Journal Article

Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA

Boettiger, Alistair N., Mateo, Leslie J., Sinnott-Armstrong, Nasa

2021

Overview

Chromatin conformation capture (3C) methods and fluorescent in situ hybridization (FISH) microscopy have been used to investigate the spatial organization of the genome. Although powerful, both techniques have limitations. Hi-C is challenging for low cell numbers and requires very deep sequencing to achieve its high resolution. In contrast, FISH can be done on small cell numbers and capture rare cell populations, but typically targets pairs of loci at a lower resolution. Here we detail a protocol for optical reconstruction of chromatin architecture (ORCA), a microscopy approach to trace the 3D DNA path within the nuclei of fixed tissues and cultured cells with a genomic resolution as fine as 2 kb and a throughput of ~10,000 cells per experiment. ORCA can identify structural features with comparable resolution to Hi-C while providing single-cell resolution and multimodal measurements characteristic of microscopy. We describe how to use this DNA labeling in parallel with multiplexed labeling of dozens of RNAs to relate chromatin structure and gene expression in the same cells. Oligopaint probe design, primary probe making, sample collection, cryosectioning and RNA/DNA primary probe hybridization can be completed in 1.5 weeks, while automated RNA/DNA barcode hybridization and RNA/DNA imaging typically takes 2–6 d for data collection and 2–7 d for the automated steps of image analysis. The authors provide experimental and computational procedures, including details on building an automated fluidic exchange system, for high-resolution imaging of multiple transcripts and chromatin structure in fixed cells or cryosectioned tissue.

• Publisher: Nature Publishing Group UK,Nature Publishing Group
• Subject: 631/1647/328/2238 / 631/337/100/101 / Analytical Chemistry / Automation / Biological Techniques / Biomedical and Life Sciences / Cell culture / Cell Line / Cell Nucleus - genetics / Cells, Cultured / Chromatin / Chromatin - metabolism / Chromatin Immunoprecipitation - methods / Chromosomes - genetics / Computational biology / Computational Biology/Bioinformatics / Computer applications / Conformation / Data collection / Deoxyribonucleic acid / DNA / DNA - chemistry / DNA - genetics / DNA Probes / Fluorescence / Fluorescence in situ hybridization / Fluorescent Dyes - chemistry / Gene expression / Gene sequencing / Genes / Genetic Techniques / Genome - genetics / Genomes / Genomics / Genomics - methods / High resolution / Humans / Hybridization / Identification and classification / Image analysis / Image processing / Image Processing, Computer-Assisted - methods / Image reconstruction / Image resolution / In Situ Hybridization, Fluorescence - methods / Labeling / Life Sciences / Marine mammals / Methods / Microarrays / Microscope and microscopy / Microscopy / Microscopy, Fluorescence - methods / Optical Restriction Mapping - methods / Organic Chemistry / Protocol / Ribonucleic acid / RNA / RNA - chemistry / RNA - genetics / RNA probes / Structure / Tissue culture