Locus-Specific DNA Methylation Analysis by Targeted Deep Bisulfite Sequencing

2018 ◽  
pp. 351-366 ◽  
Author(s):  
Elsa Leitão ◽  
Jasmin Beygo ◽  
Michael Zeschnigk ◽  
Ludger Klein-Hitpass ◽  
Marcel Bargull ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Methylation Analysis ◽  
Dna Methylation Analysis

scholarly journals Quantitative and multiplexed DNA methylation analysis using long-read single-molecule real-time bisulfite sequencing (SMRT-BS)

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Yao Yang ◽  
Robert Sebra ◽  
Benjamin S Pullman ◽  
Wanqiong Qiao ◽  
Inga Peter ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Real Time ◽  
Single Molecule ◽  
Bisulfite Sequencing ◽  
Methylation Analysis ◽  
Long Read ◽  
Dna Methylation Analysis

scholarly journals RnBeads 2.0: comprehensive analysis of DNA methylation data

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Fabian Müller ◽  
Michael Scherer ◽  
Yassen Assenov ◽  
Pavlo Lutsik ◽  
Jörn Walter ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Additional Data ◽  
Epigenetic Mark ◽  
Methylation Analysis ◽  
Data Types ◽  
Large Numbers ◽  
Computational Resources ◽  
Genome Scale ◽  
Dna Methylation Analysis

Abstract DNA methylation is a widely investigated epigenetic mark with important roles in development and disease. High-throughput assays enable genome-scale DNA methylation analysis in large numbers of samples. Here, we describe a new version of our RnBeads software - an R/Bioconductor package that implements start-to-finish analysis workflows for Infinium microarrays and various types of bisulfite sequencing. RnBeads 2.0 (https://rnbeads.org/) provides additional data types and analysis methods, new functionality for interpreting DNA methylation differences, improved usability with a novel graphical user interface, and better use of computational resources. We demonstrate RnBeads 2.0 in four re-runnable use cases focusing on cell differentiation and cancer.

scholarly journals DNA methylation analysis and editing in single mammalian oocytes

2019 ◽  
Vol 116 (20) ◽  
pp. 9883-9892 ◽  
Author(s):  
Yanchang Wei ◽  
Jingwen Lang ◽  
Qian Zhang ◽  
Cai-Rong Yang ◽  
Zhen-Ao Zhao ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Functional Analysis ◽  
Bisulfite Sequencing ◽  
High Efficiency ◽  
Coat Color ◽  
Polar Body ◽  
Methylation Analysis ◽  
Parthenogenetic Development ◽  
First Polar Body ◽  
Dna Methylation Analysis

Mammalian oocytes carry specific nongenetic information, including DNA methylation to the next generation, which is important for development and disease. However, evaluation and manipulation of specific methylation for both functional analysis and therapeutic purposes remains challenging. Here, we demonstrate evaluation of specific methylation in single oocytes from its sibling first polar body (PB1) and manipulation of specific methylation in single oocytes by microinjection-mediated dCas9-based targeted methylation editing. We optimized a single-cell bisulfite sequencing approach with high efficiency and demonstrate that the PB1 carries similar methylation profiles at specific regions to its sibling oocyte. By bisulfite sequencing of a single PB1, the methylation information regarding agouti viable yellow (Avy)-related coat color, as well as imprinting linked parthenogenetic development competency, in a single oocyte can be efficiently evaluated. Microinjection-based dCas9-Tet/Dnmt–mediated methylation editing allows targeted manipulation of specific methylation in single oocytes. By targeted methylation editing, we were able to reverse Avy-related coat color, generate full-term development of bimaternal mice, and correct familial Angelman syndrome in a mouse model. Our work will facilitate the investigation of specific methylation events in oocytes and provides a strategy for prevention and correction of maternally transmitted nongenetic disease or disorders.

scholarly journals Bisulfite sequencing Data Presentation and Compilation (BDPC) web server--a useful tool for DNA methylation analysis

2008 ◽  
Vol 36 (5) ◽  
pp. e34-e34 ◽  
Author(s):  
C. Rohde ◽  
Y. Zhang ◽  
T. P. Jurkowski ◽  
H. Stamerjohanns ◽  
R. Reinhardt ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Web Server ◽  
Sequencing Data ◽  
Methylation Analysis ◽  
Data Presentation ◽  
Bisulfite Sequencing Data ◽  
Dna Methylation Analysis

scholarly journals BitMapperBS: a fast and accurate read aligner for whole-genome bisulfite sequencing

2018 ◽  
Author(s):  
Haoyu Cheng ◽  
Yun Xu
Keyword(s):  
Dna Methylation ◽  
Bisulfite Sequencing ◽  
Standard Technique ◽  
Whole Genome ◽  
Sequencing Data ◽  
Methylation Analysis ◽  
Whole Genome Bisulfite Sequencing ◽  
Genome Bisulfite Sequencing ◽  
Computational Bottleneck ◽  
Dna Methylation Analysis

AbstractAs a gold-standard technique for DNA methylation analysis, whole-genome bisulfite sequencing (WGBS) helps researchers to study the genome-wide DNA methylation at single-base resolution. However, aligning WGBS reads to the large reference genome is a major computational bottleneck in DNA methylation analysis projects. Although several WGBS aligners have been developed in recent years, it is difficult for them to efficiently process the ever-increasing bisulfite sequencing data. Here we propose BitMapperBS, an ultrafast and memory-efficient aligner that is designed for WGBS reads. To improve the performance of BitMapperBS, we propose various strategies specifically for the challenges that are unique to the WGBS aligners, which are ignored in most existing methods. Our experiments on real and simulated datasets show that BitMapperBS is one order of magnitude faster than the state-of-the-art WGBS aligners, while achieves similar or better sensitivity and precision. BitMapperBS is freely available at https://github.com/chhylp123/BitMapperBS.

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