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Early life DNA methylation profiles are indicative of age-related transcriptome changes

https://doi.org/10.1101/557892
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Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer
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Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming
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The Hallmarks of Aging
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DNA Methylation of Transcriptional Enhancers and Cancer Predisposition
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Geroscience: Linking Aging to Chronic Disease
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Early-Life Gene Expression in Neurons Modulates Lasting Epigenetic States
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HP1 Is Involved in Regulating the Global Impact of DNA Methylation on Alternative Splicing
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Reversible Regulation of Promoter and Enhancer Histone Landscape by DNA Methylation in Mouse Embryonic Stem Cells
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Loss of Kdm5c Causes Spurious Transcription and Prevents the Fine-Tuning of Activity-Regulated Enhancers in Neurons
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Learning and Age-Related Changes in Genome-wide H2A.Z Binding in the Mouse Hippocampus
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Aging-Dependent Demethylation of Regulatory Elements Correlates with Chromatin State and Improved β Cell Function
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Age-associated changes in DNA methylation across multiple tissues in an inbred mouse model
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Eaf3 Chromodomain Interaction with Methylated H3-K36 Links Histone Deacetylation to Pol II Elongation
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Modification of Enhancer Chromatin: What, How, and Why?
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Bivalent Regions of Cytosine Methylation and H3K27 Acetylation Suggest an Active Role for DNA Methylation at Enhancers
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Caloric restriction mitigates age-associated hippocampal differential CG and non-CG methylation
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DNA methylation variability in Alzheimer's disease
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The alternative role of DNA methylation in splicing regulation
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Epigenomics of Alzheimer's disease
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Epigenetics: interaction of DNA methylation and chromatin
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Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition
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Essential role for de novo DNA methyltransferase Dnmt3a in paternal and maternal imprinting
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Genome-scale DNA methylation maps of pluripotent and differentiated cells
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Neural mechanisms of ageing and cognitive decline
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Conserved role of intragenic DNA methylation in regulating alternative promoters
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CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing
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Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer’s disease
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Disruption of DNA-methylation-dependent long gene repression in Rett syndrome
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Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome
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Epigenetic regulation of the glucocorticoid receptor in human brain associates with childhood abuse
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Dnmt1 and Dnmt3a maintain DNA methylation and regulate synaptic function in adult forebrain neurons
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DNA methylation and memory formation
inferredcites →https://doi.org/10.1038/nn.3607openalex-snapshot
Distribution, recognition and regulation of non-CpG methylation in the adult mammalian brain
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Epigenetic programming by maternal behavior
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Establishing, maintaining and modifying DNA methylation patterns in plants and animals
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Functions of DNA methylation: islands, start sites, gene bodies and beyond
inferredcites →https://doi.org/10.1038/nsmb.1659openalex-snapshot
Chromatin organization marks exon-intron structure
inferredcites →https://doi.org/10.1038/s41467-017-00607-3openalex-snapshot
Caloric restriction delays age-related methylation drift
inferredcites →https://doi.org/10.1038/s41576-018-0004-3openalex-snapshot
DNA methylation-based biomarkers and the epigenetic clock theory of ageing
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Is H3K4me1 at enhancers correlative or causative?
