Epigenomics and the regulation of aging

Identification of miRNA Changes in Alzheimer's Disease Brain and CSF Yields Putative Biomarkers and Insights into Disease Pathways

(2017) John P. Cogswell et al.   JOURNAL OF ALZHEIMERS DISEASE

Circulatory miR-34a as an RNA-based, noninvasive biomarker for brain aging

(2016) Xiaoli Li et al.   Aging-US

Sirtuins as regulators of mammalian aging

(2016) Shoshana Naiman et al.   Aging-US

Age-Related Increase in Levels of 5-Hydroxymethylcytosine in Mouse Hippocampus is Prevented by Caloric Restriction

(2014) Leonidas Chouliaras et al.   Current Alzheimer Research

Ageing, genes, environment and epigenetics: what twin studies tell us now, and in the future

(2012) Claire Joanne Steves et al.   AGE AND AGEING

Genome-wide miRNA signatures of human longevity

(2012) Abdou ElSharawy et al.   AGING CELL

Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain

(2012) Yixing Han et al.   AGING CELL

Epigenetic variation during the adult lifespan: cross-sectional and longitudinal data on monozygotic twin pairs

(2012) Rudolf P. Talens et al.   AGING CELL

DNA Methylation Does Not Stably Lock Gene Expression but Instead Serves as a Molecular Mark for Gene Silencing Memory

(2012) N. J.- M. Raynal et al.   CANCER RESEARCH

Base-Resolution Analysis of 5-Hydroxymethylcytosine in the Mammalian Genome

(2012) Miao Yu et al.   CELL

Comparative Epigenomic Annotation of Regulatory DNA

(2012) Shu Xiao et al.   CELL

piRNAs Can Trigger a Multigenerational Epigenetic Memory in the Germline of C. elegans

(2012) Alyson Ashe et al.   CELL

Rewriting the Epigenome

(2012) Benjamin R. Carone et al.   CELL

The C. elegans MicroRNA mir-71 Acts in Neurons to Promote Germline-Mediated Longevity through Regulation of DAF-16/FOXO

(2012) Konstantinos Boulias et al.   Cell Metabolism

Characterization of genome-wide enhancer-promoter interactions reveals co-expression of interacting genes and modes of higher order chromatin organization

(2012) Iouri Chepelev et al.   CELL RESEARCH

Aging and epigenetics: Longitudinal changes in gene-specific DNA methylation

(2012) Jaime Madrigano et al.   Epigenetics

piRNA-mediated transgenerational inheritance of an acquired trait

(2012) T. Grentzinger et al.   GENOME RESEARCH

Widespread plasticity in CTCF occupancy linked to DNA methylation

(2012) H. Wang et al.   GENOME RESEARCH

Impact of caloric restriction on health and survival in rhesus monkeys from the NIA study

(2012) Julie A. Mattison et al.   NATURE

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Rescue of aging-associated decline in Dnmt3a2 expression restores cognitive abilities

(2012) Ana M M Oliveira et al.   NATURE NEUROSCIENCE

Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island

(2012) Yan Zhang et al.   NUCLEIC ACIDS RESEARCH

Postnatal development- and age-related changes in DNA-methylation patterns in the human genome

(2012) Paraskevi Salpea et al.   NUCLEIC ACIDS RESEARCH

The Influence of cis-Regulatory Elements on DNA Methylation Fidelity

(2012) Mingxiang Teng et al.   PLoS One

Sequences Sufficient for Programming Imprinted Germline DNA Methylation Defined

(2012) Yoon Jung Park et al.   PLoS One

High Resolution Methylome Map of Rat Indicates Role of Intragenic DNA Methylation in Identification of Coding Region

(2012) Satish Sati et al.   PLoS One

Linking the Epigenome to the Genome: Correlation of Different Features to DNA Methylation of CpG Islands

(2012) Clemens Wrzodek et al.   PLoS One

Novel MicroRNAs Differentially Expressed during Aging in the Mouse Brain

(2012) Sachi Inukai et al.   PLoS One

Distinct DNA methylomes of newborns and centenarians

(2012) H. Heyn et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

H3K4 demethylation by Jarid1a and Jarid1b contributes to retinoblastoma-mediated gene silencing during cellular senescence

(2012) A. Chicas et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Role of DNA Methylation in Aging, Rejuvenation, and Age-Related Disease

