Fig. 4

cCRE representations learned by CREaTor suggest a new role of CTCF-bound elements. a Uniform Manifold Approximation and Projection (UMAP) of cCRE embeddings in K562. Upper: colored and numbered as clusters grouped by the Leiden algorithm. Bottom: colored and labeled by element type. b Composition of different element types in each cluster by percentage. Proximal elements: elements falling within 200 bp of an annotated TSS. Distal elements: elements more than 200 bp from any annotated TSS. Promoter-like: elements with high DNase and H3K4me3 signals. Enhancer-like: elements with high DNase and H3K27ac signals. CTCF-only: elements with high DNase and CTCF signals, as well as low H3K4me3 and H3K27ac signals. c Fold change of histone marker peaks of given types of cCREs in cluster 5 with respect to those in other clusters. Top: all cCREs. Middle: distal enhancer-like elements. Bottom: CTCF-only elements. d Expression value (log1p) distribution of genes within 10 kb of different types of CTCF-bound elements. e Average signals of H3K36me3, H3K79me2, H4K20me1, H2AFZ, H3K4me1, and H3K27me3 on different types of CTCF-bound elements. f Illustration for the proposed model of CTCF-H3K36me3 elements promoting transcription elongation