Reconfiguration of DNA methylation in aging

•Methylated cytosines have a non-random distribution throughout the genome.•DNA methylation patterns are dynamic states balanced by methylation and demethylation.•Environmental exposure and lifestyle impact the genomic methylation patterns.•Dynamic reprogramming of DNA methylation patterns in aging...

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Published in:	Mechanisms of ageing and development Vol. 151; pp. 60 - 70
Main Authors:	Zampieri, Michele, Ciccarone, Fabio, Calabrese, Roberta, Franceschi, Claudio, Bürkle, Alexander, Caiafa, Paola
Format:	Journal Article
Language:	English
Published:	Ireland Elsevier Ireland Ltd 01.11.2015
Subjects:	5-Hydroxymethylcytosine 5-Methylcytosine Aging Aging - genetics Aging - metabolism Animals CpG Islands - physiology DNA methylation DNA Methylation - physiology Epigenesis, Genetic - physiology Epigenetic reprogramming Genome, Human - physiology Humans DNMTs TET 5-Hydroxymethylcytosine 5-Methylcytosine 5caC WGBS DMRs 5mC LTR SINE BER 5hmC CGIs 5fC Epigenetic reprogramming LINE ROS DNA methylation Aging SAH SAM
ISSN:	0047-6374, 1872-6216, 1872-6216
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Abstract	•Methylated cytosines have a non-random distribution throughout the genome.•DNA methylation patterns are dynamic states balanced by methylation and demethylation.•Environmental exposure and lifestyle impact the genomic methylation patterns.•Dynamic reprogramming of DNA methylation patterns in aging A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as “epigenetic drift” which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5hmC.
AbstractList	•Methylated cytosines have a non-random distribution throughout the genome.•DNA methylation patterns are dynamic states balanced by methylation and demethylation.•Environmental exposure and lifestyle impact the genomic methylation patterns.•Dynamic reprogramming of DNA methylation patterns in aging A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as “epigenetic drift” which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5hmC. A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC.A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC. A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has highlighted the effective impact of epigenetic deregulation, particularly of DNA methylation, on aging. Age-associated alterations in DNA methylation are commonly grouped in the phenomenon known as "epigenetic drift" which is characterized by gradual extensive demethylation of genome and hypermethylation of a number of promoter-associated CpG islands. Surprisingly, specific DNA regions show directional epigenetic changes in aged individuals suggesting the importance of these events for the aging process. However, the epigenetic information obtained until now in aging needs a re-consideration due to the recent discovery of 5-hydroxymethylcytosine, a new DNA epigenetic mark present on genome. A recapitulation of the factors involved in the regulation of DNA methylation and the changes occurring in aging will be described in this review also considering the data available on 5 hmC.
Author	Franceschi, Claudio Zampieri, Michele Caiafa, Paola Ciccarone, Fabio Calabrese, Roberta Bürkle, Alexander
Author_xml	– sequence: 1 givenname: Michele surname: Zampieri fullname: Zampieri, Michele organization: Department of Cellular Biotechnologies and Hematology, “Sapienza” University of Rome, Rome 00161, Italy – sequence: 2 givenname: Fabio surname: Ciccarone fullname: Ciccarone, Fabio organization: Department of Cellular Biotechnologies and Hematology, “Sapienza” University of Rome, Rome 00161, Italy – sequence: 3 givenname: Roberta surname: Calabrese fullname: Calabrese, Roberta organization: Department of Cellular Biotechnologies and Hematology, “Sapienza” University of Rome, Rome 00161, Italy – sequence: 4 givenname: Claudio surname: Franceschi fullname: Franceschi, Claudio organization: Department of Experimental Pathology, Alma Mater Studiorum, University of Bologna, Bologna 40126, Italy – sequence: 5 givenname: Alexander surname: Bürkle fullname: Bürkle, Alexander organization: Molecular Toxicology Group, Department of Biology, University of Konstanz, Konstanz D-78457, Germany – sequence: 6 givenname: Paola surname: Caiafa fullname: Caiafa, Paola email: caiafa@bce.uniroma1.it organization: Department of Cellular Biotechnologies and Hematology, “Sapienza” University of Rome, Rome 00161, Italy
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/25708826$$D View this record in MEDLINE/PubMed
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IsDoiOpenAccess	true
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Keywords	DNMTs TET 5-Hydroxymethylcytosine 5-Methylcytosine 5caC WGBS DMRs 5mC LTR SINE BER 5hmC CGIs 5fC Epigenetic reprogramming LINE ROS DNA methylation Aging SAH SAM
Language	English
License	http://creativecommons.org/licenses/by-nc-nd/4.0 Copyright © 2015 The Authors. Published by Elsevier Ireland Ltd.. All rights reserved.
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OpenAccessLink	https://dx.doi.org/10.1016/j.mad.2015.02.002
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PublicationCentury	2000
PublicationDate	November 2015 2015-11-00 2015-Nov 20151101
PublicationDateYYYYMMDD	2015-11-01
PublicationDate_xml	– month: 11 year: 2015 text: November 2015
PublicationDecade	2010
PublicationPlace	Ireland
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PublicationTitle	Mechanisms of ageing and development
PublicationTitleAlternate	Mech Ageing Dev
PublicationYear	2015
Publisher	Elsevier Ireland Ltd
Publisher_xml	– name: Elsevier Ireland Ltd
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Snippet	•Methylated cytosines have a non-random distribution throughout the genome.•DNA methylation patterns are dynamic states balanced by methylation and... A complex interplay between multiple biological effects shapes the aging process. The advent of genome-wide quantitative approaches in the epigenetic field has...
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SubjectTerms	5-Hydroxymethylcytosine 5-Methylcytosine Aging Aging - genetics Aging - metabolism Animals CpG Islands - physiology DNA methylation DNA Methylation - physiology Epigenesis, Genetic - physiology Epigenetic reprogramming Genome, Human - physiology Humans
Title	Reconfiguration of DNA methylation in aging
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