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Exonuclease combinations reduce noises in 3D genomics technologies

ABSTRACT: Chromosome conformation-capture technologies are widely used in 3D genomics; however, experimentally, such methods have high-noise limitations and, therefore, require significant bioinformatics efforts to extract reliable distal interactions. Miscellaneous undesired linear DNAs, present during proximity-ligation, represent a main noise source which needs to be minimized or eliminated. In this study, different exonuclease combinations were tested to remove linear DNA fragments from a circularized DNA preparation. This method efficiently removed linear DNAs, raised the proportion of annulation and increased valid-pairs ratio from 30-40% to 70-80% for enhanced interaction detection in standard Hi-C. This strategy is applicable for development of various 3D genomics technologies, or optimization of Hi-C sequencing efficiency.

ORGANISM(S): Mus musculus

PROVIDER: GSE125656 | GEO | 2020/04/08

REPOSITORIES: GEO

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