Agnostic detection of genomic alterations by holistic DNA structural interrogation

Area of Science:

• Genomics
• Epigenetics
• Molecular Biology

Background:

• Established links exist between DNA sequence, chromatin structure, and gene activity.
• Variations in DNA organization properties can indicate underlying genomic changes.

Purpose of the Study:

• To demonstrate that DNA structural variations can identify diverse genomic alterations in mammalian samples.
• To compare genome-wide histone occupancy, DNA accessibility, and chromosomal conformation in modified versus unmodified mammalian cell lines and tissues.

Main Methods:

• Utilized ChIP-Seq for histone occupancy, ATAC-Seq for DNA accessibility, and Hi-C for chromosomal conformation.
• Analyzed five CRISPR/Cas9-modified mammalian cell lines and one modified tissue sample against their parent strains.

Main Results:

• Genomic alteration impact varied by mutation type, size, and location.
• Identified large genomic alterations (>200 Kb), including chromosomal rearrangements and deletions, missed by standard sequencing.
• Demonstrated a multi-level DNA organizational analysis for sensitive detection of genomic and epigenomic perturbations.

Conclusions:

• Multi-level DNA organizational analysis is a sensitive method for detecting genomic and epigenomic changes.
• This approach can identify large genomic alterations difficult to detect with standard methods.
• Applications include biomedical research and biosecurity.