Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA.
Nat Commun. 2023 Jun 6;14(1):3303. doi: 10.1038/s41467-023-38429-1.
Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact of looping on proximal interactions remains enigmatic. Here, we critically examine nuclear compartments and CTCF loop-proximal interactions using a combination of in situ Hi-C at unparalleled depth, algorithm development, and biophysical modeling. Producing a large Hi-C map with 33 billion contacts in conjunction with an algorithm for performing principal component analysis on sparse, super massive matrices (POSSUMM), we resolve compartments to 500 bp. Our results demonstrate that essentially all active promoters and distal enhancers localize in the A compartment, even when flanking sequences do not. Furthermore, we find that the TSS and TTS of paused genes are often segregated into separate compartments. We then identify diffuse interactions that radiate from CTCF loop anchors, which correlate with strong enhancer-promoter interactions and proximal transcription. We also find that these diffuse interactions depend on CTCF's RNA binding domains. In this work, we demonstrate features of fine-scale chromatin organization consistent with a revised model in which compartments are more precise than commonly thought while CTCF loops are more protracted.
核区室是三维染色质组织的突出特征，但测序深度的限制阻碍了超精细尺度的研究。CCCTC 结合因子（CTCF）环通常在更精细的尺度上进行研究，但环对近端相互作用的影响仍然是个谜。在这里，我们使用超高深度的原位 Hi-C 技术、算法开发和生物物理建模的组合，批判性地研究了核区室和 CTCF 环-近端相互作用。我们生成了一个带有 330 亿个接触点的大型 Hi-C 图谱，并结合了一种在稀疏、超大规模矩阵上执行主成分分析的算法（POSSUM），将区室分辨率提高到 500bp。我们的结果表明，即使侧翼序列不这样做，基本上所有的活性启动子和远端增强子都定位于 A 区室中。此外，我们发现暂停基因的 TSS 和 TTS 经常被分隔到不同的区室中。然后，我们确定了从 CTCF 环锚点辐射的弥散相互作用，这些相互作用与强增强子-启动子相互作用和近端转录相关。我们还发现这些弥散相互作用依赖于 CTCF 的 RNA 结合结构域。在这项工作中，我们展示了与修订模型一致的精细染色质组织特征，该模型认为区室比通常认为的更精确，而 CTCF 环则更长。
