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Updated: May 7, 2025
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Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells
Published on: April 2, 2018
11.2K
Deaminase-mediated chromatin accessibility profiling with single-allele resolution.
Biorxiv : the Preprint Server for Biology
|January 7, 2025
Summary
Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC) enhances transcription factor (TF) binding site prediction accuracy. This method reveals TF co-occupancy patterns oscillating with DNA
Area of Science:
- Epigenetics and Genomics
- Molecular Biology
- Computational Biology
Background:
- Transcription factor (TF) binding at gene regulatory elements is crucial for controlling cellular epigenetic states and gene expression.
- Existing genome-wide chromatin profiling methods possess limited resolution, hindering precise assessment of TF occupancy and co-occupancy, particularly at individual DNA alleles.
- Understanding TF binding dynamics is essential for deciphering gene regulation.
Purpose of the Study:
- To introduce Accessible Chromatin by Cytosine Editing Site Sequencing with ATAC-seq (ACCESS-ATAC), a novel technique for high-resolution TF binding site analysis.
- To optimize ACCESS-ATAC protocols for both bulk and single-cell applications.
- To improve the accuracy of TF binding site prediction compared to standard ATAC-seq.
Main Methods:
- Development and optimization of the ACCESS-ATAC protocol utilizing a double-stranded DNA cytosine deaminase (Ddd) enzyme.
- Application of optimized bulk and single-cell ACCESS-ATAC protocols in HepG2 and K562 cell lines.
- Development of computational methods for analyzing ACCESS-ATAC data and imputing TF occupancy and co-occupancy.
Main Results:
- ACCESS-ATAC significantly enhances the resolution of TF binding site prediction compared to conventional ATAC-seq.
- Genome-wide allelic occupancy and co-occupancy imputation for 64 TFs in HepG2 and K562 cells were successfully performed.
- A majority of TFs exhibit a propensity for co-occupancy at nearby motifs that oscillates with a periodicity approximating the DNA helical turn.
Conclusions:
- ACCESS-ATAC represents a significant advancement in epigenomic profiling, offering unprecedented resolution for TF binding analysis.
- The technique expands the capabilities of both bulk and single-cell epigenomic studies.
- The findings provide new insights into the spatial organization and co-occupancy dynamics of transcription factors on DNA.
