3D ATAC-PALM: super-resolution imaging of the accessible genome.
Liangqi XiePeng DongXingqi ChenTsung-Han S HsiehSambashiva BanalaMargherita De MarzioBrian P EnglishYifeng QiSeol Kyoung JungKyong-Rim Kieffer-KwonWesley R LegantAnders S HansenAnton SchulmannRafael CasellasBin ZhangEric BetzigLuke D LavisHoward Y ChangRobert Tse Nan TjianZhe J LiuPublished in: Nature methods (2020)
To image the accessible genome at nanometer scale in situ, we developed three-dimensional assay for transposase-accessible chromatin-photoactivated localization microscopy (3D ATAC-PALM) that integrates an assay for transposase-accessible chromatin with visualization, PALM super-resolution imaging and lattice light-sheet microscopy. Multiplexed with oligopaint DNA-fluorescence in situ hybridization (FISH), RNA-FISH and protein fluorescence, 3D ATAC-PALM connected microscopy and genomic data, revealing spatially segregated accessible chromatin domains (ACDs) that enclose active chromatin and transcribed genes. Using these methods to analyze genetically perturbed cells, we demonstrated that genome architectural protein CTCF prevents excessive clustering of accessible chromatin and decompacts ACDs. These results highlight 3D ATAC-PALM as a useful tool to probe the structure and organizing mechanism of the genome.
Keyphrases
- genome wide
- single molecule
- high resolution
- dna damage
- gene expression
- high throughput
- dna methylation
- transcription factor
- copy number
- living cells
- high speed
- induced apoptosis
- optical coherence tomography
- label free
- electronic health record
- endoplasmic reticulum stress
- energy transfer
- body mass index
- signaling pathway
- data analysis
- quantum dots
- nucleic acid
- fluorescence imaging