ATACsee

ATACsee is a molecular biology technique that enables in situ visualization of chromatin accessibility while also enabling genome-wide profiling by ATAC-seq. Developed to bridge imaging and sequencing, ATACsee uses the Tn5 transposase to insert fluorescently labeled adapters into regions of open chromatin in fixed cells or tissue sections. The fluorescent tags allow researchers to image the spatial distribution of accessible chromatin within individual cells using fluorescence microscopy. After imaging, the same sample is subjected to standard ATAC-seq library preparation to map accessible genomic regions across the genome, enabling direct linkage between the observed spatial patterns and the underlying DNA sequence.

Typical workflow involves fixing cells or tissue, permeabilizing, performing transposition with fluorescent adapters, washing, and imaging with appropriate filters. After imaging, the sample can be processed for library construction and sequencing. Data integration requires software to align imaging signals with sequencing peaks, and the workflow may include co-staining with nuclear markers or histone modifications to provide contextual information about chromatin state.

Applications and impact of ATACsee include studies of developmental processes, cellular differentiation, cancer cell heterogeneity, and nuclear architecture. The method enables researchers to relate spatial patterns of chromatin accessibility observed in fixed cells to genome-wide regulatory landscapes, helping to validate and interpret ATAC-seq results in a spatial context.

Limitations and considerations include that resolution is constrained by light microscopy, and the fluorescent signal provides a relative measure of accessibility at observable loci. The fixation step and the transposition process can introduce biases, and the protocol can be technically demanding, requiring careful controls and specialized imaging equipment.

See also: ATAC-seq, chromatin accessibility, Tn5 transposase.