Quantitative profiling of intrinsic dCas9-DNA recognition reveals key determinants of guide RNA performance

Evaluating high-fidelity CRISPR-Cas nucleases in nucleosomal contexts using a quantitative framework

It is demonstrated that local nucleosome sequence and structure profoundly influence Cas nuclease accessibility and specificity, with HIFIv1 emerging as the top-performing nuclease for nucleosomal targets, while evoSpCas9 excelled in exposed contexts.

CRISPR RNA-independent activation of Cas12a

It is shown that short RNAs can directly occupy the canonical crRNA-binding channel and trigger a catalytically competent trans cleavage state in the absence of PAM recognition or canonical R-loop formation.

Mapping protein-DNA interactions across biological scales: principles, scalability and applications.

A comparative overview of major PDI technologies organized according to the biological scale at which they operate is provided, including sequence- and chromatin-based binding prediction, multi-omics integration, and regulatory network inference.

Unraveling genomic regulatory complexity by adding chromatin accessibility to the long-read sequencing toolkit 2247245

Fiber-seq simultaneously profiles chromatin accessibility, DNA methylation, protein footprints, and genetic variation on single molecules at near—base-pair resolution, revealing how genetic and epigenetic features interact to regulate gene expression and provides a powerful new framework for dissecting immune cell function and disease mechanisms.

Genome-wide profiling of histone modifications and transcription factor binding at single-cell resolution by DeChIC-seq

DeChIC-seq establishes a conversion-based framework for chromatin profiling that enables mechanistic dissection of TF-driven gene regulation across rare cells, developmental systems, and disease contexts.

Programmable Allosteric DNAzyme Coupled with CRISPR/Cas12a System for Multiplexed and Sensitive Detection of Extracellular Vesicle Derived MicroRNAs