(2012) Adiv A. Johnson et al.   REJUVENATION RESEARCH

Post-developmental microRNA expression is required for normal physiology, and regulates aging in parallel to insulin/IGF-1 signaling in C. elegans

(2012) N. J. Lehrbach et al.   RNA

Dissecting the Gene Network of Dietary Restriction to Identify Evolutionarily Conserved Pathways and New Functional Genes

(2012) Daniel Wuttke et al.   PLoS Genetics

In Vivo Control of CpG and Non-CpG DNA Methylation by DNA Methyltransferases

(2012) Julia Arand et al.   PLoS Genetics

Epigenome-Wide Scans Identify Differentially Methylated Regions for Age and Age-Related Phenotypes in a Healthy Ageing Population

(2012) Jordana T. Bell et al.   PLoS Genetics

Population-specificity of human DNA methylation

(2012) Hunter B Fraser et al.   GENOME BIOLOGY

Functional annotation of the human brain methylome identifies tissue-specific epigenetic variation across brain and blood

(2012) Matthew N Davies et al.   GENOME BIOLOGY

Modeling gene expression using chromatin features in various cellular contexts

(2012) Xianjun Dong et al.   GENOME BIOLOGY

The H3K27 demethylase UTX-1 regulates C. elegans lifespan in a germline-independent, insulin-dependent manner

(2011) Travis J. Maures et al.   AGING CELL

Signals and Combinatorial Functions of Histone Modifications

(2011) Tamaki Suganuma et al.   Annual Review of Biochemistry

Transgenerational Inheritance of an Acquired Small RNA-Based Antiviral Response in C. elegans

(2011) Oded Rechavi et al.   CELL

Polycomb-Repressed Genes Have Permissive Enhancers that Initiate Reprogramming

(2011) Phillippa C. Taberlay et al.   CELL

Autophagy and Aging

(2011) David C. Rubinsztein et al.   CELL

Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification

(2011) Minjia Tan et al.   CELL

Cell cycle-dependent deacetylation of telomeric histone H3 lysine K56 by human SIRT6

(2011) Eriko Michishita et al.   CELL CYCLE

Histone Demethylase UTX-1 Regulates C. elegans Life Span by Targeting the Insulin/IGF-1 Signaling Pathway

(2011) Chunyu Jin et al.   Cell Metabolism

Age-related loss of CpG methylation in the tumour necrosis factor promoter

(2011) Isobel R. Gowers et al.   CYTOKINE

Evidence for non-CpG methylation in mammals

(2011) Jie Yan et al.   EXPERIMENTAL CELL RESEARCH

A dual epigenomic approach for the search of obesity biomarkers: DNA methylation in relation to diet-induced weight loss

(2011) Fermin I. Milagro et al.   FASEB JOURNAL

RNF20-RNF40: A ubiquitin-driven link between gene expression and the DNA damage response

(2011) Yosef Shiloh et al.   FEBS LETTERS

Dynamics of DNA damage response proteins at DNA breaks: a focus on protein modifications

(2011) S. E. Polo et al.   GENES & DEVELOPMENT

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain

(2011) J. R. Tollervey et al.   GENOME RESEARCH

Distinct DNA methylation changes highly correlated with chronological age in the human brain

(2011) Dena G. Hernandez et al.   HUMAN MOLECULAR GENETICS

Oligomerization of DNMT3A Controls the Mechanism ofde NovoDNA Methylation

(2011) Celeste Holz-Schietinger et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Deciphering a methylome: what can we read into patterns of DNA methylation?

(2011) K. B. Flores et al.   JOURNAL OF EXPERIMENTAL BIOLOGY

ICF Syndrome Mutations Cause a Broad Spectrum of Biochemical Defects in DNMT3B-Mediated De Novo DNA Methylation

(2011) Amir H. Moarefi et al.   JOURNAL OF MOLECULAR BIOLOGY

SIRT1 Deacetylates the DNA Methyltransferase 1 (DNMT1) Protein and Alters Its Activities

(2011) L. Peng et al.   MOLECULAR AND CELLULAR BIOLOGY

In Embryonic Stem Cells, ZFP57/KAP1 Recognize a Methylated Hexanucleotide to Affect Chromatin and DNA Methylation of Imprinting Control Regions

