Center for Soft Matter Research, Department of Physics, New York University, New York, NY 10003, USA.
Soft Matter. 2021 Dec 22;18(1):107-116. doi: 10.1039/d1sm00983d.
Material properties of the genome are critical for proper cellular function - they directly affect timescales and length scales of DNA transactions such as transcription, replication and DNA repair, which in turn impact all cellular processes the central dogma of molecular biology. Hence, elucidating the genome's rheology may help reveal physical principles underlying the genome's organization and function. Here, we present a novel noninvasive approach to study the genome's rheology and its response to mechanical stress in form of nuclear injection in live human cells. Specifically, we use Displacement Correlation Spectroscopy to map nucleus-wide genomic motions pre/post injection, during which we deposit rheological probes inside the cell nucleus. While the genomic motions inform on the bulk rheology of the genome pre/post injection, the probe's motion informs on the local rheology of its surroundings. Our results reveal that mechanical stress of injection leads to local as well as nucleus-wide changes in the genome's compaction, dynamics and rheology. We find that the genome pre-injection exhibits subdiffusive motions, which are coherent over several micrometers. In contrast, genomic motions post-injection become faster and uncorrelated, moreover, the genome becomes less compact and more viscous across the entire nucleus. In addition, we use the injected particles as rheological probes and find the genome to condense locally around them, mounting a local elastic response. Taken together, our results show that mechanical stress alters both dynamics and material properties of the genome. These changes are consistent with those observed upon DNA damage, suggesting that the genome experiences similar effects during the injection process.
基因组的物质属性对于正常的细胞功能至关重要——它们直接影响 DNA 转录、复制和修复等过程的时间尺度和长度尺度，而这些过程又反过来影响所有的细胞过程，这也是分子生物学中心法则的基础。因此，阐明基因组的流变特性可能有助于揭示基因组组织和功能的物理原理。在这里，我们提出了一种新的非侵入性方法来研究基因组的流变特性及其对机械力的响应，这种机械力表现为活体细胞中的核内注射。具体来说，我们使用位移相关光谱来绘制核内基因组运动的全基因组图谱，在注射前后，我们将流变探针注入到细胞核内。虽然基因组的运动反映了注射前后基因组的整体流变特性，但探针的运动反映了其周围局部的流变特性。我们的结果表明，注射带来的机械力会导致基因组的局部和整体压缩、动力学和流变特性发生变化。我们发现，在注射之前，基因组表现出亚扩散运动，这种运动在几个微米的范围内是相干的。相比之下，注射后的基因组运动变得更快且不相关，此外，基因组在整个细胞核内变得不那么紧凑，粘性也更大。此外，我们还将注入的粒子用作流变探针，发现基因组会在它们周围局部凝聚，产生局部弹性响应。总的来说，我们的结果表明，机械力会改变基因组的动力学和物质属性。这些变化与 DNA 损伤时观察到的变化一致，这表明在注射过程中基因组会经历类似的影响。
