Spatial Epigenomics Services for Chromatin Architecture Mapping
CD Genomics provides integrated spatial epigenomics services that map chromatin accessibility, histone modifications, and transcription factor binding directly on intact tissue sections — preserving the spatial coordinates that standard dissociation-based epigenomic methods destroy. Our platform combines two complementary technologies within a shared microfluidic barcoding workflow: spatial ATAC-seq for genome-wide open chromatin profiling, and spatial CUT&Tag for antibody-directed histone modification and transcription factor mapping. From tissue QC through sequencing and bioinformatics, we deliver spatially resolved epigenomic data ready for publication.
Why CD Genomics for spatial epigenomics:
- Two complementary modalities from one provider — spatial ATAC-seq for unbiased open chromatin mapping and spatial CUT&Tag for targeted histone mark and TF profiling — select one or combine both on matched sections
- Microfluidic deterministic barcoding preserves tissue coordinates at cellular-level resolution — no tissue dissociation, no loss of spatial context, genome-wide coverage
- End-to-end service from tissue QC and optimization through sequencing and publication-grade bioinformatics — peak calling, spatial clustering, motif enrichment, differential analysis, and multi-omics integration
- Validated on diverse tissue types including brain, spleen, melanoma, kidney, PDX models, embryonic tissue, gastric tumors, and prostate tumors
- Multi-omics integration with spatial transcriptomics and spatial proteomics for layered tissue atlases
Services are provided for research use only.
Technology Overview — Two Modalities, One Platform
What Are Spatial Epigenomics?
Spatial epigenomics refers to the genome-wide profiling of chromatin states — including chromatin accessibility, histone modifications, and transcription factor binding — directly on intact tissue sections while preserving the spatial coordinates of every epigenetic feature. Unlike standard epigenomic assays (bulk ATAC-seq, ChIP-seq, CUT&Tag) that require tissue dissociation and lose spatial information, or single-cell methods (scATAC-seq) that capture cellular heterogeneity but lose tissue context, spatial epigenomics maps regulatory element activity to precise tissue locations.
Our spatial epigenomics platform uses microfluidic deterministic barcoding — a technology first developed by the Rong Fan lab at Yale University — to encode two-dimensional spatial positions onto DNA fragments generated by in situ tagmentation. Two orthogonal microfluidic flow steps deliver X-axis and Y-axis DNA barcodes, creating a grid of uniquely coded spatial pixels across the tissue section. After library preparation and sequencing, each read is assigned to its pixel of origin, generating spatially resolved maps of chromatin states.
Two Complementary Technologies
| Dimension | Spatial ATAC-Seq | Spatial CUT&Tag |
|---|---|---|
| Target | All open chromatin (unbiased) | Specific histone marks or transcription factors (antibody-directed) |
| Chemistry | Tn5 transposase inserts adapters at accessible DNA | Antibody-guided pA-Tn5 fusion tagments at target-bound loci |
| Signal type | Open vs. closed chromatin | Enrichment at antibody-targeted loci |
| Sub-service page | Spatial ATAC-Seq Service | Spatial CUT&Tag Service |
For projects that require both unbiased chromatin accessibility discovery and targeted histone modification validation, we recommend running spatial ATAC-seq and spatial CUT&Tag on adjacent or serial tissue sections. Data from both modalities can be integrated through co-embedding and spatial correlation analyses. For the deepest multi-layered profiling, spatial epigenomic data can also be paired with spatial transcriptomics from matched sections.
What Spatial Epigenomic Data Reveals
| Information Layer | Technology | Biological Insight |
|---|---|---|
| Spatial chromatin accessibility | ATAC | Which regulatory elements are open in each tissue domain |
| Spatial enhancer/promoter maps | ATAC | Where gene regulatory elements are active across tissue architecture |
| Spatial histone modification domains | CUT&Tag | Active (H3K27ac, H3K4me3) vs. repressed (H3K27me3, H3K9me3) chromatin in tissue context |
| Spatial TF binding landscapes | CUT&Tag | Where transcription factors bind in situ — CTCF, RNA Pol II, cell-type-specific TFs |
| Integrated regulatory maps | ATAC + CUT&Tag | Combined accessibility and modification data for comprehensive epigenomic annotation |
Service Workflow
Our spatial epigenomics workflow proceeds through five integrated stages shared across both spatial ATAC-seq and spatial CUT&Tag, with modality-specific steps at the tagmentation stage. Quality control is performed at every checkpoint.
