Extended Data Fig. 9: Changes in POL2 and CREB1 binding or accessibility are detectable at IAPLTR1/1a in absence of DNA methylation. | Nature Genetics

Extended Data Fig. 9: Changes in POL2 and CREB1 binding or accessibility are detectable at IAPLTR1/1a in absence of DNA methylation.

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

Extended Data Fig. 9

a, Reproducibility of read counts for two independent POL2 ChIP-seq replicates from WT and DNMT-TKO neurons in promoter regions. Pearson correlation coefficients are indicated. b, Unsupervised clustering of changes in signal relative to mean for POL2 and CREB1 ChIP-seq or ATAC-seq samples in WT, DNMT-TKO (TKO) or CREB1-KO DNMT-TKO (TKO_CREB1-KO, only for ATAC-seq) neurons. Colors indicate pairwise Pearson’s correlation coefficients (PCC) of uniquely mapping read counts in 5’ LTRs of annotation-curated IAP elements that are de-repressed in absence of DNA methylation (RNA-seq, FDR < 0.05 and fold change > = 2). Different replicates are shown. Number of repeats 726 (IAPLTR1) or 844 (IAPLTR1a) c, Changes in chromatin accessibility (top tracks, ATAC-seq), POL2 binding (middle tracks, ChIP-seq) or CREB1 binding (bottom tracks, ChIP-seq) in WT and DNMT-TKO neurons at IAPLTR1/1a elements that gain expression in absence of DNA methylation (RNA-seq, FDR < 0.05 and fold change > = 2). Signal is centered at the start site of IAP elements (Methods). Orange bars depict average width of the 5’ LTR and dashed lines display the average length of an entire element including the 5’ and 3’ LTR regions. Only uniquely mapped reads are considered. Replicates are shown. n = number of elements.

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