Liu Xin, Sun Qiu, Wang Qi, Hu Chuansheng, Chen Xuecheng, Li Hua, Czajkowsky Daniel M, Shao Zhifeng
State Key Laboratory for Oncogenes and Bio-ID Center, School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
Genomics Proteomics Bioinformatics. 2022 Feb;20(1):101-109. doi: 10.1016/j.gpb.2020.06.017. Epub 2021 Feb 23.
Recent studies have characterized the genomic structures of many eukaryotic cells, often focusing on their relation to gene expression. However, these studies have largely investigated cells grown in 2D cultures, although the transcriptomes of 3D-cultured cells are generally closer to their in vivo phenotypes. To examine the effects of spatial constraints on chromosome conformation, we investigated the genomic architecture of mouse hepatocytes grown in 2D and 3D cultures using in situ Hi-C. Our results reveal significant differences in higher-order genomic interactions, notably in compartment identity and strength as well as in topologically associating domain (TAD)-TAD interactions, but only minor differences are found at the TAD level. Our RNA-seq analysis reveals an up-regulated expression of genes involved in physiological hepatocyte functions in the 3D-cultured cells. These genes are associated with a subset of structural changes, suggesting that differences in genomic structure are critically important for transcriptional regulation. However, there are also many structural differences that are not directly associated with changes in gene expression, whose cause remains to be determined. Overall, our results indicate that growth in 3D significantly alters higher-order genomic interactions, which may be consequential for a subset of genes that are important for the physiological functioning of the cell.
最近的研究已经描绘了许多真核细胞的基因组结构，通常聚焦于它们与基因表达的关系。然而，这些研究大多调查的是在二维培养条件下生长的细胞，尽管三维培养细胞的转录组通常更接近其体内表型。为了研究空间限制对染色体构象的影响，我们使用原位Hi-C技术研究了在二维和三维培养条件下生长的小鼠肝细胞的基因组结构。我们的结果揭示了高阶基因组相互作用存在显著差异，特别是在区室特征和强度以及拓扑相关结构域（TAD）-TAD相互作用方面，但在TAD水平仅发现微小差异。我们的RNA测序分析揭示了三维培养细胞中参与生理性肝细胞功能的基因表达上调。这些基因与一部分结构变化相关，这表明基因组结构的差异对转录调控至关重要。然而，也存在许多与基因表达变化没有直接关联的结构差异，其原因尚待确定。总体而言，我们的结果表明三维生长显著改变了高阶基因组相互作用，这可能对细胞生理功能重要的一部分基因产生影响。