- Study Design & Tissue QC
Your project begins with a consultative planning phase where we align tissue type, target modality (ATAC, CUT&Tag, or both), target histone marks or TFs (for CUT&Tag), and sample number with your biological questions. Fresh frozen tissue sections are assessed for morphology and chromatin preservation. QC Checkpoint: Sections with folding, tearing, necrosis exceeding ~30%, or poor nuclear morphology are flagged and discussed before proceeding.
- In Situ Tagmentation
For spatial ATAC-seq: Permeabilized tissue sections are treated with hyperactive Tn5 transposase loaded with sequencing adapters. Tn5 simultaneously fragments and tags accessible chromatin regions at nucleosome-free DNA. For spatial CUT&Tag: Tissue sections are incubated with primary antibodies targeting the histone modification or transcription factor of interest, followed by secondary antibody and pA-Tn5 fusion protein. Magnesium-activated tagmentation occurs specifically at antibody-bound loci. QC Checkpoint: Tagmentation efficiency is monitored; under- or over-tagmentation conditions are adjusted per tissue type and target.
- Spatial Barcoding
Tagmented DNA fragments are captured and spatially encoded using a microfluidic chip that delivers two orthogonal sets of DNA barcodes (X-axis and Y-axis) across the tissue section. The resulting barcode matrix creates a grid of uniquely identifiable spatial pixels. Barcoded fragments are then released from the tissue, pooled, and purified for library preparation. QC Checkpoint: Barcode distribution is assessed for uniformity; spatial pixels with inadequate barcode representation are noted.
- Library Preparation & Sequencing
Barcoded DNA fragments undergo PCR amplification, size selection, and library QC (Bioanalyzer or TapeStation trace). Libraries are sequenced on Illumina platforms at a depth calibrated to the spatial pixel resolution and tissue area. QC Checkpoint: Library fragment distribution and concentration are verified; Q30 scores and sequencing saturation are monitored.
- Bioinformatics & Data Delivery
Sequencing data are processed through our spatial epigenomics pipeline: read alignment and barcode demultiplexing, Tn5 shift correction, peak calling, spatial clustering of epigenomic profiles, transcription factor motif enrichment analysis, differential accessibility or differential modification analysis between tissue regions, and generation of spatial heatmaps, genome browser tracks, and publication-ready figures. All analysis parameters are logged for reproducibility. QC Checkpoint: Final data review against project specifications before delivery.
Sample Requirements
| Requirement | Specification |
|---|---|
| Tissue type | Fresh frozen tissue (isopentane-frozen, OCT-embedded). FFPE sections may be evaluable for some workflows after feasibility assessment. |
| Species | Human, mouse, rat, and other species (case-by-case evaluation) |
| Section thickness | 7–10 µm for standard workflows; thicker sections may require protocol adjustment |
| Slide type | Poly-L-lysine coated or other adhesive (charged) glass slides |
| Tissue area | Optimal analysis region approximately 2.5 × 2.5 mm² per sample; larger or smaller areas can be accommodated |
| Minimum samples | 3 tissue sections per condition recommended for robust spatial analysis |
| Morphology requirements | Sections should be intact without folding, tearing, or freeze-thaw damage. Necrotic and red blood cell-contaminated regions should each be kept below approximately 20% of the analysis area. |
| Shipping | Sections on slides, shipped on dry ice. Include an H&E reference section if available for morphology-guided analysis region selection. |
Tissue types successfully processed include brain, spleen, melanoma, kidney, gastric tumor, prostate tumor, PDX models, and mouse embryonic tissue (E11–E13). Protocol optimization is available for tissues not previously validated — contact our team to discuss feasibility for your tissue type.
For comprehensive sample preparation guidance and shipping instructions, contact our team during project planning.
Bioinformatics Analysis
All spatial epigenomics projects include a standard bioinformatics pipeline. Advanced and custom analyses are scoped during study design.
