Epigenetic alterations in aging.

Aging is a multifaceted process characterized by genetic and epigenetic changes in the genome. The genetic component of aging received initially all of the attention. Telomere attrition and accumulation of mutations due to a progressive deficiency in the repair of DNA damage with age remain leading causes of genomic instability. However, epigenetic mechanisms have now emerged as key contributors to the alterations of genome structure and function that accompany aging. The three pillars of epigenetic regulation are DNA methylation, histone modifications, and noncoding RNA species. Alterations of these epigenetic mechanisms affect the vast majority of nuclear processes, including gene transcription and silencing, DNA replication and repair, cell cycle progression, and telomere and centromere structure and function. Here, we summarize the lines of evidence indicating that these epigenetic defects might represent a major factor in the pathophysiology of aging and aging-related diseases, especially cancer.

[1]  D. Reinberg,et al.  SIRT1 regulates the histone methyl-transferase SUV39H1 during heterochromatin formation , 2007, Nature.

[2]  M. Fraga,et al.  Salermide, a Sirtuin inhibitor with a strong cancer-specific proapoptotic effect , 2009, Oncogene.

[3]  A. Shilatifard,et al.  An operational definition of epigenetics. , 2009, Genes & development.

[4]  R. Kuick,et al.  Infrequent occurrence of age-dependent changes in CpG island methylation as detected by restriction landmark genome scanning , 2002, Mechanisms of Ageing and Development.

[5]  O. Maes,et al.  Murine microRNAs implicated in liver functions and aging process , 2008, Mechanisms of Ageing and Development.

[6]  Hing Y Leung,et al.  Upregulation and Nuclear Recruitment of HDAC1 in Hormone Refractory Prostate Cancer , 2004, The Prostate.

[7]  William Stafford Noble,et al.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.

[8]  V. Klimenko,et al.  The 5-Methylcytosine in DNA of Rats , 1973 .

[9]  T. Ono,et al.  Age-dependent alterations in mRNA level and promoter methylation of collagen α1(I) gene in human periodontal ligament , 1999, Mechanisms of Ageing and Development.

[10]  Yang Shi,et al.  Histone Demethylation Mediated by the Nuclear Amine Oxidase Homolog LSD1 , 2004, Cell.

[11]  S. Berger The complex language of chromatin regulation during transcription , 2007, Nature.

[12]  Lin He,et al.  MicroRNAs: small RNAs with a big role in gene regulation , 2004, Nature reviews genetics.

[13]  Delin Chen,et al.  Negative Control of p53 by Sir2α Promotes Cell Survival under Stress , 2001, Cell.

[14]  Kelly M. McGarvey,et al.  Inhibition of SIRT1 Reactivates Silenced Cancer Genes without Loss of Promoter DNA Hypermethylation , 2006, PLoS genetics.

[15]  D. Reinberg,et al.  Transcription regulation by histone methylation: interplay between different covalent modifications of the core histone tails. , 2001, Genes & development.

[16]  R. Festenstein,et al.  Unravelling heterochromatin: competition between positive and negative factors regulates accessibility. , 2002, Trends in genetics : TIG.

[17]  Jin-Wu Nam,et al.  miR-29 miRNAs activate p53 by targeting p85α and CDC42 , 2009, Nature Structural &Molecular Biology.

[18]  Suk Woo Nam,et al.  Increased expression of histone deacetylase 2 is found in human gastric cancer , 2005, APMIS : acta pathologica, microbiologica, et immunologica Scandinavica.

[19]  C. Fuke,et al.  Age Related Changes in 5‐methylcytosine Content in Human Peripheral Leukocytes and Placentas: an HPLC‐based Study , 2004, Annals of human genetics.

[20]  T. Richmond,et al.  Crystal structure of the nucleosome core particle at 2.8 Å resolution , 1997, Nature.

[21]  Timothy B. Stockwell,et al.  The Sequence of the Human Genome , 2001, Science.

