The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements

Gwen Hoad, Kristina Harrison

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

Epigenetic modifications, such as DNA methylation, can contribute to gene regulation and chromosomal stability. There are several methods and techniques available for methylation analysis, ranging from global methylation to gene-specific targeted regions. Bisulfite conversion enables numerous methodologies to be used for downstream applications, including pyrosequencing which measures DNA methylation at an individual CpG site level. This allows specific regions of interest to be targeted for DNA methylation analysis. Designing and optimizing pyrosequencing assays correctly is vital for the interpretation of results.Dysregulation of DNA methylation has been implicated in human diseases, with regions such as repeat elements commonly altered. Human population studies investigating these tend to use consensus sequences to target repeat elements. However, these elements have high mutational rates, particularly Alu sequences, which could lead to assay bias and masking of changes at a regional level. Therefore, it may be more beneficial to target specific repeat elements depending upon their chromosomal location, rather than analyzing overall methylation levels.

Original languageEnglish
Title of host publicationSpringer Protocols
Subtitle of host publicationMethods in Molecular Biology
PublisherSpringer
Pages17-27
Number of pages11
DOIs
Publication statusPublished - 6 Aug 2015

Publication series

NameMethods in Molecular Biology
PublisherHumana Press
ISSN (Print)1064-3745

Fingerprint

DNA Methylation
Methylation
Chromosomal Instability
Consensus Sequence
Epigenomics
Genes
Population

Keywords

  • DNA methylation
  • epigenetics
  • pyrosequencing
  • bisulfite conversion
  • CpGs
  • bisulfite sequencing

Cite this

Hoad, G., & Harrison, K. (2015). The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements. In Springer Protocols: Methods in Molecular Biology (pp. 17-27). (Methods in Molecular Biology). Springer . https://doi.org/10.1007/7651_2015_285

The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements. / Hoad, Gwen; Harrison, Kristina.

Springer Protocols: Methods in Molecular Biology. Springer , 2015. p. 17-27 (Methods in Molecular Biology).

Research output: Chapter in Book/Report/Conference proceedingChapter

Hoad, G & Harrison, K 2015, The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements. in Springer Protocols: Methods in Molecular Biology. Methods in Molecular Biology, Springer , pp. 17-27. https://doi.org/10.1007/7651_2015_285
Hoad G, Harrison K. The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements. In Springer Protocols: Methods in Molecular Biology. Springer . 2015. p. 17-27. (Methods in Molecular Biology). https://doi.org/10.1007/7651_2015_285
Hoad, Gwen ; Harrison, Kristina. / The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements. Springer Protocols: Methods in Molecular Biology. Springer , 2015. pp. 17-27 (Methods in Molecular Biology).
@inbook{b7994f03e0d648999fcf200470503978,
title = "The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements",
abstract = "Epigenetic modifications, such as DNA methylation, can contribute to gene regulation and chromosomal stability. There are several methods and techniques available for methylation analysis, ranging from global methylation to gene-specific targeted regions. Bisulfite conversion enables numerous methodologies to be used for downstream applications, including pyrosequencing which measures DNA methylation at an individual CpG site level. This allows specific regions of interest to be targeted for DNA methylation analysis. Designing and optimizing pyrosequencing assays correctly is vital for the interpretation of results.Dysregulation of DNA methylation has been implicated in human diseases, with regions such as repeat elements commonly altered. Human population studies investigating these tend to use consensus sequences to target repeat elements. However, these elements have high mutational rates, particularly Alu sequences, which could lead to assay bias and masking of changes at a regional level. Therefore, it may be more beneficial to target specific repeat elements depending upon their chromosomal location, rather than analyzing overall methylation levels.",
keywords = "DNA methylation, epigenetics, pyrosequencing , bisulfite conversion, CpGs, bisulfite sequencing",
author = "Gwen Hoad and Kristina Harrison",
year = "2015",
month = "8",
day = "6",
doi = "10.1007/7651_2015_285",
language = "English",
series = "Methods in Molecular Biology",
publisher = "Springer",
pages = "17--27",
booktitle = "Springer Protocols",

}

TY - CHAP

T1 - The Design and Optimization of DNA Methylation Pyrosequencing Assays Targeting Region-Specific Repeat Elements

AU - Hoad, Gwen

AU - Harrison, Kristina

PY - 2015/8/6

Y1 - 2015/8/6

N2 - Epigenetic modifications, such as DNA methylation, can contribute to gene regulation and chromosomal stability. There are several methods and techniques available for methylation analysis, ranging from global methylation to gene-specific targeted regions. Bisulfite conversion enables numerous methodologies to be used for downstream applications, including pyrosequencing which measures DNA methylation at an individual CpG site level. This allows specific regions of interest to be targeted for DNA methylation analysis. Designing and optimizing pyrosequencing assays correctly is vital for the interpretation of results.Dysregulation of DNA methylation has been implicated in human diseases, with regions such as repeat elements commonly altered. Human population studies investigating these tend to use consensus sequences to target repeat elements. However, these elements have high mutational rates, particularly Alu sequences, which could lead to assay bias and masking of changes at a regional level. Therefore, it may be more beneficial to target specific repeat elements depending upon their chromosomal location, rather than analyzing overall methylation levels.

AB - Epigenetic modifications, such as DNA methylation, can contribute to gene regulation and chromosomal stability. There are several methods and techniques available for methylation analysis, ranging from global methylation to gene-specific targeted regions. Bisulfite conversion enables numerous methodologies to be used for downstream applications, including pyrosequencing which measures DNA methylation at an individual CpG site level. This allows specific regions of interest to be targeted for DNA methylation analysis. Designing and optimizing pyrosequencing assays correctly is vital for the interpretation of results.Dysregulation of DNA methylation has been implicated in human diseases, with regions such as repeat elements commonly altered. Human population studies investigating these tend to use consensus sequences to target repeat elements. However, these elements have high mutational rates, particularly Alu sequences, which could lead to assay bias and masking of changes at a regional level. Therefore, it may be more beneficial to target specific repeat elements depending upon their chromosomal location, rather than analyzing overall methylation levels.

KW - DNA methylation

KW - epigenetics

KW - pyrosequencing

KW - bisulfite conversion

KW - CpGs

KW - bisulfite sequencing

U2 - 10.1007/7651_2015_285

DO - 10.1007/7651_2015_285

M3 - Chapter

T3 - Methods in Molecular Biology

SP - 17

EP - 27

BT - Springer Protocols

PB - Springer

ER -