iscDNase-seq

iscDNase-seq profiles chromatin accessibility at single-cell resolution using a multiplex indexing approach to enable genome-wide mapping of DNase I hypersensitive sites and to link accessibility variation to gene expression.

Key Features:

• Multiplex Indexing Strategy: A three-layer indexing system uses terminal deoxynucleotidyl transferase (TdT) and T4 DNA ligase to add unique barcodes to the ends of DNase-digested chromatin, enabling simultaneous profiling of DNase I hypersensitive sites (DHSs) across more than 15,000 single cells in a single experiment.
• Enhanced Detection Capabilities: Detects DHSs with properties related to gene expression and evolutionary conservation that are not detected by scATAC-seq.
• Correlation with Gene Expression: Produces chromatin accessibility profiles that show higher correlation with single-cell RNA sequencing (scRNA-seq) than scATAC-seq, improving prediction of cell-to-cell variation in gene expression.

Scientific Applications:

• Epigenomic Studies: Reveals specific cell types and helps infer regulatory transcription factors by identifying DHSs that inform gene regulation mechanisms at single-cell resolution.
• Cellular Heterogeneity Analysis: Links cell-to-cell chromatin accessibility variation to gene expression to study epigenetic contributions to cellular diversity and states.

Methodology:

Enzymatic addition of unique barcodes to DNase-digested chromatin ends using TdT and T4 DNA ligase combined with a three-layer indexing approach and bulk cell analysis to recover genome-wide single-cell DNase I hypersensitivity profiles.