scholarly journals Single-base mapping of m6A by an antibody-independent method

2019 ◽  
Author(s):  
Zhang Zhang ◽  
Li-Qian Chen ◽  
Yu-Li Zhao ◽  
Cai-Guang Yang ◽  
Ian A Roundtree ◽  
...  
Keyword(s):  
High Throughput ◽  
High Reliability ◽  
Methylation Status ◽  
Independent Method ◽  
Location Information ◽  
Single Nucleotide ◽  
Single Base ◽  
Identification Method ◽  
Nucleotide Specificity ◽  
Base Mapping

AbstractN6-methyladenosine (m6A) is one of the most abundant mRNA modifications in eukaryotes, involved in various pivotal processes of RNA metabolism. The most popular high-throughput m6A identification method depends on the anti-m6A antibody but suffers from poor reproducibility and limited resolution. Exact location information is of great value for understanding the dynamics, machinery and functions of m6A. Here we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease (m6A-sensitive RNA-Endoribonuclease-Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic, single-base m6A maps generated by m6A-REF-seq quantitatively displayed an explicit distribution pattern with enrichment on stop codons. Independent methods were used to validate the methylation status and abundance of individual m6A sites, confirming the high reliability and accuracy of m6A-REF-seq. We applied this method on five tissues from human, mouse and rat, showing that m6A sites were conserved with single nucleotide specificity and tend to cluster among species.

scholarly journals Single-base mapping of m6A by an antibody-independent method

2019 ◽  
Vol 5 (7) ◽  
pp. eaax0250 ◽  
Author(s):  
Zhang Zhang ◽  
Li-Qian Chen ◽  
Yu-Li Zhao ◽  
Cai-Guang Yang ◽  
Ian A. Roundtree ◽  
...  
Keyword(s):  
High Throughput ◽  
Messenger Rna ◽  
High Reliability ◽  
Methylation Status ◽  
Rna Modifications ◽  
Single Nucleotide ◽  
Single Base ◽  
Identification Method ◽  
Nucleotide Specificity ◽  
Base Mapping

N6-methyladenosine (m6A) is one of the most abundant messenger RNA modifications in eukaryotes involved in various pivotal processes of RNA metabolism. The most popular high-throughput m6A identification method depends on the anti-m6A antibody but suffers from poor reproducibility and limited resolution. Exact location information is of great value for understanding the dynamics, machinery, and functions of m6A. Here, we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease recognizing ACA motif (m6A-sensitive RNA-Endoribonuclease–Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic, single-base m6A maps generated by m6A-REF-seq quantitatively displayed an explicit distribution pattern with enrichment near stop codons. We used independent methods to validate methylation status and abundance of individual m6A sites, confirming the high reliability and accuracy of m6A-REF-seq. We applied this method on five tissues from human, mouse, and rat, showing that m6A sites are conserved with single-nucleotide specificity and tend to cluster among species.

scholarly journals The development and validation of EpiComet-Chip, a modified high-throughput comet assay for the assessment of DNA methylation status

2017 ◽  
Vol 58 (7) ◽  
pp. 508-521 ◽  
Author(s):  
Todd A. Townsend ◽  
Marcus C. Parrish ◽  
Bevin P. Engelward ◽  
Mugimane G. Manjanatha
Keyword(s):  
Dna Methylation ◽  
Comet Assay ◽  
High Throughput ◽  
Methylation Status ◽  
Development And Validation

scholarly journals Precision of High-Throughput Single-Nucleotide Polymorphism Genotyping with Fingernail DNA: Comparison with Blood DNA

2008 ◽  
Vol 54 (10) ◽  
pp. 1746-1748 ◽  
Author(s):  
Mitsuko Nakashima ◽  
Masayoshi Tsuda ◽  
Akira Kinoshita ◽  
Tatsuya Kishino ◽  
Shinji Kondo ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Throughput ◽  
Single Nucleotide Polymorphism Genotyping ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide

ANALYSIS OF THE ERROR IN DETERMINING THE EQUIVALENT SIZE OF A DEFECT BY THE STANDARDLESS METHOD DURING ULTRASONIC TESTING

2021 ◽  
pp. 50-57
Author(s):  
A. N. Kireev ◽  
M. A. Kireeva
Keyword(s):  
Relative Error ◽  
High Reliability ◽  
Ultrasonic Method ◽  
Experimental Studies ◽  
Standard Samples ◽  
Defect Identification ◽  
Identification Method ◽  
Maximum Value ◽  
Software Product ◽  
The Relationship

The article provides a review and analysis of the defect identification method for determining the size of discontinuities when diagnosing various machine parts and units by the manual ultrasonic method. This method makes it possible to determine the equivalent size of discontinuities of various types without using standard samples of an enterprise: point planar and volumetric; extended planar and volumetric. The method is based on the use of the relationship between the amplitude and time characteristics of the echo signal from the discontinuity and the backside signal in the object being diagnosed and the equivalent size of the discontinuity. The article presents the mathematical apparatus for the implementation of this method. Also presented is a software product that allows you to automate calculations when using this defect identification method. The article contains experimental studies of the method for determining the equivalent dimensions of discontinuities of various types, which have shown its high reliability. The maximum value of the relative error in determining the equivalent size of a point planar discontinuity was 2.867 %. The maximum value of the relative error in determining the equivalent size of a point volumetric discontinuity was 1.986 %. The maximum value of the relative error in determining the transverse equivalent size of an extended planar discontinuity was 0.667 %. The maximum value of the relative error in determining the transverse equivalent size of an extended volumetric discontinuity was 1.95 %.

