Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, United States of America.
PLoS One. 2018 Sep 24;13(9):e0203843. doi: 10.1371/journal.pone.0203843. eCollection 2018.
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.
染色质组织对于核功能至关重要，如基因调控、DNA 复制和 DNA 修复。绝缘子结合蛋白，如果蝇边界元件相关因子（BEAF），参与染色质组织。为了进一步了解 BEAF 的作用，我们使用 4C（圆形染色体构象捕获）检测了四个 BEAF 结合区域（观点）的顺式和反式相互作用伙伴，并分析了它们与不同基因组特征的关联。以前的全基因组作图发现，BEAF 通常结合在转录起始位点附近，通常是管家基因，因此我们的观点被选择来反映这一点。我们的 4C 数据显示，我们观点的相互作用伙伴是高度可变的，通常富含活跃染色质标记。最一致的关联是与管家基因，这是我们观点的共同特征。荧光原位杂交表明，即使没有 BEAF，长距离相互作用也会发生。这些数据最符合 BEAF 与其他在活跃启动子中发现的因素冗余的模型。我们的结果指出了由活跃染色质形成的长距离相互作用的原则，支持了先前提出的模型，即浓缩染色质具有粘性，并通过拓扑关联域（TAD）之间的活跃染色质结合在一起，而 TAD 之间的空间则由活跃染色质填充，同时 TAD 相对于彼此的包装在细胞间变化。我们提出，我们检测到的高度可变的长距离相互作用是由冗余因子驱动的，这些因子打开染色质以促进转录，并与 TAD 之间的活跃染色质填充空间相结合，而 TAD 之间的相对包装则因细胞而异。
