Differential DNA methylation patterns in endo-siRNAs mediated silencing of LINE-1 retrotransposons

Long Chen; Jane E. Dahlstrom; Danny Rangasamy

doi:10.1007/978-1-4939-0931-5_15

Differential DNA methylation patterns in endo-siRNAs mediated silencing of LINE-1 retrotransposons

Long Chen, Jane E. Dahlstrom, Danny Rangasamy

Research output: Contribution to journal › Article › peer-review

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Abstract

Analyzing differences in DNA methylation is a powerful tool for assessing the effect of endo-siRNAs expression in the human genome. Here, we present a simple genome-wide DNA methylation assay that allows for a precise quantitative analysis of differences in the promoter of human long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in response to endogenous and exogenous expression of endo-siRNAs. Using the DNA bisulfite modification sequencing, we have optimized the method to detect small changes in heterogeneously methylated L1 repeats at multiple regions across the genome. We also provide guidance for analysis of primary bisulfite sequencing data and interpretation of the methylation status using the Web-based bisulfite sequencing DNA methylation (BISMA) analysis. This refined and reproducible assay can be performed even using a small amount of genomic DNA and is suitable for the analysis of clinical tissue samples.

Original language	English
Pages (from-to)	169-180
Number of pages	12
Journal	Methods in Molecular Biology
Volume	1173
DOIs	https://doi.org/10.1007/978-1-4939-0931-5_15
Publication status	Published - 2014

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title = "Differential DNA methylation patterns in endo-siRNAs mediated silencing of LINE-1 retrotransposons",

abstract = "Analyzing differences in DNA methylation is a powerful tool for assessing the effect of endo-siRNAs expression in the human genome. Here, we present a simple genome-wide DNA methylation assay that allows for a precise quantitative analysis of differences in the promoter of human long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in response to endogenous and exogenous expression of endo-siRNAs. Using the DNA bisulfite modification sequencing, we have optimized the method to detect small changes in heterogeneously methylated L1 repeats at multiple regions across the genome. We also provide guidance for analysis of primary bisulfite sequencing data and interpretation of the methylation status using the Web-based bisulfite sequencing DNA methylation (BISMA) analysis. This refined and reproducible assay can be performed even using a small amount of genomic DNA and is suitable for the analysis of clinical tissue samples.",

keywords = "Bisulfite data analysis, Breast cancer cells, DNA methylation, DNA sequencing, Endo-siRNAs, LINE-1, PCR",

author = "Long Chen and Dahlstrom, {Jane E.} and Danny Rangasamy",

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year = "2014",

doi = "10.1007/978-1-4939-0931-5_15",

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T1 - Differential DNA methylation patterns in endo-siRNAs mediated silencing of LINE-1 retrotransposons

AU - Chen, Long

AU - Dahlstrom, Jane E.

AU - Rangasamy, Danny

N1 - Publisher Copyright: © Springer Science+Business Media New York 2014.

PY - 2014

Y1 - 2014

N2 - Analyzing differences in DNA methylation is a powerful tool for assessing the effect of endo-siRNAs expression in the human genome. Here, we present a simple genome-wide DNA methylation assay that allows for a precise quantitative analysis of differences in the promoter of human long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in response to endogenous and exogenous expression of endo-siRNAs. Using the DNA bisulfite modification sequencing, we have optimized the method to detect small changes in heterogeneously methylated L1 repeats at multiple regions across the genome. We also provide guidance for analysis of primary bisulfite sequencing data and interpretation of the methylation status using the Web-based bisulfite sequencing DNA methylation (BISMA) analysis. This refined and reproducible assay can be performed even using a small amount of genomic DNA and is suitable for the analysis of clinical tissue samples.

AB - Analyzing differences in DNA methylation is a powerful tool for assessing the effect of endo-siRNAs expression in the human genome. Here, we present a simple genome-wide DNA methylation assay that allows for a precise quantitative analysis of differences in the promoter of human long interspersed nuclear element 1 (LINE-1 or L1) retrotransposons in response to endogenous and exogenous expression of endo-siRNAs. Using the DNA bisulfite modification sequencing, we have optimized the method to detect small changes in heterogeneously methylated L1 repeats at multiple regions across the genome. We also provide guidance for analysis of primary bisulfite sequencing data and interpretation of the methylation status using the Web-based bisulfite sequencing DNA methylation (BISMA) analysis. This refined and reproducible assay can be performed even using a small amount of genomic DNA and is suitable for the analysis of clinical tissue samples.

KW - Bisulfite data analysis

KW - Breast cancer cells

KW - DNA methylation

KW - DNA sequencing

KW - Endo-siRNAs

KW - LINE-1

KW - PCR

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U2 - 10.1007/978-1-4939-0931-5_15

DO - 10.1007/978-1-4939-0931-5_15

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VL - 1173

SP - 169

EP - 180

JO - Methods in Molecular Biology

JF - Methods in Molecular Biology

ER -

Differential DNA methylation patterns in endo-siRNAs mediated silencing of LINE-1 retrotransposons

Abstract

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