Exonuclease combinations reduce noises in 3D genomics technologies.
Nucleic Acids Res
; 48(8): e44, 2020 05 07.
Article
in En
| MEDLINE
| ID: mdl-32128590
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 â¼40% to â¼80% 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.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Genomics
/
Chromosomes, Mammalian
/
Exodeoxyribonucleases
Limits:
Animals
Language:
En
Journal:
Nucleic Acids Res
Year:
2020
Type:
Article
Affiliation country:
China