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Dosage compensation and DNA methylation landscape of the X chromosome in mouse liver
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ReactomePA: an R/Bioconductor package for reactome pathway analysis and visualization
inferredcites →https://doi.org/10.1073/pnas.0500398102openalex-snapshot
Epigenetic differences arise during the lifetime of monozygotic twins
inferredcites →https://doi.org/10.1073/pnas.1016071107openalex-snapshot
Histone H3K27ac separates active from poised enhancers and predicts developmental state
inferredcites →https://doi.org/10.1073/pnas.1121260109openalex-snapshot
Conserved epigenetic sensitivity to early life experience in the rat and human hippocampus
inferredcites →https://doi.org/10.1073/pnas.1618737114openalex-snapshot
DNA methylation in the gene body influences MeCP2-mediated gene repression
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Epigenomics meets splicing through the TETs and CTCF
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BEDTools: a flexible suite of utilities for comparing genomic features
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Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications
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STAR: ultrafast universal RNA-seq aligner
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Trimmomatic: a flexible trimmer for Illumina sequence data
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ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization
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Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing
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Life-Span Extension in Mice by Preweaning Food Restriction and by Methionine Restriction in Middle Age
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Nutritional Influences on Aging of Fischer 344 Rats: I. Physical, Metabolic, and Longevity Characteristics
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Aberrant patterns of DNA methylation, chromatin formation and gene expression in cancer
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DNA co-methylation analysis suggests novel functional associations between gene pairs in breast cancer samples
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Diabetes: A Candidate Disease for Efficient DNA Methylation Profiling
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The histone variant H2A.Z is an important regulator of enhancer activity
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Frequent lack of repressive capacity of promoter DNA methylation identified through genome-wide epigenomic manipulation
inferredcites →https://doi.org/10.1101/gad.254144.114openalex-snapshot
Trimethylation of Lys36 on H3 restricts gene expression change during aging and impacts life span
inferredcites →https://doi.org/10.1101/gad.263707.115openalex-snapshot
H3K36 methylation promotes longevity by enhancing transcriptional fidelity
inferredcites →https://doi.org/10.1101/gr.143503.112openalex-snapshot
DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon–intron structure
inferredcites →https://doi.org/10.1101/gr.156877.113openalex-snapshot
H2A.B facilitates transcription elongation at methylated CpG loci
inferredcites →https://doi.org/10.1101/gr.163485.113openalex-snapshot
Reconfiguration of nucleosome-depleted regions at distal regulatory elements accompanies DNA methylation of enhancers and insulators in cancer
inferredcites →https://doi.org/10.1101/gr.169011.113openalex-snapshot
H3K4me1 marks DNA regions hypomethylated during aging in human stem and differentiated cells
inferredcites →https://doi.org/10.1101/gr.176933.114openalex-snapshot
Genetic and environmental exposures constrain epigenetic drift over the human life course
inferredcites →https://doi.org/10.1101/gr.240093.118openalex-snapshot
Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses
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Methylation of ELOVL 2 gene as a new epigenetic marker of age
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Genome‐wide DNA methylation changes with age in disease‐free human skeletal muscle
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DNA methylation and healthy human aging
inferredcites →https://doi.org/10.1111/acel.12681openalex-snapshot
Sexually divergent DNA methylation patterns with hippocampal aging
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Global remodeling of the mouse DNA methylome during aging and in response to calorie restriction
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The origins of the developmental origins theory
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Gene expression profiling of aging in multiple mouse strains: identification of aging biomarkers and impact of dietary antioxidants
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DNA methylation pattern changes upon long‐term culture and aging of human mesenchymal stromal cells
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Tissue‐specific dysregulation of DNA methylation in aging
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Revisiting the genomic hypomethylation hypothesis of aging
inferredcites →https://doi.org/10.1126/science.1065848openalex-snapshot
Dnmt3L and the Establishment of Maternal Genomic Imprints
inferredcites →https://doi.org/10.1126/science.1136352openalex-snapshot
