Development of a multiplex methylation-sensitive restriction enzyme-based SNP typing system for deconvolution of semen-containing mixtures

2021 ◽  
Author(s):  
Zeqin Li ◽  
Jintao Li ◽  
Yidan Li ◽  
Na Liu ◽  
Feng Liu ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
Snp Typing ◽  
Typing System ◽  
Methylation Sensitive Restriction Enzyme

scholarly journals DNA Methylation Landscape of 16 Canine Somatic Tissues by Methylation-Sensitive Restriction Enzyme-Based Next Generation Sequencing

2021 ◽  
Author(s):  
Jumpei Yamazaki ◽  
Yuki Matsumoto ◽  
Jaroslav Jelinek ◽  
Teita Ishizaki ◽  
Shingo Maeda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Next Generation Sequencing ◽  
Restriction Enzyme ◽  
Companion Animals ◽  
Next Generation ◽  
Cpg Sites ◽  
Somatic Tissues ◽  
Methylation Sensitive Restriction Enzyme ◽  
Generation Sequencing

Abstract Background: DNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Results: Using methylation-sensitive restriction enzyme-based next generation sequencing (Canine DREAM), we obtained canine DNA methylation maps from 16 somatic tissues. In total, we evaluated 130,861 CpG sites. The majority of CpG sites were either highly methylated (>70%, 52.5%-64.6% of all CpG sites analyzed) or unmethylated (<30%, 22.5%-28.0% of all CpG sites analyzed) which are methylation patterns similar to other species. The overall methylation status of CpG sites across the 32 methylomes were remarkably similar. However, the tissue types were clearly defined by principle component analysis and hierarchical clustering analysis with DNA methylome. We found 6416 CpG sites located closely at promoter region of genes and inverse correlation between DNA methylation and gene expression of these genes. Conclusions: Our study provides basic dataset for DNA methylation profiles in dogs.

scholarly journals DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS)

PLoS ONE ◽  
2019 ◽  
Vol 14 (4) ◽  
pp. e0214368 ◽  
Author(s):  
Giancarlo Bonora ◽  
Liudmilla Rubbi ◽  
Marco Morselli ◽  
Feiyang Ma ◽  
Constantinos Chronis ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Restriction Enzyme ◽  
Bisulfite Sequencing ◽  
Methylation Sensitive Restriction Enzyme

scholarly journals msgbsR: An R package for analysing methylation-sensitive restriction enzyme sequencing data

2018 ◽  
Vol 8 (1) ◽  
Author(s):  
Benjamin T. Mayne ◽  
Shalem Y. Leemaqz ◽  
Sam Buckberry ◽  
Carlos M. Rodriguez Lopez ◽  
Claire T. Roberts ◽  
...  
Keyword(s):  
Restriction Enzyme ◽  
R Package ◽  
Sequencing Data ◽  
Methylation Sensitive Restriction Enzyme

scholarly journals Restriction enzyme analysis and ribotyping distinguish Bordetella avium and Bordetella hinzii isolates

2000 ◽  
Vol 124 (1) ◽  
pp. 83-90 ◽  
Author(s):  
R. E. SACCO ◽  
K. B. REGISTER ◽  
G. E. NORDHOLM
Keyword(s):  
Restriction Endonuclease ◽  
Restriction Enzyme ◽  
Restriction Endonucleases ◽  
Enzyme Analysis ◽  
Restriction Enzyme Analysis ◽  
Bacterial Isolates ◽  
Chromosomal Dna ◽  
Bordetella Avium ◽  
Typing System

Fifty-seven bacterial isolates previously identified as Bordetella avium or B. hinzii were characterized by restriction enzyme analysis (REA) and/or ribotyping. Twenty restriction endonucleases were evaluated for REA. Digestion of chromosomal DNA from the 42 B. avium and 15 B. hinzii isolates with Hinf I produced 8 and 7 distinct fingerprint profiles, respectively. Digestion with DdeI further discriminated these Bordetella species and produced 12 fingerprint profiles for B. avium and 4 profiles of B. hinzii. In addition, B. avium isolates were clearly distinguishable from B. hinzii isolates by ribotyping with the restriction endonuclease PvuII. The ribotype patterns of these two species of Bordetella were unique when compared to previously reported ribotype patterns for B. bronchiseptica isolates. Since it was possible to discern differences among isolates within each Bordetella species by REA analysis, we suggest that REA could be used in developing a typing system based on the fingerprint profiles generated.

scholarly journals DNA methylation estimation using methylation-sensitive restriction enzyme bisulfite sequencing (MREBS)

2017 ◽  
Author(s):  
Giancarlo Bonora ◽  
Liudmilla Rubbi ◽  
Marco Morselli ◽  
Constantinos Chronis ◽  
Kathrin Plath ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Restriction Enzyme ◽  
Large Scale ◽  
Bisulfite Sequencing ◽  
Multiple Regression Model ◽  
Reduced Representation ◽  
A Genome ◽  
Genome Bisulfite Sequencing ◽  
Methylation Sensitive Restriction Enzyme ◽  
Wide Scale