[22]  K. Kinzler,et al.  DNA methylation and genetic instability in colorectal cancer cells. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[23]  R. Jaenisch,et al.  Chromosomal Instability and Tumors Promoted by DNA Hypomethylation , 2003, Science.

[24]  T. Tollefsbol,et al.  Transcriptional control of the DNA methyltransferases is altered in aging and neoplastically-transformed human fibroblasts , 2003, Molecular and Cellular Biochemistry.

[25]  H. Erdjument-Bromage,et al.  Histone demethylation by a family of JmjC domain-containing proteins , 2006, Nature.

[26]  A. Bird,et al.  Genomic DNA methylation: the mark and its mediators. , 2006, Trends in biochemical sciences.

[27]  A. Bird CpG-rich islands and the function of DNA methylation , 1986, Nature.

[28]  Manel Esteller,et al.  MicroRNAs and cancer epigenetics: a macrorevolution , 2010, Current opinion in oncology.

[29]  Ravi Sachidanandam,et al.  Developmentally Regulated piRNA Clusters Implicate MILI in Transposon Control , 2007, Science.

[30]  Mircea Ivan,et al.  MicroRNA regulation of DNA repair gene expression in hypoxic stress. , 2009, Cancer research.

[31]  Rudolf Jaenisch,et al.  DNA hypomethylation leads to elevated mutation rates , 1998, Nature.

[32]  Cyrus Martin,et al.  The diverse functions of histone lysine methylation , 2005, Nature Reviews Molecular Cell Biology.

[33]  T. Mikkelsen,et al.  Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.

[34]  F. Slack,et al.  A Developmental Timing MicroRNA and Its Target Regulate Life Span in C. elegans , 2005, Science.

[35]  J. Herman,et al.  Methylation of the E-cadherin gene in bladder neoplasia and in normal urothelial epithelium from elderly individuals. , 2001, The American journal of pathology.

[36]  M. McVey,et al.  The SIR2/3/4 complex and SIR2 alone promote longevity in Saccharomyces cerevisiae by two different mechanisms. , 1999, Genes & development.

[37]  B. Sarg,et al.  Postsynthetic Trimethylation of Histone H4 at Lysine 20 in Mammalian Tissues Is Associated with Aging* , 2002, The Journal of Biological Chemistry.

[38]  David J. Chen,et al.  Genomic instability in laminopathy-based premature aging , 2005, Nature Medicine.

[39]  Kathryn A. O’Donnell,et al.  c-Myc-regulated microRNAs modulate E2F1 expression , 2005, Nature.

[40]  E. Li,et al.  Cloning and characterization of a family of novel mammalian DNA (cytosine-5) methyltransferases , 1998, Nature Genetics.

[41]  E. Lander,et al.  The Mammalian Epigenome , 2007, Cell.

[42]  Alain Verreault,et al.  Chromatin Challenges during DNA Replication and Repair , 2007, Cell.

[43]  T. Misteli,et al.  Lamin A-Dependent Nuclear Defects in Human Aging , 2006, Science.

[44]  S. Baylin,et al.  Aging and DNA methylation in colorectal mucosa and cancer. , 1998, Cancer research.

[45]  R. Grillari‐Voglauer,et al.  Novel modulators of senescence, aging, and longevity: Small non-coding RNAs enter the stage , 2010, Experimental Gerontology.

[46]  R. Tjian,et al.  Structure and function of a human TAFII250 double bromodomain module. , 2000, Science.

[47]  D R Turner,et al.  Human lymphocytes aged in vivo have reduced levels of methylation in transcriptionally active and inactive DNA. , 1989, Mutation research.

[48]  Peter A. Jones,et al.  Epigenetics in cancer. , 2010, Carcinogenesis.

[49]  Pingfang Liu,et al.  Genomic Instability and Aging-like Phenotype in the Absence of Mammalian SIRT6 , 2006, Cell.

