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Related Concept Videos

RNA-seq03:21

RNA-seq

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RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases. 
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
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Methyl-binding DNA capture Sequencing for Patient Tissues
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High-Throughput Deep Sequencing for Mapping Mammalian DNA Methylation.

Paul M Lizardi, Qin Yan, Narendra Wajapeyee

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    |November 18, 2016
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    Methylation Mapping by Paired-End Sequencing (Methyl-MAPS) offers a novel method for genome-wide DNA methylation analysis. This technique accurately maps methylation status across CpG dinucleotides and repetitive elements without bisulfite conversion.

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    Area of Science:

    • Genomics
    • Epigenetics
    • Molecular Biology

    Background:

    • DNA methylation is a critical epigenetic modification regulating gene expression.
    • Accurate mapping of DNA methylation is essential for understanding various biological processes and diseases.
    • Existing methods often face limitations in sensitivity, resolution, or coverage of repetitive elements.

    Purpose of the Study:

    • To introduce and validate Methylation Mapping by Paired-End Sequencing (Methyl-MAPS) as a robust protocol for genome-wide DNA methylation analysis.
    • To demonstrate the capability of Methyl-MAPS to analyze methylation status in both unique and repetitive genomic regions.
    • To highlight the advantages of Methyl-MAPS, including high coverage and the preservation of large DNA fragments.

    Main Methods:

    • Methyl-MAPS utilizes enzymatic fractionation to separate methylated and unmethylated DNA compartments.
    • Paired-end sequencing is employed to capture both sequence information and physical distances between reads.
    • The protocol generates paired-end libraries with large DNA inserts (0.8-6 kb), avoiding bisulfite modification.

    Main Results:

    • Methyl-MAPS achieves comprehensive coverage, sampling approximately 80% of CpG dinucleotides in the genome.
    • The method successfully determines the methylation status of individual genomic loci, including those within repetitive elements.
    • Paired-end mapping allows for unique alignment of reads, effectively spanning repetitive sequences.

    Conclusions:

    • Methyl-MAPS provides a powerful and accurate approach for high-resolution DNA methylation profiling.
    • The protocol overcomes limitations of bisulfite-based methods by preserving large DNA fragments and enabling analysis of complex genomic regions.
    • Methyl-MAPS is a valuable tool for advancing epigenetic research and understanding the role of DNA methylation in health and disease.