panel) calculated from the Hi-C matrices of DMSO (blue) and 6 hours dTAG-V1 (orange) treated ZFP143-FKBP cells. (B) Average cohesin (left), enhancer-promoter (E-P, middle) and promoter-promoter (P-P, right) loops in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. Value in the upper-right corner indicates the interaction strength of the loop over the background. (C) Same as in (B) but for the average ZFP143-associated loops (containing ZFP143 peak in at least one loop anchor). (D) High-resolution 4C-seq data generated for the ZFP143-bound genes Rbm41 (left panel) and Prmt6 (middle panel), and non-ZFP143-bound control gene Sik1 (right panel), using gene promoters as viewpoints. The matrix in the top panel represents interaction frequencies in a previously published high-resolution Micro-C dataset . The arrows point to detected Micro-C chromatin loops. The bottom panel shows 4C contact profiles in DMSO (blue) and in 6 hours dTAG-V1 (orange) treated ZFP143-FKBP cells. Genomic tracks show ZFP143-HA ChIP-seq (red), calibrated CTCF ChIP-seq (blue), TT-seq nascent transcription (yellow for sense and purple for antisense transcription) in control and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (E) Tornado plots of ZFP143-HA ChIP-seq signal centred at CTCF peaks in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (F) Same as in (E) but for the calibrated CTCF ChIP-seq signal centred at ZFP143-HA peaks.

Article Snippet: After systematically re-analysing the ZNF143 ChIP-seq data, we posit that the Proteintech anti-ZNF143 polyclonal antibody recognises CTCF in addition to ZNF143.

Techniques: Hi-C, Generated, Control, ChIP-sequencing

Journal: bioRxiv

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

doi: 10.1101/2024.03.08.583864

Figure Lengend Snippet: (A) Average Hi-C loops in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. Value in the upper-right corner indicates the interaction strength of the loop over the background. (B) Same as in (A) but for the average ZFP143-associated Hi-C loops (containing ZFP143 peak in at least one loop anchor). (C) High-resolution 4C-seq data generated for the Cpox and Cldn1 (left panel) and Zfp111 and Zfp108 (right panel) loci using gene promoters as viewpoints. The matrix in the top panel represents interaction frequencies in a previously published high-resolution Micro-C dataset . The arrows point to detected Micro-C chromatin loops. The bottom panel shows 4C contact profiles in DMSO (blue) and in 6 hours dTAG-V1 (orange) treated ZFP143-FKBP cells. Genomic tracks show ZFP143-HA ChIP-seq (red), calibrated CTCF ChIP-seq (blue), TT-seq nascent transcription (yellow for sense and purple for antisense transcription) in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (D) Tornado plots of calibrated CTCF ChIP-seq signal centred at CTCF peaks in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (E) Genomic tracks showing ZFP143-HA ChIP-seq (red) in DMSO and calibrated CTCF ChIP-seq (blue) in DMSO and 6 hours dTAG-V1 treated ZFP143-FKBP cells. (F) Venn diagram showing the overlap between ZFP143-HA (red) and CTCF (blue) peaks.

Article Snippet: After systematically re-analysing the ZNF143 ChIP-seq data, we posit that the Proteintech anti-ZNF143 polyclonal antibody recognises CTCF in addition to ZNF143.

Techniques: Hi-C, Generated, ChIP-sequencing

Journal: bioRxiv

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

doi: 10.1101/2024.03.08.583864

Figure Lengend Snippet: (A) Overlap between ZNF143/ZFP143 peaks from re-analysed publicly available data and CTCF peaks from CISTROME for human (left panel) and mouse (right panel) datasets. Box plots for each ZNF143/ZFP143 dataset represent the median overlap with CTCF peaks. Each dot represents the overlap between the indicated ZNF143/ZFP143 peak set with an individual CTCF peak set. Colours represent the antibody used for chromatin immunoprecipitation, as indicated below. (B) Venn diagram showing the overlap between ZNF143 peaks detected by Proteintech (light pink) and FLAG (light green) antibodies in K562 cells. (C) Heatmap showing the enrichment of SBS (i.e. ZNF143) and CTCF motifs in common, Proteintech-specific, and FLAG-specific peaks in K562 cells. (D) Tornado plots of ChIP-seq signals detected by Proteintech (light pink), FLAG (light green), and custom (orange) antibodies, and CTCF signal (blue) in K562 cells. The ChIP-seq signals are centred on common (top) and Proteintech-specific (bottom) peaks. (E) Genomic tracks showing ChIP-seq signals for CTCF (blue) and signals detected by Proteintech (pink), FLAG (light green), and custom12 (orange) antibodies in K562 cells. Rectangles indicate common (left) and Proteintech-specific (middle and right) peaks in the region. (F) Scatter plot of the percentage of loop anchors overlapping the peak (x-axis) against the fold enrichment of peaks in loop anchors (y-axis) for a number of DNA binding proteins and for Proteintech-specific, FLAG-specific and common peaks in K562 cells.

Article Snippet: After systematically re-analysing the ZNF143 ChIP-seq data, we posit that the Proteintech anti-ZNF143 polyclonal antibody recognises CTCF in addition to ZNF143.