[50]  B. Kennedy,et al.  Mutation in the silencing gene S/R4 can delay aging in S. cerevisiae , 1995, Cell.

[51]  C. López-Otín,et al.  Defective prelamin A processing and muscular and adipocyte alterations in Zmpste24 metalloproteinase–deficient mice , 2002, Nature Genetics.

[52]  Peter A. Jones,et al.  Epigenetic Activation of Tumor Suppressor MicroRNAs in Human Cancer Cells , 2006, Cell cycle.

[53]  A. Bird,et al.  Epigenetic regulation of gene expression: how the genome integrates intrinsic and environmental signals , 2003, Nature Genetics.

[54]  M. Blasco The epigenetic regulation of mammalian telomeres , 2007, Nature Reviews Genetics.

[55]  C. Croce,et al.  Frequent deletions and down-regulation of micro- RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[56]  M. Roizen SIRT1 redistribution on chromatin promotes genomic stability but alters gene expression during aging , 2009 .

[57]  J. Workman,et al.  Alteration of nucleosome structure as a mechanism of transcriptional regulation. , 1998, Annual review of biochemistry.

[58]  S. Lowe,et al.  A microRNA polycistron as a potential human oncogene , 2005, Nature.

[59]  R. Jaenisch,et al.  Activation and transposition of endogenous retroviral elements in hypomethylation induced tumors in mice , 2008, Oncogene.

[60]  S. Baylin,et al.  Methylation of the oestrogen receptor CpG island links ageing and neoplasia in human colon , 1994, Nature Genetics.

[61]  S. Baylin,et al.  Switch from monoallelic to biallelic human IGF2 promoter methylation during aging and carcinogenesis. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[62]  O. Kovalchuk,et al.  Loss of DNA methylation and histone H4 lysine 20 trimethylation in human breast cancer cells is associated with aberrant expression of DNA methyltransferase 1, Suv4-20h2 histone methyltransferase and methyl-binding proteins , 2006, Cancer biology & therapy.

[63]  D. Sinclair,et al.  The role of nuclear architecture in genomic instability and ageing , 2007, Nature Reviews Molecular Cell Biology.

[64]  A. Bird DNA methylation patterns and epigenetic memory. , 2002, Genes & development.

[65]  C. Allis,et al.  The language of covalent histone modifications , 2000, Nature.

[66]  V. Klimenko,et al.  The 5-methylcytosine in DNA of rats. Tissue and age specificity and the changes induced by hydrocortisone and other agents. , 1973, Gerontologia.

[67]  T. Kouzarides Histone methylation in transcriptional control. , 2002, Current opinion in genetics & development.

[68]  D. Reinberg,et al.  The key to development: interpreting the histone code? , 2005, Current opinion in genetics & development.

[69]  C. Allis,et al.  Roles of histone acetyltransferases and deacetylases in gene regulation , 1998, BioEssays : news and reviews in molecular, cellular and developmental biology.

[70]  K. Yanagisawa,et al.  Identification of hypoxia-inducible factor-1 alpha as a novel target for miR-17-92 microRNA cluster. , 2008, Cancer research.

[71]  George A Calin,et al.  MiR-15a and MiR-16 control Bmi-1 expression in ovarian cancer. , 2009, Cancer research.

[72]  Abena B. Redwood,et al.  Loss of A-type lamins and genomic instability , 2009, Cell cycle.

[73]  R. Weinberg,et al.  hSIR2SIRT1 Functions as an NAD-Dependent p53 Deacetylase , 2001, Cell.

[74]  C. Burge,et al.  Most mammalian mRNAs are conserved targets of microRNAs. , 2008, Genome research.

[75]  George A. Calin,et al.  A MicroRNA Signature of Hypoxia , 2006, Molecular and Cellular Biology.

[76]  Lei Zeng,et al.  Structure and ligand of a histone acetyltransferase bromodomain , 1999, Nature.

[77]  S. Grewal,et al.  Heterochromatin revisited , 2007, Nature Reviews Genetics.

