Rahman Fariha, Augoustides Victoria, Tyler Emma, Daugird Timothy A, Arthur Christian, Legant Wesley R
Lampe Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, Chapel Hill, NC, USA.
Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
Nat Commun. 2025 Jul 1;16(1):6042. doi: 10.1038/s41467-025-61358-0.
The nucleus coordinates many different processes. Visualizing how these are spatially organized requires imaging protein complexes, epigenetic marks, and DNA across scales from single molecules to the whole nucleus. To accomplish this, we develop a multiplexed imaging protocol to localize 13 different nuclear targets with nanometer precision. Within single cells, we show that nuclear specification into active and repressive states exists along a spectrum of length scales, emerging below one micron and becoming strengthened at the nanoscale with unique organizational principles in both heterochromatin and euchromatin. HP1α was positively correlated with DNA at the microscale but uncorrelated at the nanoscale. RNA Polymerase II, p300, and CDK9 were positively correlated at the microscale but became partitioned below 300 nm. Perturbing histone acetylation or transcription disrupted nanoscale organization but had less effect at the microscale. We envision that our imaging and analysis pipeline will be useful to reveal the organizational principles not only of the cell nucleus but also other cellular compartments.
细胞核协调许多不同的过程。要可视化这些过程是如何在空间上组织的，需要对从单分子到整个细胞核的不同尺度上的蛋白质复合物、表观遗传标记和DNA进行成像。为了实现这一点，我们开发了一种多重成像方案，以纳米精度定位13种不同的核靶点。在单细胞内，我们表明，细胞核向激活状态和抑制状态的特化存在于一系列长度尺度上，在亚微米尺度下出现，并在纳米尺度上通过异染色质和常染色质中独特的组织原则而得到强化。HP1α在微米尺度上与DNA呈正相关，但在纳米尺度上不相关。RNA聚合酶II、p300和CDK9在微米尺度上呈正相关，但在300 nm以下开始分离。干扰组蛋白乙酰化或转录会破坏纳米尺度的组织，但在微米尺度上影响较小。我们设想，我们的成像和分析流程不仅将有助于揭示细胞核的组织原则，也将有助于揭示其他细胞区室的组织原则。
