Systems Biology


    Protocols in Current Issue
    A Molecular Cloning and Sanger Sequencing-based Protocol for Detecting Site-specific DNA Methylation
    Authors:  Wei Guo, Anthony Cannon and Damon Lisch, date: 05/05/2022, view: 519, Q&A: 0

    DNA methylation is a conserved chemical modification, by which methyl groups are added to the cytosine of DNA molecules. Methylation can influence gene expression without changing the sequence of a particular gene. This epigenetic effect is an intriguing phenomenon that has puzzled biologists for years. By probing the temporal and spatial patterns

    Whole-genome Methylation Analysis of APOBEC Enzyme-converted DNA (~5 kb) by Nanopore Sequencing

    In recent years, DNA methylation research has been accelerated by the advent of nanopore sequencers. However, read length has been limited by the constraints of base conversion using the bisulfite method, making analysis of chromatin content difficult. The read length of the previous method combining bisulfite conversion and long-read sequencing

    Detecting Differentially Methylated Promoters in Genes Related to Disease Phenotypes Using R
    Authors:  Jordi Martorell Marugán and Pedro Carmona-Sáez, date: 06/05/2021, view: 2010, Q&A: 0

    DNA methylation in gene promoters plays a major role in gene expression regulation, and alterations in methylation patterns have been associated with several diseases. In this context, different software suites and statistical methods have been proposed to analyze differentially methylated positions and regions. Among them, the novel statistical

    Reduced Representation Bisulfite Sequencing in Maize
    Authors:  Fei-Man Hsu, Chung-Ju Rachel Wang and Pao-Yang Chen, date: 03/20/2018, view: 6523, Q&A: 0
    [Abstract] DNA methylation is an epigenetic modification that regulates plant development (Law and Jacobsen, 2010). Whole genome bisulfite sequencing (WGBS) is a state-of-the-art method for profiling genome-wide methylation patterns with single-base resolution (Cokus et al., 2008). However, for an organism with a large genome, e.g., the 2.1 ...
    Whole Genome Bisulfite Sequencing and DNA Methylation Analysis from Plant Tissue
    Authors:  Daniela Pignatta, George W. Bell and Mary Gehring, date: 02/20/2015, view: 18439, Q&A: 0
    [Abstract] This protocol describes whole genome bisulfite-sequencing library preparation from plant tissue and subsequent data analysis. Allele-specific methylation analysis and genome-wide identification of differentially methylated regions are additional features of the analysis procedure.
    Library Construction for Genome-wide Bisulfite Sequencing in Plants
    Authors:  David Moraga Amador, Chenggang Wang, Kevin H. Holland and Zhonglin Mou, date: 12/20/2013, view: 13164, Q&A: 0
    [Abstract] DNA methylation is the most studied epigenetic modification, which involves the addition of a methyl group to the carbon-5 position of cytosine residues in DNA. DNA methylation is important for the regulation of gene expression. Bisulfite sequencing is the gold standard technique for determining genome-wide DNA methylation profiles in eukaryotes. ...
    Quantitative Methylation Specific PCR (qMSP)
    Authors:  Triantafillos Liloglou and Georgios Nikolaidis, date: 08/20/2013, view: 30033, Q&A: 0
    [Abstract] Detection of low copies of methylated DNA targets in clinical specimens is challenging. The quantitative Methylation-Specific PCR (qMSP) assays were designed to specifically amplify bisulphite-converted methylated DNA target sequences in the presence of an excess of unmethylated counterpart sequences. These qMSP assays are real-time PCR assays ...
    Detection of DNA Methylation Changes Surrounding Transposable Elements
    Authors:  Beery Yaakov and Khalil Kashkush, date: 06/05/2013, view: 10177, Q&A: 0
    [Abstract] Transposable elements (TEs) are a major component of all genomes, thus the epigenetic mechanisms controlling their activity is an important field of study. Cytosine methylation is one of the factors regulating the transcription and transposition of TEs, alongside Histone modifications and small RNAs. Adapter PCR-based methods [such as Amplified ...
    DNA Methylation Profiling Using Infinium Methylation Assay
    [Abstract] The Infinium Human Methylation 450 BeadChip technology allows the rapid quantitative DNA methylation analysis of more than 485,000 CpG dinucleotides located across the genome. The method utilizes sodium bisulfite treatment of genomic DNA to convert unmethylated cytosine residues into uracils whereas methylated cytosines remain unchanged. Modified ...

    We use cookies on this site to enhance your user experience. By using our website, you are agreeing to allow the storage of cookies on your computer.