(2011) Simon Quenneville et al.   MOLECULAR CELL

MMSET regulates histone H4K20 methylation and 53BP1 accumulation at DNA damage sites

(2011) Huadong Pei et al.   NATURE

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Regulation of Caenorhabditis elegans lifespan by sir-2.1 transgenes

(2011) Mohan Viswanathan et al.   NATURE

Absence of effects of Sir2 overexpression on lifespan in C. elegans and Drosophila

(2011) Camilla Burnett et al.   NATURE

Genome-wide mapping of 5-hydroxymethylcytosine in embryonic stem cells

(2011) William A. Pastor et al.   NATURE

Dynamic regulation of 5-hydroxymethylcytosine in mouse ES cells and during differentiation

(2011) Gabriella Ficz et al.   NATURE

Dnmt3a is essential for hematopoietic stem cell differentiation

(2011) Grant A Challen et al.   NATURE GENETICS

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

Sensitive and specific single-molecule sequencing of 5-hydroxymethylcytosine

(2011) Chun-Xiao Song et al.   NATURE METHODS

Neuronal activity modifies the DNA methylation landscape in the adult brain

(2011) Junjie U Guo et al.   NATURE NEUROSCIENCE

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

Transcription initiation platforms and GTF recruitment at tissue-specific enhancers and promoters

(2011) Frederic Koch et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

MethylomeDB: a database of DNA methylation profiles of the brain

(2011) Yurong Xin et al.   NUCLEIC ACIDS RESEARCH

Epigenetic Predictor of Age

(2011) Sven Bocklandt et al.   PLoS One

Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans

(2011) N. O. Burton et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Age-associated changes in expression of small, noncoding RNAs, including microRNAs, in C. elegans

(2011) M. Kato et al.   RNA

Tet-Mediated Formation of 5-Carboxylcytosine and Its Excision by TDG in Mammalian DNA

(2011) Y.-F. He et al.   SCIENCE

Tet Proteins Can Convert 5-Methylcytosine to 5-Formylcytosine and 5-Carboxylcytosine

(2011) S. Ito et al.   SCIENCE

Taking a “good” look at free radicals in the aging process

(2011) Siegfried Hekimi et al.   TRENDS IN CELL BIOLOGY

Dynamic Chromatin Localization of Sirt6 Shapes Stress- and Aging-Related Transcriptional Networks

(2011) Tiara L. A. Kawahara et al.   PLoS Genetics

MicroRNA Predictors of Longevity in Caenorhabditis elegans

(2011) Zachary Pincus et al.   PLoS Genetics

A Genome-Wide Study of DNA Methylation Patterns and Gene Expression Levels in Multiple Human and Chimpanzee Tissues

(2011) Athma A. Pai et al.   PLoS Genetics

Insufficient DNA methylation affects healthy aging and promotes age-related health problems

(2011) Liang Liu et al.   Clinical Epigenetics

Longevity is not influenced by prenatal programming of body size

(2010) Cheryl A. Conover et al.   AGING CELL

Long non-coding RNAs in nervous system function and disease

(2010) Irfan A. Qureshi et al.   BRAIN RESEARCH

ATM-Dependent Chromatin Changes Silence Transcription In cis to DNA Double-Strand Breaks

(2010) Niraj M. Shanbhag et al.   CELL

Apoptosis and aging: increased resistance to apoptosis enhances the aging process

(2010) Antero Salminen et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

MicroRNAs Both Promote and Antagonize Longevity in C. elegans

(2010) Alexandre de Lencastre et al.   CURRENT BIOLOGY

Distinct roles of GCN5/PCAF-mediated H3K9ac and CBP/p300-mediated H3K18/27ac in nuclear receptor transactivation

(2010) Qihuang Jin et al.   EMBO JOURNAL

How increased oxidative stress promotes longevity and metabolic health: The concept of mitochondrial hormesis (mitohormesis)

(2010) Michael Ristow et al.   EXPERIMENTAL GERONTOLOGY

Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes

(2010) K.-M. Schmitz et al.   GENES & DEVELOPMENT

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Chromatin and sequence features that define the fine and gross structure of genomic methylation patterns

