Repository of the analyses of the NAR manuscript titled "Epigenetic characterization of housekeeping core promoters and their importance in tumor suppression".
Abstract of publication: The precise control of gene transcription in humans requires the interaction of different cis-regulatory elements (CREs), as enhancers and promoters, to ensure the accurate transcription of genes. There has been extensive research on the description of cell type-specific (CTS) regulatory interactions, especially between enhancers and promoters. However, constitutively active interactions between CREs have been less studied. In this research, we elucidate the presence of around 11,000 housekeeping CREs (HK-CREs) and describe their main characteristics. Contrary to expectations, our findings indicate that the majority of the ubiquitously active CREs (around 83%) are not the core promoters of housekeeping genes and are involved in a broader role beyond housekeeping gene regulation. HK-CREs are conserved regions rich in unmethylated CpG sites. Their distribution across chromosomes highly correlates with the number of protein-coding genes and they interact with a large number of target genes in long-distance interactions, mostly through promoter-promoter interactions. In the context of cancer, we observed a reduction in the activity of a subset of HK-CREs, particularly those located near the telomere at the end of chromosome 19 and associated with zinc finger genes, that implicates them as important elements to maintain the integrity of the cell. Overall, our work unravels the presence of ubiquitously active CREs essential for the maintenance and stability of cells.