[78]  S. Nishizuka,et al.  Multiple tumor suppressor genes are increasingly methylated with age in non‐neoplastic gastric epithelia , 2006, Cancer science.

[79]  C. Allis,et al.  Translating the Histone Code , 2001, Science.

[80]  M. Fraga,et al.  Loss of acetylation at Lys16 and trimethylation at Lys20 of histone H4 is a common hallmark of human cancer , 2005, Nature Genetics.

[81]  Nick Gilbert,et al.  Chromatin Architecture of the Human Genome Gene-Rich Domains Are Enriched in Open Chromatin Fibers , 2004, Cell.

[82]  Yang Shi,et al.  Reversal of Histone Lysine Trimethylation by the JMJD2 Family of Histone Demethylases , 2006, Cell.

[83]  Abena B. Redwood,et al.  Novel roles for A‐type lamins in telomere biology and the DNA damage response pathway , 2009, EMBO Journal.

[84]  L. Guarente,et al.  Negative control of p53 by Sir2alpha promotes cell survival under stress. , 2001, Cell.

[85]  S. Khorasanizadeh The Nucleosome From Genomic Organization to Genomic Regulation , 2004, Cell.

[86]  C. Morrison,et al.  MicroRNA-29 family reverts aberrant methylation in lung cancer by targeting DNA methyltransferases 3A and 3B , 2007, Proceedings of the National Academy of Sciences.

[87]  T. Jenuwein,et al.  An epigenetic road map for histone lysine methylation , 2003, Journal of Cell Science.

[88]  Peter A. Jones,et al.  Histone H3-lysine 9 methylation is associated with aberrant gene silencing in cancer cells and is rapidly reversed by 5-aza-2'-deoxycytidine. , 2002, Cancer research.

[89]  Laura Scott,et al.  Recurrent de novo point mutations in lamin A cause Hutchinson–Gilford progeria syndrome , 2003, Nature.

[90]  M. Esteller,et al.  How epigenetics can explain human metastasis: A new role for microRNAs , 2009 .

[91]  Peter A. Jones,et al.  The putative tumor suppressor microRNA-101 modulates the cancer epigenome by repressing the polycomb group protein EZH2. , 2009, Cancer research.

[92]  Danny Reinberg,et al.  Histone lysine methylation: a signature for chromatin function. , 2003, Trends in genetics : TIG.

[93]  L. Guarente,et al.  Increased dosage of a sir-2 gene extends lifespan in Caenorhabditis elegans , 2001, Nature.

[94]  F. Collins,et al.  Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[95]  E. Ballestar,et al.  Methyl-CpG-binding proteins in cancer: blaming the DNA methylation messenger. , 2005, Biochemistry and cell biology = Biochimie et biologie cellulaire.

[96]  T. Kouzarides Chromatin Modifications and Their Function , 2007, Cell.

[97]  E. Wang,et al.  Epigenetic Control of MicroRNA Expression and Aging , 2009, Current genomics.

[98]  A. Feinberg,et al.  Intra-individual change over time in DNA methylation with familial clustering. , 2008, JAMA.

[99]  M. Fraga,et al.  The role of epigenetics in aging and age-related diseases , 2009, Ageing Research Reviews.

[100]  D. Reinberg,et al.  Human SirT1 interacts with histone H1 and promotes formation of facultative heterochromatin. , 2004, Molecular cell.

[101]  Z. Hall Cancer , 1906, The Hospital.

[102]  Namjin Chung,et al.  Sirt1 promotes fat mobilization in white adipocytes by repressing PPAR-γ , 2004, Nature.

[103]  J. Issa,et al.  P14 methylation in human colon cancer is associated with microsatellite instability and wild-type p53. , 2003, Gastroenterology.

[104]  D. Haber,et al.  DNA Methyltransferases Dnmt3a and Dnmt3b Are Essential for De Novo Methylation and Mammalian Development , 1999, Cell.