(2010) J. R. Edwards et al.   GENOME RESEARCH

Widespread and tissue specific age-related DNA methylation changes in mice

(2010) S. Maegawa et al.   GENOME RESEARCH

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

Exercise Effects on Methylation ofASCGene

(2010) K. Nakajima et al.   INTERNATIONAL JOURNAL OF SPORTS MEDICINE

MOF and Histone H4 Acetylation at Lysine 16 Are Critical for DNA Damage Response and Double-Strand Break Repair

(2010) G. G. Sharma et al.   MOLECULAR AND CELLULAR BIOLOGY

Regulation of the Histone H4 Monomethylase PR-Set7 by CRL4Cdt2-Mediated PCNA-Dependent Degradation during DNA Damage

(2010) Hisanobu Oda et al.   MOLECULAR CELL

H2A.Z Maintenance during Mitosis Reveals Nucleosome Shifting on Mitotically Silenced Genes

(2010) Theresa K. Kelly et al.   MOLECULAR CELL

Members of the H3K4 trimethylation complex regulate lifespan in a germline-dependent manner in C. elegans

(2010) Eric L. Greer et al.   NATURE

Conserved role of intragenic DNA methylation in regulating alternative promoters

(2010) Alika K. Maunakea et al.   NATURE

Epigenetic choreographers of neurogenesis in the adult mammalian brain

(2010) Dengke K Ma et al.   NATURE NEUROSCIENCE

Reduced histone biosynthesis and chromatin changes arising from a damage signal at telomeres

(2010) Roderick J O'Sullivan et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Genome-wide analysis of miRNA expression reveals a potential role for miR-144 in brain aging and spinocerebellar ataxia pathogenesis

(2010) Stephan Persengiev et al.   NEUROBIOLOGY OF AGING

Examination of the specificity of DNA methylation profiling techniques towards 5-methylcytosine and 5-hydroxymethylcytosine

(2010) Seung-Gi Jin et al.   NUCLEIC ACIDS RESEARCH

DNA Methylation as a Biomarker for Cardiovascular Disease Risk

(2010) Myungjin Kim et al.   PLoS One

The Behaviour of 5-Hydroxymethylcytosine in Bisulfite Sequencing

(2010) Yun Huang et al.   PLoS One

microRNA Expression Patterns Reveal Differential Expression of Target Genes with Age

(2010) Nicole Noren Hooten et al.   PLoS One

Altered Histone Acetylation Is Associated with Age-Dependent Memory Impairment in Mice

(2010) S. Peleg et al.   SCIENCE

Sirt1 improves healthy ageing and protects from metabolic syndrome-associated cancer

(2010) Daniel Herranz et al.   Nature Communications

Aging and Chronic Sun Exposure Cause Distinct Epigenetic Changes in Human Skin

(2010) Elke Grönniger et al.   PLoS Genetics

Essential Functions of the Histone Demethylase Lid

(2010) Ling Li et al.   PLoS Genetics

Contrasting chromatin organization of CpG islands and exons in the human genome

(2010) Jung Kyoon Choi   GENOME BIOLOGY

The ageing epigenome: Damaged beyond repair?

(2009) David A. Sinclair et al.   AGEING RESEARCH REVIEWS

Next-generation sequencing in aging research: Emerging applications, problems, pitfalls and possible solutions

(2009) João Pedro de Magalhães et al.   AGEING RESEARCH REVIEWS

Delayed kinetics of DNA double-strand break processing in normal and pathological aging

(2009) Olga A. Sedelnikova et al.   AGING CELL

CTCF: Master Weaver of the Genome

(2009) Jennifer E. Phillips et al.   CELL

Np95 interacts with de novo DNA methyltransferases, Dnmt3a and Dnmt3b, and mediates epigenetic silencing of the viral CMV promoter in embryonic stem cells

(2009) Daniela Meilinger et al.   EMBO REPORTS

MicroRNA group disorganization in aging

(2009) Joel Lanceta et al.   EXPERIMENTAL GERONTOLOGY

Age-dependent decreases in DNA methyltransferase levels and low transmethylation micronutrient levels synergize to promote overexpression of genes implicated in autoimmunity and acute coronary syndromes

(2009) YePeng Li et al.   EXPERIMENTAL GERONTOLOGY

Glucose restriction can extend normal cell lifespan and impair precancerous cell growth through epigenetic control of hTERT and p16 expression

