A team of researchers has introduced a groundbreaking technique known as Deaminase-Assisted single-molecule chromatin Fiber sequencing, or DAF-seq. This innovative method allows for the detailed mapping of chromatin fiber architectures at a single-cell level, significantly enhancing our understanding of gene regulation in diploid organisms.
Gene regulation is a complex process that involves the co-binding of proteins along chromosome-length chromatin fibers within individual cells. The challenge has been the difficulty in resolving the heterogeneity of protein occupancy between haplotypes and across different cells. DAF-seq addresses this issue by enabling single-molecule footprinting with near-nucleotide resolution. This capability allows researchers to simultaneously profile chromatin states and DNA sequences of individual molecules, providing insights into cooperative protein occupancy at regulatory elements.
The implications of DAF-seq extend to the study of somatic variants and rare chromatin epialleles. The technique generates chromosome-length protein co-occupancy maps, covering approximately 99% of each cell’s mappable genome. Notably, the research revealed a remarkable level of chromatin plasticity, with chromatin actuation varying by 61% between haplotypes within a single cell and 63% between different cells.
In addition to these findings, the team discovered that regulatory elements are preferentially co-actuated along the same fiber in a distance-dependent manner. This pattern aligns with the behaviors seen in cohesin-mediated loops, suggesting a sophisticated level of organization within chromatin structures.
The research, conducted by scientists at the University of Washington and published in relevant scientific journals, highlights the potential of DAF-seq to transform our understanding of gene regulation. The method not only captures the intricate architectures of chromatin but also allows for the characterization of protein occupancy with unprecedented precision—single-nucleotide, single-molecule, single-haplotype, and single-cell accuracy.
Funding for this pivotal study was provided by various organizations, including the National Institutes of Health (NIH) and the Chan Zuckerberg Initiative. The lead researchers, including A.B. Stergachis, expressed gratitude for the support received from associated labs and institutions, which facilitated the extensive data collection and analysis.
DAF-seq represents a significant advancement in genomic research, offering a powerful tool for unraveling the complexities of gene regulation at the cellular level. As researchers continue to explore the implications of this technique, it is poised to contribute to a deeper understanding of genetic mechanisms and their roles in health and disease.
