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Coupling CRISPR scanning with targeted chromatin accessibility profiling using a double-stranded DNA deaminase.
Heejin Roh1,2, Simon P Shen1,2, Yan Hu2,3
1Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
Nature Methods
|September 11, 2025
Summary
We developed targeted deaminase-accessible chromatin sequencing (TDAC-seq) to profile chromatin accessibility in single DNA molecules. This genome editing method links genetic changes to chromatin accessibility with single-nucleotide resolution.
Area of Science:
- Genomics
- Epigenetics
- Molecular Biology
Background:
- Genome editing advances understanding of cis-regulatory elements.
- Current methods struggle to profile chromatin accessibility on single, long DNA molecules.
Purpose of the Study:
- To develop a method for profiling chromatin accessibility at specific genomic loci on single chromatin fibers.
- To link genome editing outcomes to chromatin accessibility changes at single-nucleotide resolution.
Main Methods:
- Developed targeted deaminase-accessible chromatin sequencing (TDAC-seq) using cytidine deaminases.
- Applied TDAC-seq with CRISPR perturbations for sequence-function mapping.
- Utilized long-read sequencing for high-resolution analysis of targeted loci.
Main Results:
- TDAC-seq successfully profiled chromatin accessibility at endogenous loci.
- Integrated TDAC-seq with CRISPR edits to map effects on fetal hemoglobin activation in HSPCs.
- Applied TDAC-seq to analyze variants in a GFI1B enhancer linked to myeloproliferative neoplasms.
Conclusions:
- TDAC-seq provides high-resolution, single-molecule mapping of chromatin accessibility.
- The method enables linking genome editing to chromatin accessibility changes.
- TDAC-seq is a scalable tool for interrogating regulatory element function and disease-associated variants.
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