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Genome-Wide Profiling of DNA Double-Strand Breaks by the BLESS and BLISS Methods
Reza Mirzazadeh1, Tomasz Kallas1, Magda Bienko2
1Science for Life Laboratory, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.
Abstract:
DNA double-strand breaks (DSBs) are major DNA lesions that are constantly formed during physiological processes such as DNA replication, transcription, and recombination, or as a result of exogenous agents such as ionizing radiation, radiomimetic drugs, and genome editing nucleases. Unrepaired DSBs threaten genomic stability by leading to the formation of potentially oncogenic rearrangements such as translocations. In past few years, several methods based on next-generation sequencing (NGS) have been developed to study the genome-wide distribution of DSBs or their conversion to translocation events. We developed Breaks Labeling, Enrichment on Streptavidin, and Sequencing (BLESS), which was the first method for direct labeling of DSBs in situ followed by their genome-wide mapping at nucleotide resolution (Crosetto et al., Nat Methods 10:361-365, 2013). Recently, we have further expanded the quantitative nature, applicability, and scalability of BLESS by developing Breaks Labeling In Situ and Sequencing (BLISS) (Yan et al., Nat Commun 8:15058, 2017). Here, we first present an overview of existing methods for genome-wide localization of DSBs, and then focus on the BLESS and BLISS methods, discussing different assay design options depending on the sample type and application.
Insights
DNA double-strand breaks (DSBs) are critical DNA lesions. New sequencing methods like BLESS and BLISS enable precise, genome-wide mapping of DSBs and translocations, enhancing genomic stability studies.
Area of Science:
- Molecular Biology
- Genomics
- DNA Repair
Background:
- DNA double-strand breaks (DSBs) are significant DNA lesions arising from physiological processes or exogenous agents.
- Unrepaired DSBs can lead to oncogenic genomic rearrangements, such as translocations, threatening genomic stability.
- Next-generation sequencing (NGS) methods have advanced the study of DSB distribution and translocation events.
Purpose of the Study:
- To provide an overview of genome-wide DSB localization methods.
- To focus on the BLESS and BLISS techniques for DSB mapping.
- To discuss assay design considerations for BLESS and BLISS based on sample type and application.
Main Methods:
- Breaks Labeling, Enrichment on Streptavidin, and Sequencing (BLESS) for direct in situ DSB labeling and genome-wide mapping at nucleotide resolution.
- Breaks Labeling In Situ and Sequencing (BLISS) as an advancement of BLESS, enhancing quantitative capabilities, applicability, and scalability.
- Comparison and discussion of various assay design options for BLESS and BLISS.
Main Results:
- BLESS was the pioneering method for direct, high-resolution, genome-wide DSB mapping.
- BLISS offers improved quantitative analysis, broader applicability, and enhanced scalability for DSB studies.
- The study provides insights into optimizing BLESS and BLISS methodologies for different research contexts.
Conclusions:
- BLESS and BLISS are powerful NGS-based tools for studying the genome-wide distribution of DSBs and their role in genomic instability.
- These methods facilitate the understanding of DSB formation and repair mechanisms.
- The discussed assay design options aid researchers in effectively applying BLESS and BLISS to their specific research questions.