ABSTRACTWhole-genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) are widely used for measuring DNA methylation levels on a genome-wide scale(1). Both methods have limitations: WGBS is expensive and prohibitive for most large-scale projects; RRBS only interrogates 6-12% of the CpGs in the human genome(16,19). Here, we introduce methylation-sensitive restriction enzyme bisulfite sequencing (MREBS) which has the reduced sequencing requirements of RRBS, but significantly expands the coverage of CpG sites in the genome. We built a multiple regression model that combines the two features of MREBS: the bisulfite conversion ratios of single cytosines (as in WGBS and RRBS) as well as the number of reads that cover each locus (as in MRE-seq(12)). This combined approach allowed us to estimate differential methylation across 60% of the genome using read count data alone, and where counts were sufficiently high in both samples (about 1.5% of the genome), our estimates were significantly improved by the single CpG conversion information. We show that differential DNA methylation values based on MREBS data correlate well with those based on WGBS and RRBS. This newly developed technique combines the sequencing cost of RRBS and DNA methylation estimates on a portion of the genome similar to WGBS, making it ideal for large-scale projects of mammalian genomes.

scholarly journals DNA methylation landscape of 16 canine somatic tissues by methylation-sensitive restriction enzyme-based next generation sequencing

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jumpei Yamazaki ◽  
Yuki Matsumoto ◽  
Jaroslav Jelinek ◽  
Teita Ishizaki ◽  
Shingo Maeda ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Next Generation Sequencing ◽  
Restriction Enzyme ◽  
Companion Animals ◽  
Next Generation ◽  
Cpg Sites ◽  
Somatic Tissues ◽  
Methylation Sensitive Restriction Enzyme ◽  
Generation Sequencing

AbstractDNA methylation plays important functions in gene expression regulation that is involved in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in companion animals like dog. Using methylation-sensitive restriction enzyme-based next generation sequencing (Canine DREAM), we obtained canine DNA methylation maps of 16 somatic tissues from two dogs. In total, we evaluated 130,861 CpG sites. The majority of CpG sites were either highly methylated (> 70%, 52.5–64.6% of all CpG sites analyzed) or unmethylated (< 30%, 22.5–28.0% of all CpG sites analyzed) which are methylation patterns similar to other species. The overall methylation status of CpG sites across the 32 methylomes were remarkably similar. However, the tissue types were clearly defined by principle component analysis and hierarchical clustering analysis with DNA methylome. We found 6416 CpG sites located closely at promoter region of genes and inverse correlation between DNA methylation and gene expression of these genes. Our study provides basic dataset for DNA methylation profiles in dogs.

scholarly journals Hypermethylated RASSF1A in Maternal Plasma: A Universal Fetal DNA Marker that Improves the Reliability of Noninvasive Prenatal Diagnosis

2006 ◽  
Vol 52 (12) ◽  
pp. 2211-2218 ◽  
Author(s):  
KC Allen Chan ◽  
Chunming Ding ◽  
Ageliki Gerovassili ◽  
Sze W Yeung ◽  
Rossa WK Chiu ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Restriction Enzyme ◽  
False Negative ◽  
Chorionic Villus ◽  
Maternal Plasma ◽  
Enzyme Digestion ◽  
Restriction Enzyme Digestion ◽  
Fetal Dna ◽  
Prenatal Diagnostic ◽  
Methylation Sensitive Restriction Enzyme

Abstract Background: We recently demonstrated that the promoter of the RASSF1A gene is hypermethylated in the placenta and hypomethylated in maternal blood cells. This methylation pattern allows the use of methylation-sensitive restriction enzyme digestion for detecting the placental-derived hypermethylated RASSF1A sequences in maternal plasma. Methods: We performed real-time PCR after methylation-sensitive restriction enzyme digestion to detect placental-derived RASSF1A sequences in the plasma of 28 1st-trimester and 43 3rd-trimester pregnant women. We used maternal plasma to perform prenatal fetal rhesus D (RhD) blood group typing for 54 early-gestation RhD-negative women, with hypermethylated RASSF1A as the positive control for fetal DNA detection. Results: Hypermethylated RASSF1A sequences were detectable in the plasma of all 71 pregnant women. The genotype of plasma RASSF1A after enzyme digestion was identical to the fetal genotype in each case, thus confirming its fetal origin. Nineteen of the 54 pregnant women undergoing prenatal fetal RhD genotyping showed undetectable RHD sequences in their plasma DNA samples. The fetal DNA control, RASSF1A, was not detectable in 4 of the 19 women. Subsequent chorionic villus sample analysis revealed that 2 of these 4 women with negative RHD and RASSF1A signals were in fact carrying RhD-positive fetuses. Conclusions: Hypermethylated RASSF1A is a universal marker for fetal DNA and is readily detectable in maternal plasma. When applied to prenatal RhD genotyping, this marker allows the detection of false-negative results caused by low fetal DNA concentrations in maternal plasma. This new marker can also be applied to many other prenatal diagnostic and monitoring scenarios.

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