Functional Activity of Transcription Factors Is Associated with Detection Frequency of Human Open Chromatin Regions

Chromatin organization determines the epigenetic regulation of gene expression, and open chromatin regions (OCRs) represent active regulatory elements that provide DNA accessibility for transcription factors (TFs). However, the overlap of such regions identified experimentally is often low even under similar experimental conditions. This variability may reflect both technical artifacts and biological differences between samples. The study tested the hypothesis that the OCR detection frequency across experiments performed in similar conditions is associated with functional properties of TFs, including pioneer activity and the type of regulatory effect (activation or repression). Bulk data from more than 1000 ATAC-seq and DNase-seq experiments and ChIP-seq, RNA-seq (TF knockout), and scATAC-seq data were retrieved from the GTRD database ( http://gtrd.biouml.org/ ). OCR detection frequencies were compared with TF binding sites, and scATAC-seq data were used to estimate the fraction of cells containing the corresponding regions. It was shown that rarely detected OCRs may be associated with specific cell subpopulations. These regions are enriched in binding sites for pioneer TFs (e.g., FOXA1, GATA3, and SPI1) in some cases. In addition, genomic regions interacting with transcriptional activators are detected more frequently on average than regions associated with repressors. The findings are supported by the analysis of TF knockout data from the KnockTF database ( http://www.licpathway.net/KnockTFv2/index.php ). The results indicate that functional properties of TFs and cell heterogeneity contribute to shaping the OCR landscape and highlight the importance of integrating single-cell sequencing data for the interpretation of rarely detected OCRs in ATAC-seq and DNase-seq datasets.