Cell type-specific enhancers are critically important for lineage specification. The mechanisms that determine cell type-specificity of enhancer activity, however, are not fully understood. Most current models for how enhancers function invoke physical proximity between enhancer elements and their target genes. Here, we use an imaging-based approach to examine the spatial relationship of cell type-specific enhancers and their target genes with single cell resolution. Using high-throughput microscopy, we measure the spatial distance from target promoters to their cell type-specific active and inactive enhancers in individual pancreatic cells derived from distinct lineages. These images were processed to identify nuclei and the loci within them. The shared dataset is composed of spot positions for promoter and enhancer probes in individual cells. It is comprised of 14 separate files, each corresponding to an individual plate imaged on a different day. Column headers and contents are consistent between individual files.

DNA FISH

High-throughput fluorescence in-situ hybridization was performed as described previously (Finn and Misteli 2021). Probes were generated from Bacterial Artificial Chromosomes (BACs) containing target regions. Bacteria from a single colony was grown into a large-scale culture and target DNA was purified via alkaline lysis using the Nucleobond BAC 100 Maxiprep kit (from Takara). DNA was then quantified and stored at -20°C for future use. Probes were generated from BAC DNA by a nick translation reaction incubated at 16°C for 1 hr 20 min with the following mix: 40 ng/uL DNA, 0.05 M Tris-HCl pH 8.0, 5 mM MgCl2, 0.05 mg/ml BSA, 0.05 mM dNTPs with all dTTP replaced with fluorescently labeled dUTP, 1 mM β-mercaptoethanol, 0.5 U/μL E. coli DNA Polymerase and 0.5 μg/μL DNAse I. The reaction was stopped with the addition of 1 μL EDTA per 50 μL reaction volume and heat shocked to 72°C for 10 min, then stored at −20°C overnight. QC gels were run in 2% agarose to verify successful nick translation with a smear of less than 1 kb. Combinations of two probes (1 μg per probe) were mixed, ethanol precipitated, resuspended in 15 μL of hybridization buffer (50% formamide pH 7.0, 10% Dextran Sulfate, and 1% Tween-20 in 2X SSC) per well and warmed to 72°C before plating.

Cells were plated at an appropriate density and grown overnight at 37°C before fixation for 10 minutes in 4% PFA, two PBS rinses, and storage in 70% ethanol at -20°C. To perform DNA FISH, cells were warmed to room temperature and rinsed three times in PBS to remove ethanol. Cells were then permeabilized in 0.5% w/v saponin/0.5% v/v Triton X-100 in PBS at room temperature for 20 min, rinsed twice with PBS, deproteinated for 15 minutes at room temperature in 0.1 N HCl, and neutralized for 5 min at room temperature in 2X SSC before equilibration in 50% formamide/2X SSC for at least 20 min at room temperature. 13.5 μL of resuspended probe mix was added per well, pipetting to mix before adding, and plates were spun to remove air bubbles. Cells were denatured for 7.5 min at 85°C and immediately moved to a 37°C water for 72 hour hybridization. After hybridization, plates were rinsed once at room temperature with 2X SSC, and then thrice each with 1X SSC and 0.1X SSC both warmed to 45°C. Cells were stained with DAPI for 15 min, rinsed, and mounted in PBS, and imaged. All experiments were performed in twelve technical replicate wells per experiment.

Imaging

Automated imaging was performed in three channels (405, 488, and 561 nm excitation lasers) on a CV8000 dual spinning disc confocal microscope with a 60X water immersion lens (NA = 1.2) and no pixel binning for a final pixel size of 108 nm. We imaged 16 fields per well with a z-stack of 10 μm at 1 μm intervals. In the first exposure, cells were excited with the 405 nm laser and the light path included a short pass emission dichroic mirror and an sCMOS camera in front of a 445/45 nm bandpass filter. In the second exposure, cells were excited with both 488 and 561 nm lasers and emission detected through the same light path by two sCMOS cameras in front of 525/50 nm and 600/37 nm bandpass emission filters respectively. Laser power and exposure time was optimized per experiment to ensure good signal-to-noise ratios.

Image analysis

Analysis of imaging data was carried out using HiTIPS, a high-throughput image analysis software to analyze DNA FISH data (Keikhosravi et al. 2023). For each experimental plate, specific analysis parameters were selected and tailored to align with the average nucleus size, as well as the size and brightness of the DNA FISH spots observed. Within HiTIPS, the GPU-based CellPose algorithm for nuclei segmentation was used in conjunction with the Laplacian of Gaussian method for spot detection (Stringer et al. 2021). Parameter selection was guided by real-time visual feedback, enabling iterative refinement of measurement parameters.  Image processing was done on the NIH HPC Biowulf cluster (NIH Biowulf HPC Cluster). Well-specific metadata were appended to the processed data using R.