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High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3

BACKGROUND: Methylation of DNA at CpG sites is an epigenetic modification and a potential modifier of disease risk, possibly mediating environmental effects. Currently, DNA methylation is commonly assessed using specific microarrays that sample methylation at a few % of all methylated sites. METHODS...

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Autores principales: Söderhäll, Cilla, Reinius, Lovisa E., Salmenperä, Pertteli, Gentile, Massimiliano, Acevedo, Nathalie, Konradsen, Jon R., Nordlund, Björn, Hedlin, Gunilla, Scheynius, Annika, Myllykangas, Samuel, Kere, Juha
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
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Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111952/
https://www.ncbi.nlm.nih.gov/pubmed/33971943
http://dx.doi.org/10.1186/s13148-021-01093-7
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author Söderhäll, Cilla
Reinius, Lovisa E.
Salmenperä, Pertteli
Gentile, Massimiliano
Acevedo, Nathalie
Konradsen, Jon R.
Nordlund, Björn
Hedlin, Gunilla
Scheynius, Annika
Myllykangas, Samuel
Kere, Juha
author_facet Söderhäll, Cilla
Reinius, Lovisa E.
Salmenperä, Pertteli
Gentile, Massimiliano
Acevedo, Nathalie
Konradsen, Jon R.
Nordlund, Björn
Hedlin, Gunilla
Scheynius, Annika
Myllykangas, Samuel
Kere, Juha
author_sort Söderhäll, Cilla
collection PubMed
description BACKGROUND: Methylation of DNA at CpG sites is an epigenetic modification and a potential modifier of disease risk, possibly mediating environmental effects. Currently, DNA methylation is commonly assessed using specific microarrays that sample methylation at a few % of all methylated sites. METHODS: To understand if significant information on methylation can be added by a more comprehensive analysis of methylation, we set up a quantitative method, bisulfite oligonucleotide-selective sequencing (Bs-OS-seq), and compared the data with microarray-derived methylation data. We assessed methylation at two asthma-associated genes, IL13 and ORMDL3, in blood samples collected from children with and without asthma and fractionated white blood cell types from healthy adult controls. RESULTS: Our results show that Bs-OS-seq can uncover vast amounts of methylation variation not detected by commonly used array methods. We found that high-density methylation information from even one gene can delineate the main white blood cell lineages. CONCLUSIONS: We conclude that high-resolution methylation studies can yield clinically important information at selected specific loci missed by array-based methods, with potential implications for future studies of methylation-disease associations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13148-021-01093-7.
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spelling pubmed-81119522021-05-11 High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3 Söderhäll, Cilla Reinius, Lovisa E. Salmenperä, Pertteli Gentile, Massimiliano Acevedo, Nathalie Konradsen, Jon R. Nordlund, Björn Hedlin, Gunilla Scheynius, Annika Myllykangas, Samuel Kere, Juha Clin Epigenetics Research BACKGROUND: Methylation of DNA at CpG sites is an epigenetic modification and a potential modifier of disease risk, possibly mediating environmental effects. Currently, DNA methylation is commonly assessed using specific microarrays that sample methylation at a few % of all methylated sites. METHODS: To understand if significant information on methylation can be added by a more comprehensive analysis of methylation, we set up a quantitative method, bisulfite oligonucleotide-selective sequencing (Bs-OS-seq), and compared the data with microarray-derived methylation data. We assessed methylation at two asthma-associated genes, IL13 and ORMDL3, in blood samples collected from children with and without asthma and fractionated white blood cell types from healthy adult controls. RESULTS: Our results show that Bs-OS-seq can uncover vast amounts of methylation variation not detected by commonly used array methods. We found that high-density methylation information from even one gene can delineate the main white blood cell lineages. CONCLUSIONS: We conclude that high-resolution methylation studies can yield clinically important information at selected specific loci missed by array-based methods, with potential implications for future studies of methylation-disease associations. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13148-021-01093-7. BioMed Central 2021-05-10 /pmc/articles/PMC8111952/ /pubmed/33971943 http://dx.doi.org/10.1186/s13148-021-01093-7 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Research
Söderhäll, Cilla
Reinius, Lovisa E.
Salmenperä, Pertteli
Gentile, Massimiliano
Acevedo, Nathalie
Konradsen, Jon R.
Nordlund, Björn
Hedlin, Gunilla
Scheynius, Annika
Myllykangas, Samuel
Kere, Juha
High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3
title High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3
title_full High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3
title_fullStr High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3
title_full_unstemmed High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3
title_short High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3
title_sort high-resolution targeted bisulfite sequencing reveals blood cell type-specific dna methylation patterns in il13 and ormdl3
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8111952/
https://www.ncbi.nlm.nih.gov/pubmed/33971943
http://dx.doi.org/10.1186/s13148-021-01093-7
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