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Fig. 4 | Epigenetics & Chromatin

Fig. 4

From: Characterizing chromatin interactions of regulatory elements and nucleosome positions, using Hi-C, Micro-C, and promoter capture Micro-C

Fig. 4

Regulatory elements and nucleosome-depleted regions (NDRs) that are involved in loops. A Genome browser screenshots of ChIP-seq (H3K4me3, H3K27ac, CTCF, H3K27me3, H3K9me3), NOMe-seq (DNA methylation, chromatin accessibility, nucleosome-depleted regions (NDRs)), Hi-C, Micro-C, and RefSeq Genes are shown. B Fractions of regulatory elements that intersect with loop anchors identified from Hi-C 1 billion, Micro-C 1 billion, 2 billion, and 3 billion data are plotted (left). A fraction of regulatory elements that intersect with loop anchors from any datasets is shown in grey (in loop) while the one not in loop is shown in orange (not in loop) (right). C Numbers of loops belong to different loop categories defined by intersecting the loop anchors with different types of regulatory elements (red: active promoter, orange: active enhancer, purple: active insulator, green: NDRs without features, grey: repressed region, pink: heterochromatin region, and white: none) are shown. They are in rank order with the most frequent category at the top and the 28th most frequent category at the bottom. Chromatin loops are called at 5 kb resolution using Micro-C 3 billion data. D Comparison of number of promoter–enhancer loops identified from Hi-C 1 billion, Micro-C 1 billion, 2 billion and 3 billion data. E Significance of chromatin interaction (q-value identified by Mustache) for top 5 loop categories. A mean q-value is shown in red. A median q-value is shown in blue

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