Need to get swiftly up to date with recent advances to the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-Seq) technique? Well, slow down and read on for the latest single-cell spatial and multimodal updates to your chromatin toolbox!
Our first study gives us a quick lowdown on Spatial-ATAC-seq, a technique to capture spatial chromatin accessibility from intact tissues at the cell level and genome scale; meanwhile, a multimodal report rapidly fills us in on ISSAAC-seq, a new method to interrogate both chromatin accessibility and gene expression in a single cell!
Spatial-ATAC-seq Accelerates the Spatial Resolution of Chromatin Accessibility Profiling
The ability to spatially resolve chromatin accessibility from single cells within intact tissue provides a speedy means to delineate cell functions/states in a native environment and understand how local environments impact cell function. Advances accelerating research towards this aim have included single-cell (sc)ATAC-seq, imaging chromatin accessibility in fixed cells via ATAC-see, and the application of scATAC-seq to microdissected tissues.
Now, a talented team led by Gonçalo Castelo-Branco (Karolinska Institutet) and Rong Fan (Yale University) provide a single-cell spatial update to ATAC-seq by integrating in situ Tn5 transposition chemistry and microfluidic deterministic barcoding to create spatial-ATAC-seq, which supports the high-spatial-resolution genome-wide mapping of chromatin accessibility in intact tissues using next-generation sequencing.
Let’s hear from Deng and colleagues on how spatial-ATAC-seq can accelerate tissue-based epigenetic research:
- Delineation of the epigenetic landscape of organogenesis by spatial-ATAC-seq profiling of intact early mouse embryos identifies all major tissue types with a distinct chromatin accessibility state, reveals the spatiotemporal alterations that occur during development, and defines the gene regulators involved in central nervous system development
- Mapping the accessible genome in post-natal mouse brain coronal sections and adult archival human coronal brain sections (including the hippocampus and choroid plexus) via spatial-ATAC-seq readily reveals the intricate arealization of brain regions
- Applying spatial-ATAC-seq to human tonsil tissue resolves the spatially distinct organization of immune cell types and states in lymphoid follicles and extrafollicular zones
- Analysis reveals the dynamics of B cell activation to the germinal center reaction (the basis of T-dependent humoral immunity against foreign pathogens and the expression of adaptive immune responses) and putative target genes of fine-mapped autoimmune genome-wide association studies genetic variants
Overall, spatial-ATAC-seq provides a cutting-edge means of profiling spatially-resolved chromatin accessibility under normal developmental and pathological conditions, which may hastily improve our understanding of how epigenetics impacts cell identity, state, and fate decisions. Ongoing developments in this technology include improving resolution through increased barcodes or more intricate microfluidic channels, implementing additional modalities to enable spatial multiomic profiling (See below!), and evaluating tissue samples from human patients with various diseases/disorders.
“We’ll get an unbiased global view, and a much finer resolution view, of all possible cell states, and more importantly, ‘see’ where they are in a tissue,” study co-leader Rong Fan said. “It’s a powerful tool for building cell maps and cell atlases.” Study co-leader Gonçalo Castelo-Branco adds that “Applying spatial ATAC-Seq in diseased tissues might allow us in the near future to identify transitions between epigenetic states in specific cells in the context of the disease niche, which will give insights of the molecular mechanisms that mediating the acquisition of pathological cellular states.”
ISSAAC-seq Speeds Up Gene Regulatory Insight with Multimodal Multitasking
A multitasking team by Wenfei Jin and Xi Chen (Southern University of Science and Technology, Shenzhen, China) also aimed to update ATAC-seq – this time by providing the ability to simultaneously profile gene expression and chromatin accessibility in the same single nucleus.
The team now describes how their sensitive and flexible multimodal single-cell technique – in situ sequencing hetero RNA–DNA-hybrid after assay for transposase-accessible chromatin-sequencing or ISSAAC-seq – can help us to understand the function of tissue-resident cell types and cell state alterations during dynamic processes.
Let’s hear from Xu, Yang, and colleagues on updating ATAC-seq to multimodal technique:
- Joint profiling by ISSAAC-seq in complex tissue (over 10,000 nuclei from the frozen adult mouse cerebral cortex) uncovers major and rare cell types and reveals cell-type-specific gene regulatory programs
- This approach successfully identifies twelve types of excitatory neurons (Rbfox3+, Slc32a1−, Slc17a7+), seven types of inhibitory neurons (Rbfox3+, Slc32a1+, Slc17a7−), and four types of non-neuron (Rbfox3-)
- ATAC-seq results exhibit clear and specific chromatin accessibility results around marker gene loci
- Direct comparisons of ATAC and RNA profiles from the same cell uncover a level of heterogeneity missed by analysis using a single modality
- A deeper analysis of oligodendrocyte lineage cells (oligodendrocyte progenitor cells [Pdgfra] and mature oligodendrocytes [Mbp]) via ISSAAC-seq reveals the distinct dynamics and relationships of gene expression and chromatin accessibility during oligodendrocyte maturation
- Decreased Pdgfra and increased Mbp gene expression during maturation link tightly to gene activity scores measured by chromatin accessibility, demonstrating how ISSAAC-seq can decipher gene regulatory mechanisms associated with dynamic processes such as cell differentiation
- These findings also demonstrate that alterations to chromatin accessibility often precede gene expression changes, in agreement with previous studies
Overall, the authors report ISSAAC-seq, a multimodal update to ATAC-seq, as a powerful and highly sensitive means of investigating gene expression and chromatin accessibility within the same cell. Interestingly, they note that their approach offers high-quality results at a cheaper price than commercially available kits and can be combined with fluorescence-activated cell sorting for limited cell numbers or droplet-based systems for high-throughput cell profiling. Furthermore, they note that integrating ISSAAC-seq with antibody-oligo conjugates to capture protein information may support an additional multiomic update in the future.
Updates to Updates – Epigenetic Analysis in the Fast Lane!
A quick-fire pair of updates have brought the analysis of chromatin accessibility up to speed for those working in the fast lane of epigenetics; however, a recent preprint from Gonçalo Castelo-Branco and Rong Fan now brings updates to these updates! They describe how co-profiling chromatin accessibility and gene expression (spatial-ATAC-RNA-seq) or histone modification and gene expression (spatial-CUT&Tag-RNA-seq) within the same tissue section at a near single-cell resolution.
See Nature, August 2022 for more on how spatial-ATAC-seq can accelerate epigenetic research through the spatial resolution of single-cell chromatin accessibility profiling, and head to Nature Methods, September 2022 for all the details on how a multimodal update to ATAC-seq makes ISSAAC-seq an affordable and sensitive means to study cell-specific regulatory programs.