Gene Body-Specific Methylation on the Active X Chromosome
inferredcites →https://doi.org/10.1126/science.1190485openalex-snapshot
Dnmt3a-Dependent Nonpromoter DNA Methylation Facilitates Transcription of Neurogenic Genes
inferredcites →https://doi.org/10.1126/science.1237905openalex-snapshot
Global Epigenomic Reconfiguration During Mammalian Brain Development
inferredcites →https://doi.org/10.1146/annurev-cellbio-092910-154121openalex-snapshot
The Role of MeCP2 in the Brain
inferredcites →https://doi.org/10.1146/annurev-genom-090413-025437openalex-snapshot
Non-CG Methylation in the Human Genome
inferredcites →https://doi.org/10.1155/2016/6072357openalex-snapshot
DNA Methylation and Chromatin Remodeling: The Blueprint of Cancer Epigenetics
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The 5-Methylcytosine in DNA of Rats
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Aberrant DNA methylation patterns in diabetic nephropathy
inferredcites →https://doi.org/10.1186/gb-2008-9-9-r137openalex-snapshot
Model-based Analysis of ChIP-Seq (MACS)
inferredcites →https://doi.org/10.1186/gb-2012-13-10-r97openalex-snapshot
Aging effects on DNA methylation modules in human brain and blood tissue
inferredcites →https://doi.org/10.1186/gb-2013-14-10-r115openalex-snapshot
DNA methylation age of human tissues and cell types
inferredcites →https://doi.org/10.1186/gb-2013-14-9-r102openalex-snapshot
Differential DNA methylation with age displays both common and dynamic features across human tissues that are influenced by CpG landscape
inferredcites →https://doi.org/10.1186/s12864-017-4353-7openalex-snapshot
DNA methylation regulates discrimination of enhancers from promoters through a H3K4me1-H3K4me3 seesaw mechanism
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DNA methylation patterns associated with oxidative stress in an ageing population
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Sexually divergent induction of microglial-associated neuroinflammation with hippocampal aging
inferredcites →https://doi.org/10.1186/s13059-014-0550-8openalex-snapshot
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
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The Ensembl Regulatory Build
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Diverse interventions that extend mouse lifespan suppress shared age-associated epigenetic changes at critical gene regulatory regions
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Dietary restriction protects from age-associated DNA methylation and induces epigenetic reprogramming of lipid metabolism
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Multi-tissue DNA methylation age predictor in mouse
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Absence of genomic hypomethylation or regulation of cytosine-modifying enzymes with aging in male and female mice
inferredcites →https://doi.org/10.1186/s13072-018-0191-3openalex-snapshot
Age-related DNA methylation changes are tissue-specific with ELOVL2 promoter methylation as exception
inferredcites →https://doi.org/10.1186/s13148-016-0228-zopenalex-snapshot
Epigenetic age acceleration predicts cancer, cardiovascular, and all-cause mortality in a German case cohort
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A novel Alzheimer’s disease drug candidate targeting inflammation and fatty acid metabolism
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Age-Specific Epigenetic Drift in Late-Onset Alzheimer's Disease
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Continuous Aging of the Human DNA Methylome Throughout the Human Lifespan
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Whole-Genome Sequencing of the World’s Oldest People
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Beneficial Effects of Caloric Restriction on Chronic Kidney Disease in Rodent Models: A Meta-Analysis and Systematic Review
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Principles Governing DNA Methylation during Neuronal Lineage and Subtype Specification
inferredcites →https://doi.org/10.18632/aging.100908openalex-snapshot
DNA methylation levels at individual age-associated CpG sites can be indicative for life expectancy
inferredcites →https://doi.org/10.18632/aging.101414openalex-snapshot
An epigenetic biomarker of aging for lifespan and healthspan
inferredcites →https://doi.org/10.18632/aging.101590openalex-snapshot
A multi-tissue full lifespan epigenetic clock for mice
inferredcites →https://doi.org/10.18632/aging.101666openalex-snapshot
Cell and tissue type independent age-associated DNA methylation changes are not rare but common
inferredcites →https://doi.org/10.18632/oncotarget.7383openalex-snapshot
Epigenetic clock analyses of cellular senescence and ageing
inferredcites →https://doi.org/10.2217/epi.11.6openalex-snapshot
Epigenetic Mechanisms in Memory and Synaptic Function
inferredcites →https://doi.org/10.2217/epi.15.119openalex-snapshot
DNA Methylation Dynamics in Neurogenesis
inferredcites →https://doi.org/10.3389/fgene.2012.00277openalex-snapshot
The Genetics of Extreme Longevity: Lessons from the New England Centenarian Study
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DNA Methylation, Its Mediators and Genome Integrity
inferredcites →https://doi.org/10.7554/elife.00726openalex-snapshot
DNA methylation presents distinct binding sites for human transcription factors
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