CTCF is widely recognized for its essential role in mediating chromatin loops to regulate gene expression, particularly by modulating enhancer-promoter (EP) interactions. However, acute depletion of CTCF has minimal impact on these interactions and gene expression, leaving much of its regulatory mechanism still unclear.
To systematically investigate the transcriptional regulatory function of CTCF, this study identified differentially expressed genes (DEGs) in a CTCF degradation system. The findings revealed that most downregulated genes contain CTCF binding sites at their promoters, which aligns with the classical model in which CTCF facilitates EP interactions to activate transcription. However, the authors demonstrated that CTCF promotes the expression of these downregulated genes independently of its looping function. Mechanistically, CTCF selectively stabilizes the genomic binding of chromatin remodelers CHD4 and CHD8, enhancing local chromatin accessibility at CTCF binding sites. Furthermore, CTCF preferentially binds approximately 60 base pairs upstream of the transcription start site of target genes, highlighting a position-dependent mechanism for transcriptional activation.
In contrast, the influence of CTCF loops on EP or promoter-promoter (PP) interactions is relatively limited. This restricted impact stems from several key mechanistic factors: for CTCF loops to effectively enhance EP/PP interactions, CTCF must bind to one or both interaction anchors in a convergent orientation; effective insulation requires a strong CTCF loop; and importantly, nearly half of EP/PP interactions are surrounded by multiple CTCF loops with either promoting or insulating roles, which may counteract each other and reduce the overall effect of CTCF loops on these interactions. Additionally, most altered EP/PP interactions do not correlate with significant changes in transcription. As a result, only a small subset of DEGs is regulated through CTCF-mediated loops.
In summary, this study highlights the dual role of CTCF as both a loop-dependent and loop-independent transcriptional regulator, with the loop-independent functions being more predominant in the acute degradation system. These findings provide new mechanistic insights into the diverse roles of CTCF in genome regulation.
DOI：10.1093/procel/pwaf087