Standard Analysis (Included)
- Read alignment & quality filtering
- Spatial barcode demultiplexing & error correction
- Tn5 shift correction & fragment file generation
- Peak calling per spatial pixel (MACS2)
- Spatial clustering of epigenomic profiles
- Differential accessibility / modification between tissue regions
- Transcription factor motif enrichment (JASPAR, HOMER)
- Spatial heatmap generation
- Genome browser tracks (bigWig format)
- HOMER annotatePeaks for genomic feature assignment
Optional Advanced Analysis
- Multi-omics integration with spatial transcriptomics — co-embedding, spatial correlation, regulatory network inference
- ATAC + CUT&Tag integrated analysis — combined accessibility and histone modification annotation
- Cell-type deconvolution of spatial pixels using scATAC-seq or scRNA-seq reference data
- Ligand-receptor interaction inference incorporating epigenomic regulatory potential
- Custom genome alignment for non-standard reference genomes
- Interactive HTML report with zoomable spatial heatmaps
Deliverables
| Deliverable | Description |
|---|---|
| Raw sequencing data (FASTQ) | Demultiplexed FASTQ files for all spatial barcoded libraries |
| Processed data matrices | Spatial pixel × peak count matrix, spatial pixel × gene activity score matrix (ATAC), spatial pixel × histone modification enrichment matrix (CUT&Tag) |
| Spatial epigenomic maps | High-resolution spatial heatmaps of chromatin accessibility, histone modification enrichment, or TF binding across the tissue section |
| Peak annotations | Genomic feature assignment (promoter, enhancer, intron, intergenic) for all called peaks |
| TF motif enrichment report | Enriched transcription factor binding motifs per spatial cluster or tissue region, with statistical significance |
| Differential analysis tables | Differentially accessible peaks or differentially enriched histone modification regions between user-defined tissue compartments |
| Genome browser tracks | bigWig format tracks for visualization in IGV, UCSC Genome Browser, or Ensembl |
| Bioinformatics report | Methods documentation, QC metrics, analysis parameter logs, and publication-ready figures (PDF/PNG/SVG) |
| Data archive | All intermediate files, analysis scripts, and processing logs archived for reproducibility |
Applications
Spatial epigenomics is most informative when regulatory element activity varies across tissue architecture — a common feature of development, immune responses, and disease.
Tumor microenvironment and cancer epigenetics
Map enhancer activation and repressive domains in tumor core, invasive margin, and adjacent stroma. Identify spatially restricted regulatory elements associated with immune exclusion, epithelial-to-mesenchymal transition, and drug-tolerant persister niches. Spatial ATAC-seq and CUT&Tag have been applied to gastric adenocarcinoma and prostate tumor sections, revealing tumor-stroma epigenetic interactions.
Neuroscience and brain architecture
Profile chromatin state differences across cortical layers, hippocampal subfields, and white vs. grey matter. Spatial epigenomic maps of mouse brain have demonstrated layer-specific chromatin accessibility and H3K4me3/H3K27me3 domain boundaries aligned with anatomical structures.
Developmental biology
Characterize spatiotemporal chromatin dynamics during embryogenesis and organogenesis. Spatial CUT&Tag profiling of mouse embryos (E11) has revealed tissue-boundary-specific histone modification patterns that precede transcriptional activation.
Immunology and lymphoid tissue organization
Map chromatin accessibility and transcription factor binding associated with immune cell activation, differentiation, and spatial organization in lymphoid organs and inflammatory infiltrates.
Biomarker discovery and target identification
Identify spatially restricted regulatory elements, enhancer RNAs, or histone modification signatures linked to pathology for downstream validation and therapeutic targeting.
Case Study: Spatial Epigenomic Profiling of Tissue Chromatin States
Source: Deng Y, Bartosovic M, Ma S, et al. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature 609, 375–383 (2022).
Background: Chromatin accessibility varies substantially across tissue regions, but traditional ATAC-seq requires tissue dissociation, destroying the spatial coordinates that link open chromatin to tissue anatomy. Understanding where specific regulatory elements become accessible within intact tissue is critical for identifying spatially restricted gene regulatory programs in development and disease.
