Targeted DNA methylation analysis by next-generation sequencing

Journal of Visualized Experiments : JoVE
Dustin R MasserWillard M Freeman

Abstract

The role of epigenetic processes in the control of gene expression has been known for a number of years. DNA methylation at cytosine residues is of particular interest for epigenetic studies as it has been demonstrated to be both a long lasting and a dynamic regulator of gene expression. Efforts to examine epigenetic changes in health and disease have been hindered by the lack of high-throughput, quantitatively accurate methods. With the advent and popularization of next-generation sequencing (NGS) technologies, these tools are now being applied to epigenomics in addition to existing genomic and transcriptomic methodologies. For epigenetic investigations of cytosine methylation where regions of interest, such as specific gene promoters or CpG islands, have been identified and there is a need to examine significant numbers of samples with high quantitative accuracy, we have developed a method called Bisulfite Amplicon Sequencing (BSAS). This method combines bisulfite conversion with targeted amplification of regions of interest, transposome-mediated library construction and benchtop NGS. BSAS offers a rapid and efficient method for analysis of up to 10 kb of targeted regions in up to 96 samples at a time that can be performed by...Continue Reading

Associated Clinical Trials

Citations

Apr 2, 2016·Proceedings of the National Academy of Sciences of the United States of America·Huibin ZhangSwaine L Chen
Aug 31, 2016·Environmental Science & Technology·David C VolzYinsheng Wang
Jan 13, 2018·GeroScience·Dustin R MasserWillard M Freeman
Nov 23, 2019·Essays in Biochemistry·Quentin Gouil, Andrew Keniry
Oct 22, 2016·Molecular Ecology Resources·Jean-René ArseneauMark Laflamme
Sep 28, 2017·BMB Reports·Sang-Eun JungHwan Young Lee
Mar 3, 2020·Frontiers in Plant Science·Jun Hyung LeeC Neal Stewart
Jul 6, 2018·Epigenetics & Chromatin·Simone RoehNadine Provençal
Mar 1, 2019·Life Science Alliance·Florian NoackFederico Calegari
Mar 1, 2017·International Journal of Molecular Sciences·Nicole van der MerweMaritha J Kotze
Oct 18, 2020·Proceedings of the National Academy of Sciences of the United States of America·Eric J KochMargaret McFall-Ngai
Nov 21, 2020·Communications Biology·Ana J Chucair-ElliottWillard M Freeman
Oct 27, 2020·Epigenetics : Official Journal of the DNA Methylation Society·Mayur DokeThangavel Samikkannu
Oct 11, 2017·Environmental Science & Technology Letters·Allison KupscoDavid C Volz

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Methods Mentioned

BETA
deamination
Amplicon Sequencing
PCR
electrophoresis
chip
DNA assay

Software Mentioned

fastq
NGS Core Tools
Ignore
Trim Sequences
BSAS
Trim
fasta
Map Reads to Reference

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