4C-seq characterization of Drosophila BEAF binding regions provides evidence for highly variable long-distance interactions between active chromatin

Abstract

Chromatin organization is crucial for nuclear functions such as gene regulation, DNA replication and DNA repair. Insulator binding proteins, such as the Drosophila Boundary Element-Associated Factor (BEAF), are involved in chromatin organization. To further understand the role of BEAF, we detected cis- and trans-interaction partners of four BEAF binding regions (viewpoints) using 4C (circular chromosome conformation capture) and analyzed their association with different genomic features. Previous genome-wide mapping found that BEAF usually binds near transcription start sites, often of housekeeping genes, so our viewpoints were selected to reflect this. Our 4C data show the interaction partners of our viewpoints are highly variable and generally enriched for active chromatin marks. The most consistent association was with housekeeping genes, a feature in common with our viewpoints. Fluorescence in situ hybridization indicated that the long-distance interactions occur even in the absence of BEAF. These data are most consistent with a model in which BEAF is redundant with other factors found at active promoters. Our results point to principles of long-distance interactions made by active chromatin, supporting a previously proposed model in which condensed chromatin is sticky and associates into topologically associating domains (TADs) separated by active chromatin. We propose that the highly variable long-distance interactions we detect are driven by redundant factors that open chromatin to promote transcription, combined with active chromatin filling spaces between TADs while packing of TADs relative to each other varies from cell to cell.

M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity

“…Why M1BP is only partially dependent on CP190 for binding is unclear, but these results are consistent with the known ability of M1BP to bind DNA directly 30 , whereas CP190 is believed to require interaction with a specific DNA-binding protein in order to associate with chromatin 8,17,18,42,43 . Aside from the insulator protein BEAF-32, which binds an AT-rich dual core sequence 44 , we did not generally observe a large extent of overlap between M1BP and other DNA-binding insulator proteins that have been shown to be involved in recruiting CP190 to DNA. Future studies may reveal a possible functional relationship between M1BP and BEAF-32 in insulator activity or regulation of gene expression.…”

M1BP cooperates with CP190 to activate transcription at TAD borders and promote chromatin insulator activity

“…Why M1BP is only partially dependent on CP190 for binding is unclear, but these results are consistent with the known ability of M1BP to bind DNA directly 30 whereas CP190 is believed to require interaction with a specific DNA-binding protein in order to associate with chromatin 7, 17, 18, 45, 46 . Aside from the insulator protein BEAF-32, which binds an AT-rich dual core sequence 47 , we did not generally observe a large extent of overlap between M1BP and other DNA-binding insulator proteins that have been shown to be involved in recruiting CP190 to DNA. Future studies may reveal a possible functional relationship between M1BP and BEAF-32 in insulator activity or regulation of gene expression.…”

Promoter-Proximal Chromatin Domain Insulator Protein BEAF Mediates Local and Long-Range Communication with a Transcription Factor and Directly Activates a Housekeeping Promoter in Drosophila

“…We previously reported that BEAF is usually found near housekeeping promoters (JIANG et al 2009;SHRESTHA et al 2018). In the course of these experiments, we found that promoterproximal BEAF can activate two housekeeping promoters on its own but does not have this effect on a developmental promoter.…”

“…We extended this by compiling lists of genes with a TSS within 300 bp of the center of BEAF peaks from various additional sources (BUSHEY et al 2009;NEGRE et al 2010;LIANG et al 2014) and compared them to lists of housekeeping genes as defined by low variance in expression levels in various tissues, cell types and developmental stages (LAM et al 2012;ULIANOV et al 2016). We found that roughly 85% of BEAF-associated genes are housekeeping genes (SHRESTHA et al 2018). Note that the minimal RpS12 promoter has the DREF binding site (HIROSE et al 1993) deleted, and presumably so are the sequences responsible for a BEAF peak near this promoter.…”