Fig. 7: MBD-2 non-NuRD and NuRD-overlapping gene targets shows variable expression level and divergent MBD-2 binding patterns. | Nature Communications

Fig. 7: MBD-2 non-NuRD and NuRD-overlapping gene targets shows variable expression level and divergent MBD-2 binding patterns.

From: Dual genomic localizations and gene regulatory functions of MBD-2 with and without NuRD in Caenorhabditis elegans which lacks DNA methylation

Fig. 7: MBD-2 non-NuRD and NuRD-overlapping gene targets shows variable expression level and divergent MBD-2 binding patterns.The alternative text for this image may have been generated using AI.

A Venn diagrams depicting overlaps of genes identified from ChIP-seq data (single-end reads with a non-zero read count in at least one RNA-seq sample (N2, P0 or F1 mbd-2-/-) with non-NuRD-overlapping MBD-2 peaks (pink) and NuRD-overlapping MBD-2 peaks (red) at their TSS ± 2 kb, dysregulated genes ( ≥ 2 fold and Benjamini-adjusted two-tailed Wald test p-values < 0.05), either upregulated (purple) or downregulated (green) in P0 mbd-2-/- RNA-seq. Exclusive non-NuRD-overlapping and exclusive NuRD-overlapping MBD-2 gene targets are defined by genes with only non-NuRD-overlapping and NuRD-overlapping MBD-2 peaks, respectively. B, C Box-and-whiskers plots with median (middle line), 25th, 75th percentile (box) and minima, maxima (whiskers) depicting transcript per million (TPM) of protein-coding genes in wildtype (N2) worms with a non-zero read count in at least one RNA-seq sample (N2, P0 or F1 mbd-2-/-). B TPM of all protein-coding genes, exclusive non-NuRD-overlapping and exclusive NuRD-overlapping MBD-2 gene targets, C TPM of all protein-coding genes, genes with either exclusive non-NuRD-overlapping and exclusive NuRD-overlapping MBD2 peaks, which has either no change, downregulated or upregulated in P0 mbd-2-/-. Genes with TPM ≥ 500 are flattened on the red dotted line. The two-tailed t-test p-value of the TPM difference in different MBD-2 target types (exclusive non-NuRD-overlapping or exclusive NuRD-overlapping, and P0 mbd-2-/- upregulated or downregulated) versus all protein-coding genes was indicated on top. n = number of genes. Source data of B and C are provided as Source Data files. D, E Metaplot showing the binding patterns of MBD-2 (count per million (CPM) normalized reads over input) at its gene targets. All left panels show the binding pattern with TSS as the reference point ( ± 2 kb), while all right panels show the binding pattern across the gene, with a 1500-bp scaled region from TSS + 300 bp to TES-50 bp. (TSS-2 kb to TSS + 300 bp, and TES-50 bp to TES + 500 bp are excluded from scaling.) D MBD-2 binding pattern on non-NuRD-overlapping (blue) and NuRD-overlapping (green) targets. E MBD-2 binding pattern on genes upregulated (blue) and downregulated (green) ≥ 5-fold in P0 mbd-2-/- RNA-seq.

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