Corrette John, Li Jiachun, Shao Hanjuan, Veerasubramanian Praveen Krishna, Spakowitz Andrew, Downing Timothy L, Allard Jun
Mathematical, Computational and Systems Biology, University of California Irvine, Irvine, CA, 92797, United States.
Department of Biomedical Engineering, University of California Irvine, Irvine, CA, 92797, United States.
Nucleic Acids Res. 2025 Jul 19;53(14). doi: 10.1093/nar/gkaf670.
The 3D organization of the genome-in particular, which two regions of DNA are in contact with each other-plays a role in regulating gene expression. Several factors influence genome 3D organization. Nucleosomes (where ∼100 base pairs of DNA wrap around histone proteins) bend, twist, and compactify chromosomal DNA, altering its polymer mechanics. How much does the positioning of nucleosomes between gene loci influence contacts between those gene loci? And to what extent are polymer mechanics responsible for this? To address this question, we combine a stochastic polymer mechanics model of chromosomal DNA including twists and wrapping induced by nucleosomes with two data-driven pipelines. The first estimates nucleosome positioning from ATAC-seq data in regions of high accessibility. Most of the genome is low accessibility, so we combine this with a novel image analysis method that estimates the distribution of nucleosome spacing from electron microscopy data. There are no fit parameters in the biophysical model. We apply this method to IL-6, IL-15, CXCL9, and CXCL10, inflammatory marker genes in macrophages, before and after inflammatory stimulation, and compare the predictions with contacts measured by conformation capture experiments (4C-seq). We find that within a 500-kb genomic region, polymer mechanics with nucleosomes can explain 71% of close contacts. These results suggest that, while genome contacts on 100 kb scales are multifactorial, they may be amenable to mechanistic, physical explanation. Our work also highlights the role of nucleosomes, not just at the loci of interest, but between them, and not just the total number of nucleosomes, but their specific placement. The method generalizes to other genes, and can be used to address whether a contact is under active regulation by the cell (e.g. a macrophage during inflammatory stimulation).
基因组的三维组织——特别是DNA的哪两个区域相互接触——在调节基因表达中发挥作用。有几个因素会影响基因组的三维组织。核小体（约100个碱基对的DNA缠绕在组蛋白周围）会使染色体DNA弯曲、扭曲并压缩，改变其聚合物力学性质。核小体在基因座之间的定位对这些基因座之间的接触有多大影响？聚合物力学在多大程度上对此负责？为了解决这个问题，我们将一个包含核小体诱导的扭曲和缠绕的染色体DNA随机聚合物力学模型与两个数据驱动的管道相结合。第一个管道根据高可及性区域的ATAC-seq数据估计核小体定位。基因组的大部分区域可及性较低，因此我们将其与一种新颖的图像分析方法相结合，该方法根据电子显微镜数据估计核小体间距的分布。生物物理模型中没有拟合参数。我们将此方法应用于巨噬细胞中炎症刺激前后的炎症标记基因IL-6、IL-15、CXCL9和CXCL10，并将预测结果与通过构象捕获实验（4C-seq）测量的接触进行比较。我们发现，在一个500 kb的基因组区域内，带有核小体的聚合物力学可以解释71%的紧密接触。这些结果表明，虽然100 kb尺度上的基因组接触是多因素的，但它们可能适合用机械的、物理的解释。我们的工作还强调了核小体的作用，不仅在感兴趣的基因座处，而且在它们之间，不仅是核小体的总数，还有它们的特定位置。该方法可推广到其他基因，并可用于确定一种接触是否受到细胞的主动调节（例如炎症刺激期间的巨噬细胞）。
