Center for Genomics and Systems Biology, New York University Abu Dhabi (NYUAD), P.O. Box 129188, Abu Dhabi, United Arab Emirates.
Department of Biology, New York University, New York, NY, 10003, USA.
Genome Biol. 2023 Jan 25;24(1):18. doi: 10.1186/s13059-023-02853-9.
Recent work has demonstrated that three-dimensional genome organization is directly affected by changes in the levels of nuclear cytoskeletal proteins such as β-actin. The mechanisms which translate changes in 3D genome structure into changes in transcription, however, are not fully understood. Here, we use a comprehensive genomic analysis of cells lacking nuclear β-actin to investigate the mechanistic links between compartment organization, enhancer activity, and gene expression.
Using HiC-Seq, ATAC-Seq, and RNA-Seq, we first demonstrate that transcriptional and chromatin accessibility changes observed upon β-actin loss are highly enriched in compartment-switching regions. Accessibility changes within compartment switching genes, however, are mainly observed in non-promoter regions which potentially represent distal regulatory elements. Our results also show that β-actin loss induces widespread accumulation of the enhancer-specific epigenetic mark H3K27ac. Using the ABC model of enhancer annotation, we then establish that these epigenetic changes have a direct impact on enhancer activity and underlie transcriptional changes observed upon compartment switching. A complementary analysis of fibroblasts undergoing reprogramming into pluripotent stem cells further confirms that this relationship between compartment switching and enhancer-dependent transcriptional change is not specific to β-actin knockout cells but represents a general mechanism linking compartment-level genome organization to gene expression.
We demonstrate that enhancer-dependent transcriptional regulation plays a crucial role in driving gene expression changes observed upon compartment-switching. Our results also reveal a novel function of nuclear β-actin in regulating enhancer function by influencing H3K27 acetylation levels.
最近的研究表明，核细胞骨架蛋白（如β-肌动蛋白）水平的变化会直接影响三维基因组结构。然而，将三维基因组结构的变化转化为转录变化的机制尚不完全清楚。在这里，我们使用缺乏核β-肌动蛋白的细胞的综合基因组分析来研究区室组织、增强子活性和基因表达之间的机制联系。
使用 HiC-Seq、ATAC-Seq 和 RNA-Seq，我们首先证明，在β-肌动蛋白缺失时观察到的转录和染色质可及性变化在区室转换区域中高度富集。然而，区室转换基因内的可及性变化主要发生在非启动子区域，这些区域可能代表远端调控元件。我们的结果还表明，β-肌动蛋白缺失诱导广泛积累增强子特异性表观遗传标记 H3K27ac。使用增强子注释的 ABC 模型，我们随后确定这些表观遗传变化对增强子活性有直接影响，是观察到的区室转换时转录变化的基础。对成纤维细胞重编程为多能干细胞的互补分析进一步证实，区室转换和增强子依赖性转录变化之间的这种关系不仅是β-肌动蛋白敲除细胞所特有的，而且代表了一种将区室水平基因组组织与基因表达联系起来的一般机制。
我们证明了增强子依赖性转录调控在驱动区室转换时观察到的基因表达变化中起着至关重要的作用。我们的结果还揭示了核β-肌动蛋白通过影响 H3K27 乙酰化水平调节增强子功能的新功能。
