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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 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.

SUBMITTER: Kong S

PROVIDER: S-EPMC7192622 | biostudies-literature | 2020 May

REPOSITORIES: biostudies-literature

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Exonuclease combinations reduce noises in 3D genomics technologies.

Kong Siyuan S Li Qing Q Zhang Gaolin G Li Qiujia Q Huang Qitong Q Huang Lei L Zhang Hui H Huang Yinghua Y Peng Yanling Y Qin Baoming B Zhang Yubo Y

Nucleic acids research 20200501 8

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 circularize ...[more]

PMID: 32128590

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Project description:The objective of this study was to compare the influence of beef production systems using additive combinations of growth-promotant technologies on meat quality. Steer calves (n = 120) were assigned to 1 of 4 treatments: 1) no technology (NT; control), 2) antibiotic treated (ANT; NT plus therapeutic antibiotics, monensin, and tylosin), 3) implant treated (IMP; ANT plus a series of three implants), and 4) beta-agonist treated (BA; IMP plus ractopamine-HCl). Muscle biopsy samples from the longissimus lumborum were extracted from a subset (n = 4 per treatment) of steers to evaluate expression of calpain-1, calpain-2, and calpastatin using real-time RT-PCR. Following carcass chilling, objective color (L*, a*, and b*) was evaluated. The right strip loin was removed from each carcass, portioned into 2.54-cm steaks, and designated to 7, 14, or 21 d postmortem aging periods for analysis of cook loss and Warner-Bratzler shear force (WBSF). The anterior face of each strip loin was used for analysis of crude fat and moisture. Treatment influenced (P < 0.001) L*, a*, and b*. The NT and IMP treatments had greater (P < 0.01) L* values, ANT was intermediate, and BA had the lowest (P < 0.01) L* values. The NT and IMP treatments had higher (P < 0.01) a* and b* values compared with ANT, which were higher (P < 0.01) than BA. Steaks from implanted steers (IMP and BA) tended (P ≤ 0.067) to exhibit higher a* and b* than steaks from nonimplanted steers. Cattle in the NT and ANT treatments produced steaks with increased (P < 0.01) crude fat percentage compared with the IMP and BA treatments, which were similar (P > 0.05). Percent moisture of NT steaks was lower (P < 0.01) than all other treatments, ANT was intermediate, and IMP and BA were similar (P > 0.05) and had the highest (P < 0.01) moisture content. Cook loss tended to be greater (P = 0.088) for implanted steers (IMP and BA) compared to nonimplanted steers (NT and ANT). Steaks from NT and ANT treatments were more tender (P < 0.05) than IMP and BA, which were similar (P > 0.05). Thus, WBSF was lower (P < 0.001) in nonimplanted than implanted steaks. Expression of calpastatin was increased (P ≤ 0.025) in ANT and BA treatments, and there was a tendency for expression of calpain-2 to be increased (P = 0.081) in ANT compared to NT. These results suggest that production systems with limited use of growth promoting technology produced strip loins with more crude fat, less moisture and cook loss, and improved tenderness.

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Exonuclease combinations reduce noises in 3D genomics technologies.

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Exonuclease combinations reduce noises in 3D genomics technologies.

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