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. 2023 Mar 23;51(11):5364–5376. doi: 10.1093/nar/gkad207

Figure 4.

Figure 4.

The methylation effect of CTCF recognition is negatively regulated by the strength of upstream sites. (A) Known cytosine methylation and modification pathways in human. (B) Methyl-Spec-seq libraries design testing various C-to-xC effects at position 2 with altered upstream sites. Barcodes at –19 and –18 indicate the type of modifications. (C) Variants distribution of binding energy with different modifications and constructs; M, H, F, K are short for methylated, hemimethylated, formyl, and carboxyl cytosines respectively. (D) Relationship between observed C-to-mC substitution effects and the strength of upstream site, which is defined by the energy of corresponding unmethylated site. (E) Comparison of C-to-xC substitution effects between wildtype and R567W mutant constructs; The dashed lines indicate linear regression of high affinity sites (with energy of unmethylated sites below 0.4kT). (F) Structural comparison of existing CTCF-DNA complexes; Two structures were aligned over bases C2 and G2; Only CG at position 2 and finger 7 were shown. (G) Proposed Upstream Regulation model of CTCF.