Mapping the nuclear landscape with multiplexed super-resolution fluorescence microscopy.
Fariha RahmanVictoria AugoustidesEmma TylerTimothy A DaugirdChristian ArthurWesley R LegantPublished in: bioRxiv : the preprint server for biology (2024)
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 developed a multiplexed imaging protocol to localize 13 different nuclear targets with nanometer precision in 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. HP1-α 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.
Keyphrases
- high resolution
- single cell
- single molecule
- atomic force microscopy
- dna methylation
- circulating tumor
- gene expression
- induced apoptosis
- high throughput
- cell free
- genome wide
- photodynamic therapy
- mass spectrometry
- cell cycle
- transcription factor
- bone marrow
- fluorescence imaging
- signaling pathway
- mesenchymal stem cells
- cell death
- cell cycle arrest
- endoplasmic reticulum stress
- quantum dots
- label free