Fig. 3: liCHi-C identifies enhancer–promoter pairs and proteins involved in chromatin organization.

A Heatmap representing enrichment (expressed in terms of z-scores) of promoters (top) and non-promoter promoter-interacting regions (npPIRs) (bottom) for histone marks. PIRs and promoters were classified by the quartiles level of FPKM expression of the associated gene. HSC hematopoietic stem cell, CMP common myeloid progenitor, CLP common B-cell lymphoid progenitor, MK megakaryocytes, Mon monocytes, Ery erythroblast, nB naive B cell, nCD4 naive CD4⁺ cells, nCD8 naive CD8⁺ cells. B GATA3 regulatory landscape in naive B (top), naive CD4⁺ T (middle), and naive CD8⁺ T (bottom) cells according to histone modifications and liCHi-C data. Green shade depicts the gene promoter, while yellow shades depict putative enhancer regions for that gene in any of these cell types. Arrows symbolize gene placement and orientation along the genomic window. C Scatterplot plot of chromatin assortativity (ChAs) of six histone marks computed for the promoter—pPIR sub-network (x axis) against the promoter—npPIR (y axis) for common myeloid progenitor cells. Dot size depends on the abundancy of each histone mark. D H3K9me3-centered interaction network (arcs) for common myeloid progenitor cells. Top graph depicts whole chromosome 19, while bottom graph shows a zoom centered on a ZNF gene cluster. Arrows symbolize gene placement and orientation along the genomic window.