Gene Expression Variability Linked to Chromatin Clique Configurations and cis-Regulatory Elements

This study explores the relationship between combinations of ENCODE cis-Regulatory Elements (cCREs) within topological elements of chromatin interaction networks and gene expression patterns. We assign cCRE annotations to the nodes of chromatin interaction networks and categorize the network's topological elements, particularly cliques of size 3, based on their cCRE composition, studying how these compositions relate to gene expression profiles. Our findings show that cliques enriched with multiple enhancer-like or promoter-like elements are generally linked to higher expression levels with some notable exceptions, while those containing a mix of CTCF elements and DNase-only sites display generally lower expression levels. In addition, we identify a specific effect where larger cliques appear to show correspondingly increasing expression values, indicating a separate chromatin aggregation effect from the annotations present.