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Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues

DNA methylation of CpGs located in two types of repetitive elements—LINE1 (L1) and Alu—is used to assess “global” changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitiv...

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Autores principales: Price, E. Magda, Cotton, Allison M., Peñaherrera, Maria S., McFadden, Deborah E., Kobor, Michael S., Robinson, Wendy
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Landes Bioscience 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398992/
https://www.ncbi.nlm.nih.gov/pubmed/22531475
http://dx.doi.org/10.4161/epi.20221
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author Price, E. Magda
Cotton, Allison M.
Peñaherrera, Maria S.
McFadden, Deborah E.
Kobor, Michael S.
Robinson, Wendy
author_facet Price, E. Magda
Cotton, Allison M.
Peñaherrera, Maria S.
McFadden, Deborah E.
Kobor, Michael S.
Robinson, Wendy
author_sort Price, E. Magda
collection PubMed
description DNA methylation of CpGs located in two types of repetitive elements—LINE1 (L1) and Alu—is used to assess “global” changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNA methylation. Few studies have investigated whether repetitive element DNA methylation is associated with DNA methylation at other genomic regions, or the biological and technical factors that influence potential associations. Here, we assess L1 and Alu DNA methylation by Pyrosequencing of consensus sequences and using subsets of probes included in the Illumina Infinium HumanMethylation27 BeadChip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNA methylation. Additionally, we compare Pyrosequencing results for repetitive elements to average DNA methylation of CpG islands, as assessed by array probes classified into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNA methylation. Correlation of DNA methylation suggests an association between L1 and weak CpG island DNA methylation in some of the tissues examined. We caution, however, that L1, Alu and CpG island DNA methylation are distinct measures of dispersed DNA methylation and one should not be used in lieu of another. Analysis of DNA methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways.
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spelling pubmed-33989922012-07-18 Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues Price, E. Magda Cotton, Allison M. Peñaherrera, Maria S. McFadden, Deborah E. Kobor, Michael S. Robinson, Wendy Epigenetics Research Paper DNA methylation of CpGs located in two types of repetitive elements—LINE1 (L1) and Alu—is used to assess “global” changes in DNA methylation in studies of human disease and environmental exposure. L1 and Alu contribute close to 30% of all base pairs in the human genome and transposition of repetitive elements is repressed through DNA methylation. Few studies have investigated whether repetitive element DNA methylation is associated with DNA methylation at other genomic regions, or the biological and technical factors that influence potential associations. Here, we assess L1 and Alu DNA methylation by Pyrosequencing of consensus sequences and using subsets of probes included in the Illumina Infinium HumanMethylation27 BeadChip array. We show that evolutionary age and assay method affect the assessment of repetitive element DNA methylation. Additionally, we compare Pyrosequencing results for repetitive elements to average DNA methylation of CpG islands, as assessed by array probes classified into strong, weak and non-islands. We demonstrate that each of these dispersed sequences exhibits different patterns of tissue-specific DNA methylation. Correlation of DNA methylation suggests an association between L1 and weak CpG island DNA methylation in some of the tissues examined. We caution, however, that L1, Alu and CpG island DNA methylation are distinct measures of dispersed DNA methylation and one should not be used in lieu of another. Analysis of DNA methylation data is complex and assays may be influenced by environment and pathology in different or complementary ways. Landes Bioscience 2012-06-01 /pmc/articles/PMC3398992/ /pubmed/22531475 http://dx.doi.org/10.4161/epi.20221 Text en Copyright © 2012 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited.
spellingShingle Research Paper
Price, E. Magda
Cotton, Allison M.
Peñaherrera, Maria S.
McFadden, Deborah E.
Kobor, Michael S.
Robinson, Wendy
Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues
title Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues
title_full Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues
title_fullStr Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues
title_full_unstemmed Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues
title_short Different measures of “genome-wide” DNA methylation exhibit unique properties in placental and somatic tissues
title_sort different measures of “genome-wide” dna methylation exhibit unique properties in placental and somatic tissues
topic Research Paper
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3398992/
https://www.ncbi.nlm.nih.gov/pubmed/22531475
http://dx.doi.org/10.4161/epi.20221
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