scholarly journals Flow Cytometric Platform for High-Throughput Single Nucleotide Polymorphism Analysis

BioTechniques ◽  
2001 ◽  
Vol 30 (3) ◽  
pp. 661-669 ◽  
Author(s):  
J.D. Taylor ◽  
D. Briley ◽  
Q. Nguyen ◽  
K. Long ◽  
M.A. Iannone ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
High Throughput ◽  
Polymorphism Analysis ◽  
Single Nucleotide Polymorphism Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Flow Cytometric

scholarly journals Investigation of Genetic Relationships within Miscanthus using SNP Markers Identified using SLAF-Seq

2021 ◽  
Author(s):  
ZHIYONG Chen ◽  
Yancen He ◽  
Yasir Iqbal ◽  
Yanlan Shi ◽  
Hongmei Huang ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Genetic Relationships ◽  
Female Parent ◽  
Snp Markers ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Sequencing Method ◽  
Specific Locus

Abstract Background: Miscanthus, which is a leading dedicated-energy grass in Europe and in parts of Asia, is expected to play a key role in the development of the future bioeconomy. However, due to its complex genetic background, it is difficult to investigate phylogenetic relationships and the evolution of gene function in this genus. Here, we investigated 50 Miscanthus germplasms: 1 female parent (M. lutarioriparius), 30 candidate male parents (M. lutarioriparius, M. sinensis, and M. sacchariflorus), and 19 offspring. We used high-throughput Specific-Locus Amplified Fragment sequencing (SLAF-seq) to identify informative single nucleotide polymorphisms (SNPs) in all germplasms.Results: We identified 800,081 SLAF tags, of which 160,368 were polymorphic. Each tag was 264–364 bp long. The obtained SNPs were used to investigate genetic relationships within Miscanthus. We constructed a phylogenetic tree of the 50 germplasms using the obtained SNPs, and found that the germplasms fell into two clades: one clade of M. sinensis only and one clade that included the offspring, M. lutarioriparius, and M. sacchariflorus. Genetic cluster analysis indicated that M. lutarioriparius germplasm C3 was the most likely male parent of the offspring.Conclusions: As a high-throughput sequencing method, SLAF-seq can be used to identify informative SNPs in Miscanthus germplasms and to rapidly characterize genetic relationships within this genus. Our results will support the development of breeding programs utilizing Miscanthus cultivars with elite biomass- or fiber-production potential.

scholarly journals The presence of a single-nucleotide mismatch in linker increases the fluorescence of guanine-enhanced DNA-templated Ag nanoclusters and their application for highly sensitive detection of cyanide

RSC Advances ◽  
2018 ◽  
Vol 8 (72) ◽  
pp. 41464-41471 ◽  
Author(s):  
Jun Peng ◽  
Jian Ling ◽  
Qiu-Lin Wen ◽  
Yu Li ◽  
Qiu-E. Cao ◽  
...  
Keyword(s):  
Sensitive Detection ◽  
Single Nucleotide ◽  
Single Base ◽  
Highly Sensitive ◽  
Nucleotide Mismatch ◽  
Single Nucleotide Mismatch ◽  
Ag Nanoclusters ◽  
Ag Ncs ◽  
Highly Sensitive Detection

Single-base mismatched G-rich enhanced DNA-Ag NCs for cyanide detection.

The Phenolyzer Suite: Prioritizing the Candidate Genes Involved in Microtia

2019 ◽  
Vol 128 (6) ◽  
pp. 556-562 ◽  
Author(s):  
Huang Xin ◽  
Wang Changchen ◽  
Liu Lei ◽  
Yang Meirong ◽  
Zhang Ye ◽  
...  
Keyword(s):  
Candidate Genes ◽  
High Throughput ◽  
Potential Candidate ◽  
Single Nucleotide Variants ◽  
Gene Score ◽  
Single Nucleotide ◽  
Research Directions ◽  
Score System ◽  
Pathogenic Genes ◽  
First Time

Objective: Microtia is a congenital malformation of the external ear. Great progress about the genetic of microtia has been made in recent years. This article was to prioritize the potential candidate pathogenic genes of microtia based on existing studies and reports, with the purpose of narrowing the range of following study scientifically and quickly. Method: A computational tool called Phenolyzer (phenotype-based gene analyzer) was used to prioritize microtia genes. Microtia, as a query term, was input in the interface of Phenolyzer. After several steps, including disease match, gene query, gene score system, seed gene growth, and gene ranking, the final results about genetic information of microtia were provided. Then we tracked details of the top 10 genes ranked by Phenolyzer on the basis of previous reports. Results: We detected 10 348 genes associated with microtia or related syndromes, and 78 genes of those genes belonged to seed genes. Every gene was given a score, and the gene with higher scores was more likely influence microtia. The top 10 ranked genes included HOXA2, CHD7, CDT1, ORC1, ORC4, ORC6, CDC6, MED12, TWIST1, and GLI3. Otherwise, four gene-gene interactions were displayed. Conclusion: This article prioritized candidate genes of microtia for the first time. High-throughput methods provide tens of thousands of single-nucleotide variants, indels, and structural variants, and only a handful are relevant to microtia or associated syndromes. Combine the ranked potential pathogenic genes list from Phenolyzer with the results of samples provided by high-throughput methods, and more precise research directions are presented.

Sign in / Sign up

Export Citation Format

Share Document