Exonuclease Combinations Reduce Noises in 3D Genomics Technologies

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2020 Mar 5

PMID 32128590

Citations 5

Authors

Siyuan Kong

Qing Li

Gaolin Zhang

Qiujia Li

Qitong Huang

Lei Huang

Hui Zhang

Yinghua Huang

Yanling Peng

Baoming Qin

Yubo Zhang

Affiliations

Soon will be listed here.

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 the valid-pairs ratio from ∼40% to ∼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.

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