Systems Biology


    Protocols in Current Issue
    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: 7814, 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: 6472, 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: 12283, 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: 5229, 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 ...