Our bodies contain diverse cell types, each with the same DNA but performing different functions. Understanding these cellular differences is a challenge in biology. Single-cell ATAC sequencing (scATAC-seq) is a scientific tool that explores these differences by examining how DNA is packaged within individual cells.
How Single Cell ATAC Sequencing Works
DNA within a cell is tightly wound around proteins, forming chromatin. Chromatin can be imagined as a library where some “books” (genes) are open and accessible, while others are closed. ScATAC-seq identifies these open regions, which are accessible for cellular machinery.
The “ATAC” stands for “Assay for Transposase-Accessible Chromatin.” This technique uses the Tn5 transposase enzyme. This enzyme cuts and tags DNA only in accessible chromatin regions. Tightly packed, “closed” regions are not affected by the Tn5 enzyme.
This process is performed on thousands of individual cells, often isolated into tiny droplets. The tagged DNA fragments from each cell are then sequenced. This generates an accessibility map for each cell, indicating where its chromatin was open or closed.
What Chromatin Accessibility Reveals
The accessibility map from scATAC-seq provides insights into which genes a cell is poised to activate. Open chromatin regions often correspond to active gene promoters or enhancers that boost gene activity. Closed chromatin regions indicate inactive genes.
This information helps distinguish different cell types within complex tissues, like neuronal subtypes in the brain or immune cells in blood. A muscle cell, for example, shows a distinct open chromatin pattern compared to a liver cell. This allows researchers to identify cell populations based on their regulatory landscapes.
ScATAC-seq also helps understand the regulatory landscape of gene expression. By identifying accessible enhancer and promoter regions, scientists can pinpoint DNA “switches” that control gene activity. Observing changes in chromatin accessibility over time can also show how cells transform, such as during embryonic development as stem cells differentiate.
Integration with Other Cellular Data
While scATAC-seq reveals the potential for gene activity, combining it with other data offers a more comprehensive view of cell function. ScATAC-seq shows which genes could be active, but not which genes are actively expressed. This distinction is important for a complete picture of cellular states.
Single-cell RNA sequencing (scRNA-seq) measures mRNA molecules in individual cells, indicating active gene expression. By integrating scATAC-seq and scRNA-seq data, scientists can link gene expression potential to its actual expression. This combined approach provides a more complete understanding of cellular identity, function, and regulatory mechanisms.
This multi-omics approach allows researchers to correlate changes in chromatin accessibility with gene expression. For example, if an enhancer becomes accessible in scATAC-seq data, scientists can check if the regulated gene shows increased expression in scRNA-seq data. This integrated analysis helps build better models of gene regulation and cellular behavior.
Applications in Biological Research
Single-cell ATAC sequencing is applied across various biological research fields, providing insights into cellular processes and disease mechanisms. In cancer research, scATAC-seq helps understand how cancer cells develop therapy resistance. It has identified chromatin accessibility changes that allow melanoma cells to evade treatment, pointing to new therapeutic targets.
In developmental biology, scATAC-seq helps map cell differentiation. Researchers track how a fertilized egg develops into diverse cell types. This involves observing how chromatin accessibility patterns change as stem cells differentiate into specific lineages.
Immunology benefits from scATAC-seq, as it helps understand dynamic changes within immune cells. This technique reveals how immune cells activate and alter gene regulation to fight infections or how they malfunction in autoimmune diseases. Identifying specific regulatory elements accessible during immune responses can uncover novel pathways involved in disease progression or protection.