(2009) Yuanyuan Li et al.   FASEB JOURNAL

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

(2009) M. J. Fullwood et al.   GENOME RESEARCH

Lineage-specific DNA methylation in T cells correlates with histone methylation and enhancer activity

(2009) C. Schmidl et al.   GENOME RESEARCH

One-Pot Shotgun Quantitative Mass Spectrometry Characterization of Histones

(2009) Mariana D. Plazas-Mayorca et al.   JOURNAL OF PROTEOME RESEARCH

Selective Anchoring of DNA Methyltransferases 3A and 3B to Nucleosomes Containing Methylated DNA

(2009) S. Jeong et al.   MOLECULAR AND CELLULAR BIOLOGY

The DNA-damage response in human biology and disease

(2009) Stephen P. Jackson et al.   NATURE

An oestrogen-receptor-α-bound human chromatin interactome

(2009) Melissa J. Fullwood et al.   NATURE

Histone H4 lysine 16 acetylation regulates cellular lifespan

(2009) Weiwei Dang et al.   NATURE

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells

(2009) Madeleine P Ball et al.   NATURE BIOTECHNOLOGY

DNA Damage, Aging, and Cancer

(2009) Jan H.J. Hoeijmakers   NEW ENGLAND JOURNAL OF MEDICINE

Caloric Restriction Delays Disease Onset and Mortality in Rhesus Monkeys

(2009) R. J. Colman et al.   SCIENCE

Conversion of 5-Methylcytosine to 5-Hydroxymethylcytosine in Mammalian DNA by MLL Partner TET1

(2009) M. Tahiliani et al.   SCIENCE

Genome-wide DNA methylation profiling using Infinium®assay

(2009) Marina Bibikova et al.   Epigenomics

Aging and Environmental Exposures Alter Tissue-Specific DNA Methylation Dependent upon CpG Island Context

(2009) Brock C. Christensen et al.   PLoS Genetics

SIRT1 Redistribution on Chromatin Promotes Genomic Stability but Alters Gene Expression during Aging

(2008) Philipp Oberdoerffer et al.   CELL

Resveratrol Delays Age-Related Deterioration and Mimics Transcriptional Aspects of Dietary Restriction without Extending Life Span

(2008) Kevin J. Pearson et al.   Cell Metabolism

The emergence of DNA methylation as a key modulator of aberrant cell death in prostate cancer

(2008) T M Murphy et al.   ENDOCRINE-RELATED CANCER

Small RNA guides for de novo DNA methylation in mammalian germ cells

(2008) A. A. Aravin et al.   GENES & DEVELOPMENT

A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning

(2008) A. Valouev et al.   GENOME RESEARCH

Intra-individual Change Over Time in DNA Methylation With Familial Clustering

(2008) Hans T. Bjornsson   JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION

Di-methyl H4 Lysine 20 Targets the Checkpoint Protein Crb2 to Sites of DNA Damage

(2008) Nikole T. Greeson et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Genomic DNA hypomethylation as a biomarker for bladder cancer susceptibility in the Spanish Bladder Cancer Study: a case–control study

(2008) Lee E Moore et al.   LANCET ONCOLOGY

Decline in genomic DNA methylation through aging in a cohort of elderly subjects

(2008) Valentina Bollati et al.   MECHANISMS OF AGEING AND DEVELOPMENT

Histone Ubiquitination: Triggering Gene Activity

(2008) Vikki M. Weake et al.   MOLECULAR CELL

A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice

(2008) Alexei A. Aravin et al.   MOLECULAR CELL

SIRT6 is a histone H3 lysine 9 deacetylase that modulates telomeric chromatin

(2008) Eriko Michishita et al.   NATURE

Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning

(2008) Shawn J. Cokus et al.   NATURE

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

Combinatorial patterns of histone acetylations and methylations in the human genome

(2008) Zhibin Wang et al.   NATURE GENETICS

UHRF1 binds G9a and participates in p21 transcriptional regulation in mammalian cells

(2008) Jong Kyong Kim et al.   NUCLEIC ACIDS RESEARCH

Frequent switching of Polycomb repressive marks and DNA hypermethylation in the PC3 prostate cancer cell line

(2008) E. N. Gal-Yam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Epigenetic Role for Maternally Inherited piRNAs in Transposon Silencing

(2008) J. Brennecke et al.   SCIENCE