Techniques: Chromatin Immunoprecipitation, ChIP-sequencing, DNA Binding Assay

Journal: bioRxiv

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

doi: 10.1101/2024.03.08.583864

Figure Lengend Snippet: (A) Tornado plots of CTCF ChIP-seq signal from two biological replicates in wild-type (WT) and ZNF143-knockout (KO) haematopoietic stem and progenitor cells (HSPC) centred at ZNF143-related (top) and ZNF143-unrelated (bottom) CTCF peaks . (B) Same as in (A) but for the CTCF ChIP-seq signal in HSPC from two orthogonal studies , . (C) Rolling mean of the normalised CTCF motifs scores, annotated for the ZNF143-related (top) and ZNF143-unrelated (bottom) CTCF peaks. (D) Violin plots showing the fraction of ZNF143-related (left) and ZNF143-unrelated (right) CTCF peaks overlapping CTCF peaks from the CISTROME database . (E) GC bias scores calculated for CTCF ChIP-seq data generated from WT and ZNF143-KO HSPC samples . Note the divergence of the first WT CTCF replicate from the rest of the samples. (F) Genomic tracks showing CTCF ChIP-seq signal from two biological replicates in WT and ZNF143-KO HSPC , CTCF ChIP-seq signal from two other HSPC samples , , and GC content. Horizontal bars indicate ZNF143-related and ZNF143-unrelated CTCF peaks . Note the overlap of ZNF143-related peaks with GC-rich regions. (G) Tornado plots of ZNF143 ChIP-nexus signal from control and CTCF-depleted HEC1B cells centred at ZNF143-only (top) and shared ZNF143 and CTCF (bottom) peaks . (H) Genomic tracks showing ZNF143 ChIP-nexus signal from control and CTCF-depleted HEC1B cells . Horizontal bars indicate ZNF143-only and shared ZNF143 and CTCF peaks. Note the specific loss of signal at shared peaks upon CTCF depletion. (I) Venn diagram showing the overlap between ZNF143-CTCF motif pairs located 37 bp apart from each other and SINE/B2 repeat elements in the mouse genome from RepeatMasker. (J) Tornado plots of CTCF and ZNF143 ChIP-seq signal centred at ZNF143-CTCF motif pairs located 37 bp apart from each other .

Article Snippet: After systematically re-analysing the ZNF143 ChIP-seq data, we posit that the Proteintech anti-ZNF143 polyclonal antibody recognises CTCF in addition to ZNF143.

Techniques: ChIP-sequencing, Knock-Out, Generated, Control

Journal: bioRxiv

Article Title: Axial Nephron Fate Switching Demonstrates a Plastic System Tunable on Demand

doi: 10.1101/2025.03.29.646044

Figure Lengend Snippet: (a) Annotated unsupervised clustering of PAX2 + nephron-like DD14 control and DE organoid cells represented in a UMAP. (Inset) Sample contribution of each condition. (b) Violin plot with annotations of select gene markers (top x axis) showing expression levels (bottom x axis) in the DD14 organoid dataset. The y axis shows cluster numbers and sample origin (gray square – control organoids, pink square – DE organoids). (c) Volcano plot of DESeq analysis comparing DD14 DMSO control and DE organoid nephron scRNA sequencing data. Dashed lines show 0.05 p-value cutoff (horizontal) and ±1.5-fold change cutoff (vertical). (d) Bar plot showing normalized percent contribution of cells expressing select nephron markers (log 2 FC > 0) separated by sample origin. Numbers in bars show raw cell counts. (e) Feature plots of select genes in the DD14 DE organoid dataset. (f) Immunofluorescence stain of week 16 human kidney from SSB-CLSN stage marking DCT/CNT precursor and loop of Henle/macula densa precursor segments. (g) Immunofluorescence stains of DD14 control and DE organoids showing expression of DCT/CNT precursor and loop of Henle/macula densa precursor markers. Yellow arrow – autofluorescence. Scale bar: 50 microns.

Article Snippet: The primary antibodies used were as follows: Laminin β1 (Santa Cruz Biotechnology, sc-33709, 1:250), HNF4A (R&D Systems, MAB4605, 1:200), POU3F3 (Thermo Scientific, PA564311, 1:100), Mafb (Novus (R&D), MAB3810, 1:500), GATA3 (Novus (R&D), AF2605, 1:200), Jag1 (Novus (R&D), AF599, 1:100), SLC12A1 (Sigma-Aldrich, HPA018107, 1:200), PAX8 (abcam, ab189249, 1:100), WT1 (abcam, ab89901, 1:500), LEF1 (Cell signaling, 2286S, 1:200), CDH1 (BD Laboratories, 610181, 1:200), PAPPA2 (R&D Systems, AF1668, 1:100), HNF1B (Thermo Scientific, MA5-24605, 1:500), Pax2 (Thermo Scientific, 716000, 1:100), TFAP2A (Santa Cruz Biotechnology, sc-12726, 1:200), IRX1 (Sigma-Aldrich, HPA043160, 1:200), SIX1 (Cell signaling, 12891S, 1:300), Pax2 (R&D Systems, AF3364, 1:50), TMEM52B (Novus (R&D), NBP2-49272, 1:100), MEIS1/2/3 (Active Motif, 39096, 1:1000), ZO-1 (Thermo Scientific, 33-9100, 1:200), PODXL (R&D Systems, AF1658, 1:300), Renin (R&D Systems, AF4090, 1:100), MECOM (R&D Systems, MAB75061, 1:100), hErbB4 (R&D Systems, MAB1131, 1:100), LEF1 (Santa Cruz Biotechnology, sc-374412, 1:200), CD31 (abcam, ab9498, 1:250), ESRRγ (Sigma-Aldrich, HPA044678, 1:100), GATA3 (Cell Signaling Technology, 5852T, 1:100), and acetyl-alpha tubulin (Sigma-Aldrich, MABT868, 1:500).

Techniques: Control, Expressing, Sequencing, Immunofluorescence, Staining