Cytosine methylation and the ecology of intragenomic parasites

Yoder, Jeffrey A.; Walsh, Colum P.; Bestor, Timothy H.

doi:10.1016/s0168-9525(97)01181-5

Cited by 1,724 publications

(1,255 citation statements)

References 48 publications

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“…Repetitive regions showed decreasing methylation with age. These changes in retrotransposons may promote the expression of these elements and increase damage to the genome in late life (Robertson & Wolffe, 2000; Yoder, Walsh, & Bestor, 1997). …”

Section: Discussionmentioning

confidence: 99%

Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction

2018

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SummaryAging is characterized by numerous molecular changes, such as accumulation of molecular damage and altered gene expression, many of which are linked to DNA methylation. Here, we characterize the blood DNA methylome across 16 age groups of mice and report numerous global, region‐ and site‐specific features, as well as the associated dynamics of methylation changes. Transition of the methylome throughout lifespan was not uniform, with many sites showing accelerated changes in late life. The associated genes and promoters were enriched for aging‐related pathways, pointing to a fundamental link between DNA methylation and control of the aging process. Calorie restriction both shifted the overall methylation pattern and was accompanied by its gradual age‐related remodeling, the latter contributing to the lifespan‐extending effect. With age, both highly and poorly methylated sites trended toward intermediate levels, and aging was accompanied by an accelerated increase in entropy, consistent with damage accumulation. However, the entropy effects differed for the sites that increased, decreased and did not change methylation with age. Many sites trailed behind, whereas some followed or even exceeded the entropy trajectory and altered the developmental DNA methylation pattern. The patterns we observed in certain genomic regions were conserved between humans and mice, suggesting common principles of functional DNA methylome remodeling and its critical role in aging. The highly resolved DNA methylome remodeling provides an excellent model for understanding systemic changes that characterize the aging process.

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Section: Discussionmentioning

confidence: 99%

Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction

2018

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“…The ''genome defense'' hypothesis suggests that CpG methylation initially arose in evolution for silencing and neutralizing the gene activities of transposable elements and was subsequently recruited for repression of genes (59) but there are other hypotheses on the evolutionary origin of DNA methylation. (60) It is not known how cells recognize newly transposed elements and induce chromatin and DNA methylation but, in some eukaryotic organisms (S.pombe, C.elegans, D.melanogaster, A.thaliana), duplex RNA formed by transcripts from both strands of RT is cleaved with specific RNase III (DICER) and the resulting small RNAs (<30 nt) are captured by complexes containing an ARGONAUTE (Ago) protein, which either induce cleavage of RT transcripts (RISC complexes) or induce histone H3 methylation at lysine-9 in chromatin and de novo DNA methylation of RT genomic sequences (RITS complexes) (reviewed in Ref.…”

Section: Modulation Of Biological Effects Of Retroelements By Their Ementioning

confidence: 99%

Regulation of mammalian gene expression by retroelements and non‐coding tandem repeats

Tomilin

2008

BioEssays

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Genomes of higher eukaryotes contain abundant non‐coding repeated sequences whose overall biological impact is unclear. They comprise two categories. The first consists of retrotransposon‐derived elements. These are three major families of retroelements (LINEs, SINEs and LTRs). SINEs are clustered in gene‐rich regions and are found in promoters of genes while LINEs are concentrated in gene‐poor regions and are depleted from promoters. The second class consists of non‐coding tandem repeats (satellite DNAs and TTAGGG arrays), which are associated with mammalian centromeres, heterochromatin and telomeres. Terminal TTAGGG arrays are involved in telomere capping and satellite DNAs are located in heterochromatin, which is implicated in transcription silencing by gene repositioning (relocalization). It is unknown whether interstitial TTAGGG sequences, which are present in many vertebrates, have a function. Here, evidence will be presented that retroelements and TTAGGG arrays are involved in regulation of gene expression. Retroelements can provide binding sites for transcription factors and protect promoter CpG islands from repressive chromatin modifications, and may be also involved in nuclear compartmentalization of transcriptionally active and inactive domains. Interstitial telomere‐like sequences can form dynamically maintained three‐dimensional nuclear networks of transcriptionally inactive domains, which may be involved in transcription silencing like classic heterochromatin. BioEssays 30:338–348, 2008. © 2008 Wiley Periodicals, Inc.

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“…To maintain the genome stability, DNA methylation induced gene silencing on the integrated virus DNA is crucial for mammalian cells to subdue the intruder's DNA. Exogenous retroviral DNAs can be inactivated due to de novo DNA methylation and were able to integrate into human genome to become part of it [34]. Indeed, human genome contains DNA sequences resembling the retroviral long terminal repeats (LTRs) [35] and the transposable elements.…”

Section: Virus Infection Epigenetics Alter-ations and Carcinogenesismentioning

confidence: 99%

Epigenetic changes in virus-associated human cancers

Leu

Chang

2005

Cell Res

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Epigenetics of human cancer becomes an area of emerging research direction due to a growing understanding of specific epigenetic pathways and rapid development of detection technologies. Aberrant promoter hypermethylation is a prevalent phenonmena in human cancers. Tumor suppressor genes are often hypermethylated due to the increased activity or deregulation of DNMTs. Increasing evidence also reveals that viral genes are one of the key players in regulating DNA methylation. In this review, we will focus on hypermethylation and tumor suppressor gene silencing and the signal pathways that are involved, particularly in cancers closely associated with the hepatitis B virus, simian virus 40 (SV40), and Epstein-Barr virus. In addition, we will discuss current technologies for genome-wide detection of epigenetically regulated targets, which allow for systematic DNA hypermethylation analysis. The study of epigenetic changes should provide a global view of gene profile in cancer, and epigenetic markers could be used for early detection, prognosis, and therapy of cancer.

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Cytosine methylation and the ecology of intragenomic parasites

Cited by 1,724 publications

References 48 publications

Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction

Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction

Regulation of mammalian gene expression by retroelements and non‐coding tandem repeats

Epigenetic changes in virus-associated human cancers

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