Methods: The study developed spatial-ATAC-seq, which performs Tn5 tagmentation directly on intact tissue sections followed by microfluidic deterministic barcoding to encode spatial coordinates onto tagged DNA fragments. The method was applied to mouse embryo (E13) sagittal sections and human tonsil tissue. A companion method, spatial-CUT&Tag, was developed in parallel for antibody-targeted histone modification profiling (Deng et al., Science, 2022). Both modalities use the same microfluidic barcoding platform, enabling matched epigenomic profiling from adjacent tissue sections.
Results: Spatial-ATAC-seq revealed region-specific chromatin accessibility patterns across the developing mouse brain, with distinct open chromatin domains corresponding to anatomical structures such as the cortex, thalamus, and cerebellum. In human tonsil, the method resolved germinal center-specific accessibility programs. Integration with spatial-CUT&Tag data distinguished active enhancers (open + H3K27ac) from poised enhancers (open + H3K4me1, low H3K27ac) in a spatially resolved manner. The protocol was subsequently formalized in Nature Protocols (2024), and extended to multi-omics workflows capable of co-profiling epigenome and transcriptome from the same tissue section (Nature Protocols, 2025).
Conclusion: Spatial-ATAC-seq enables spatially resolved, genome-wide chromatin accessibility profiling at cellular resolution from intact tissues. The technology has been applied to diverse tissue types including brain, tonsil, gastric adenocarcinoma, and prostate tumors, and is now available as a validated service through CD Genomics.
Spatial ATAC-Seq vs. Spatial CUT&Tag — Choosing the Right Approach
| Decision Factor | Choose Spatial ATAC-Seq | Choose Spatial CUT&Tag |
|---|---|---|
| Research goal | Discovery — map all open chromatin and identify candidate regulatory elements | Hypothesis-driven — test whether a specific histone mark or TF shows spatial patterning |
| Prior knowledge | No prior target selection needed | Requires validated antibody against target of interest |
| Data type | Genome-wide accessibility | Target-specific enrichment |
| Multi-omics pairing | Best paired with spatial CUT&Tag (H3K27ac or H3K4me3) for active regulatory element annotation | Best paired with spatial ATAC-seq to distinguish accessible vs. modified chromatin |
| Antibody requirement | None | Requires high-quality, ChIP/CUT&Tag-validated antibody |
| Sensitivity for low-abundance targets | General — captures all open chromatin | High — specific enrichment at antibody-bound loci |
| Sample consumption | One tissue section per run | One tissue section per target; multiple targets require adjacent sections |
Combined approach recommendation: For comprehensive spatial epigenomic atlasing, we recommend spatial ATAC-seq on one section (unbiased accessibility) plus spatial CUT&Tag for H3K27ac (active enhancers/promoters) and/or H3K27me3 (repressive domains) on adjacent sections. This combination distinguishes active, poised, and repressed regulatory elements in their tissue context — an annotation depth not achievable by either modality alone.
Frequently Asked Questions (FAQ)
References
- Deng Y, Bartosovic M, Ma S, et al. Spatial profiling of chromatin accessibility in mouse and human tissues. Nature. 2022;609:375–383. DOI: 10.1038/s41586-022-05094-1.
- Deng Y, Bartosovic M, Kukanja P, et al. Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level. Science. 2022;375(6581):681–686. DOI: 10.1126/science.abg7216.
- Farzad N, Enninful A, Bao S, et al. Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue. Nature Protocols. 2024;19:3389–3425. DOI: 10.1038/s41596-024-01013-y.
- Li H, Bao S, Farzad N, et al. Spatially resolved genome-wide joint profiling of epigenome and transcriptome with spatial-ATAC-RNA-seq and spatial-CUT&Tag-RNA-seq. Nature Protocols. 2025;20:2383–2417. DOI: 10.1038/s41596-025-01145-9.
- Llorens-Bobadilla E, Zamboni M, Marklund M, et al. Solid-phase capture and profiling of open chromatin by spatial ATAC. Nature Biotechnology. 2023;41:1085–1088. DOI: 10.1038/s41587-022-01603-9.
- Noronha K, Decker S, Rojas G, et al. Revolutionizing epigenomic analysis in cancer: high-resolution spatial CUT&Tag and spatial ATAC-seq mapping at the single-nucleus level. Journal for ImmunoTherapy of Cancer. 2024;12(Suppl 2):A1524. DOI: 10.1136/jitc-2024-SITC2024.1361.
