Extended Data Fig. 8: CRE is important for IAP activity and bound by methylation-sensitive CREB1. | Nature Genetics

Extended Data Fig. 8: CRE is important for IAP activity and bound by methylation-sensitive CREB1.

From: Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation

Extended Data Fig. 8

a, Curated RepeatMasker annotation for IAP elements. IAPLTR1a (orange) and IAPEz-int (dark grey) fragments of same ID and subfamily are merged if within 1024 bp. b, IAPs differentially expressed in DNMT-TKO (red, FDR < 0.05, |log2FC| >= 1) using uniquely mapping RNA reads and the curated annotation. c, Related IAPs are similarly de-repressed in DNMT-TKO neurons. d, TF motifs (black) in 5’LTR of expressed IAPLTR1/1a. Significance (Bonferroni-corrected one-sided Wilcoxon test) of expression difference (DNMT-TKO vs WT) between IAPLTR1 and 1a elements plus/minus motif. Cluster of motifs (red) reproducibly enriched in IAPLTR1 and 1a elements expressed in DNMT-TKO. Unbiased clustering (right) indicates that most resemble the CRE motif (TGACGTCA). e, Reporter activity in ES cells similar to Fig. 5b. IAPLTR1a reporter is silent in WT and only moderately active in DNMT-TKO ES cells. Seven biological replicates each, error bar indicates SEM. P = 0.0012, two-sided t-test. f, Reproducibility of read counts for three CREB1 ChIP-seq replicates from WT and DNMT-TKO neurons in all peak regions. Coefficients from pearson correlation. g, Top motif found by de novo motif search in the top 500 CREB1 ChIP-seq peaks shared between WT or DNMT-TKO neurons. h, Fraction of peaks with a CRE sequence for different bins of CREB1 enrichment in WT (left) or DNMT-TKO (right) neurons across three replicates. n = Number of peaks per enrichment bin. i, CREB1 peaks are located in unmethylated CpG-island promoters. n = Number of datapoints. Boxplots as in Fig. 2d. j, Gene expression of CREB1-bound and -unbound promoters in neurons. Boxplots as in Fig. 2d. k, Gene Ontology (GO) terms enriched in genes with CREB1-bound promoters (top 500). Dots represent top 10 terms with highest gene ratio (fraction of genes represented in the GO term). Dot size and color representing gene counts and adjusted P value (Fisher’s exact test), respectively. l, CREB1 binding (ChIP-seq) in DNMT-TKO versus WT cells at peak regions across cell lines indicated by red or blue circles. PCC indicated. m, CREB1 binding in WT neurons at all peak regions identified in WT and DNMT-TKO cells binned by motif methylation. Boxplots as in Fig. 2d.

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