Studies On Transcriptional Regulation By The Interplay Among Transcription Factors, Chromatin Remodeling Factors And Long-range Chromatin Interactions

Transcriptional regulation is a complex process that is orchestrated by the action of a large number of trans-acting factors including sequence-specific transcription factors, histone modification enzymes and chromatin remodeling enzymes. This process occurs in a context of chromatin structure, which also impacts the transcriptional regulation.To understand how chromatin structure functions in transcriptional regulation, we investigated the function of CTCF, which is known to play roles in long-range chromatin interaction. Recent genome-wide studies have shown that the mammalian genomes are organized into topologically associated domains(TADs) and sub-functional domains(Lieberman-Aiden et al. 2009; Duan et al. 2010; Tanizawa et al. 2010; Dixon et al. 2012; Nora et al. 2012; Sexton et al. 2012). The insulator-binding protein, CTCF, is established as a key player to maintain the chromatin domain boundaries(Cuddapah et al. 2009; Dixon et al. 2012; Nora et al. 2012; Schwartz et al. 2012; Phillips-Cremins et al. 2013; Sofueva et al. 2013; Dowen et al. 2014; Zuin et al. 2014). However, the vast majority of CTCF binding sites are interwoven with enhancers within chromatin domains and do not display chromatin boundary functions. Here we report a positive correlation between the intradomain CTCF binding sites with the function of their nearby enhancers.1. Using a modified high-resolution Super-C protocol, we identify 90,518 and 81,773 high-confidence interactions among promoters, p300-bound enhancers and CTCF-bound insulators in murine ES and CD4 T cells, respectively.2. Analysis of these unprecedentedly high-resolution interaction maps reveals that CTCF binding sites and enhancers are interspersed and extensively interact with each other, and are positively correlated with enhancer-promoter interactions and enhancer activity.3. Cell-specific gene expression is positively correlated with cell-specific long-distance enhancer-promoter interactions.4. Deletion of CTCF sites using CRISPR/Cas9 severely compromises the enhancer-promoter interaction and enhancer function, suggesting that one major function of CTCF is to facilitate formation of looping between enhancers and promoters by directly interacting with these regions.5. We further demonstrate that knockdown of CTCF results in increased cell-cell variation of gene expression, suggesting that stable promoter-enhancer interaction mediated by CTCF plays an important role in maintaining the stability of gene expression programs.Despite of a large number of studies on different transcription factors and histone modification enzymes, many questions remain unanswered on the specific mechanisms how these different factors act together to regulate transcription. Thus we investigated how the sequence-specific factors IRF1 and IRF2 act together with the BAF chromatin remodeling complexes to regulate the expression of the TLR3 gene, which is critically involved in the antiviral activities. We found that:6. IRF2 is critically required for the induction of the TLR3 and other interferon-inducible genes in a chromatin environment.7. While both IRF1 and IRF2 directly interact with the BAF chromatin remodeling complex, IRF2 is associated with the TLR3 promoter in the unstimulated state and IRF1 binding to the promoter is strongly induced by stimulation with interferon, suggesting that these two factors may function at different stages of gene induction in the recruitment of the BAF complex.8. IRF2 acts to maintain an open chromatin structure by recruiting the BAF complex to the TLR3 promoter in the unstimulated state, while IRF1 serves to rapidly activate the promoter upon stimulation. Therefore, the division of labor between the IRF transcription factor family members plays a pivotal role in coordinating the transcriptional activation in the cellular antiviral response.All these results will be great helpful for understanding the detail mechnaim of transcriptional regulation.