Nuclear architecture is the organization of the genome within a cell nucleus with respect to different nuclear landmarks such as the nuclear lamina, nuclear matrix or nucleoli. Recently, nuclear architecture has emerged as a major regulator of gene expression in mammalian cells. However, studies connecting nuclear architecture with gene expression are largely population-averaged and do not report on the heterogeneity in genome organization or gene expression within a population. In this report we present a method for combining 3D DNA fluorescence in situ hybridization (FISH) with single-molecule RNA FISH (smFISH) and immunofluorescence to study nuclear architecture-dependent gene regulation on a cell-by-cell basis. We further combine our method with imaging-based cell cycle staging to correlate nuclear architecture with gene expression across the cell cycle. We present this in the context of the cyclin-A2 (CCNA2) gene, which has known cell cycle-dependent expression. We show that, across the cell cycle, the expression of a CCNA2 gene copy is stochastic and depends neither on its sub-nuclear position – which usually lies close to nuclear lamina – nor on the expression from other copies of the gene.

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核结构是细胞核内基因组相对于不同核标志（例如核纤层、核基质或核仁）的组织。最近，核结构已成为哺乳动物细胞基因表达的主要调节因子。然而，将核结构与基因表达联系起来的研究主要是群体平均，并且没有报告群体内基因组组织或基因表达的异质性。在本报告中，我们提出了一种将 3D DNA 荧光原位杂交 (FISH) 与单分子 RNA FISH (smFISH) 和免疫荧光相结合的方法，以逐个细胞地研究核结构依赖性基因调控。我们进一步将我们的方法与基于成像的细胞周期分期相结合，将核结构与整个细胞周期的基因表达相关联。我们在细胞周期蛋白 A2 ( CCNA2 ) 基因的背景下提出了这一点，该基因具有已知的细胞周期依赖性表达。我们发现，在整个细胞周期中， CCNA2基因拷贝的表达是随机的，既不依赖于其亚核位置（通常靠近核纤层）也不依赖于该基因其他拷贝的表达。

本文有对该论文第一作者的相关第一人称采访。