[105]  V. Ambros,et al.  The Caenorhabditis elegans Heterochronic Regulator LIN-14 Is a Novel Transcription Factor That Controls the Developmental Timing of Transcription from the Insulin/Insulin-Like Growth Factor Gene ins-33 by Direct DNA Binding , 2005, Molecular and Cellular Biology.

[106]  V. L. Wilson,et al.  DNA methylation decreases in aging but not in immortal cells. , 1983, Science.

[107]  M. Thakur,et al.  Methylation of chromosomal proteins and DNA of rat brain and its modulation by estradiol and calcium during aging , 1981, Experimental Gerontology.

[108]  C. Mello,et al.  Revealing the world of RNA interference , 2004, Nature.

[109]  Gregory J. Hannon,et al.  microRNAs join the p53 network — another piece in the tumour-suppression puzzle , 2007, Nature Reviews Cancer.

[110]  T. Ono,et al.  Alterations of c-fos gene methylation in the processes of aging and tumorigenesis in human liver. , 1996, Mutation research.

[111]  V. Ambros,et al.  The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14 , 1993, Cell.

[112]  Tom Misteli,et al.  The Cell Nucleus and Aging: Tantalizing Clues and Hopeful Promises , 2005, PLoS biology.

[113]  Brian Burke,et al.  Loss of a-Type Lamin Expression Compromises Nuclear Envelope Integrity Leading to Muscular Dystrophy , 1999, The Journal of cell biology.

[114]  Pierre Cau,et al.  Lamin A Truncation in Hutchinson-Gilford Progeria , 2003, Science.

[115]  Bradley R. Cairns,et al.  Chromatin remodelling: the industrial revolution of DNA around histones , 2006, Nature Reviews Molecular Cell Biology.

[116]  Paul Tempst,et al.  JHDM2A, a JmjC-Containing H3K9 Demethylase, Facilitates Transcription Activation by Androgen Receptor , 2006, Cell.

[117]  M. Grunstein Histone acetylation in chromatin structure and transcription , 1997, Nature.

[118]  M. Turunen,et al.  Hypoxia induces microRNA miR‐210 in vitro and in vivo , 2008, FEBS letters.

[119]  H. Horvitz,et al.  MicroRNA expression profiles classify human cancers , 2005, Nature.

[120]  Y. Kwan,et al.  Identification of histone methylation multiplicities patterns in the brain of senescence-accelerated prone mouse 8 , 2010, Biogerontology.

[121]  Manel Esteller,et al.  Epigenetics and aging: the targets and the marks. , 2007, Trends in genetics : TIG.

[122]  L. Bonetta Edible vaccines: not quite ready for prime time , 2002, Nature Medicine.

[123]  Peter A. Jones,et al.  The Epigenomics of Cancer , 2007, Cell.

[124]  Stuart L. Schreiber,et al.  Active genes are tri-methylated at K4 of histone H3 , 2002, Nature.

[125]  D. Bartel MicroRNAs: Target Recognition and Regulatory Functions , 2009, Cell.

[126]  A. Feinberg,et al.  The emerging science of epigenomics. , 2006, Human molecular genetics.

[127]  R. Jaenisch,et al.  DNA Methylation in the Human Cerebral Cortex Is Dynamically Regulated throughout the Life Span and Involves Differentiated Neurons , 2007, PloS one.

[128]  B. Rogina,et al.  Sir2 mediates longevity in the fly through a pathway related to calorie restriction. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[129]  Mala Murthy,et al.  Redistribution of Silencing Proteins from Telomeres to the Nucleolus Is Associated with Extension of Life Span in S. cerevisiae , 1997, Cell.

[130]  M. Blasco,et al.  Role of Rb Family in the Epigenetic Definition of Chromatin , 2005, Cell cycle.

[131]  M. Esteller Epigenetics in cancer. , 2008, The New England journal of medicine.

[132]  T. Jenuwein,et al.  The many faces of histone lysine methylation. , 2002, Current opinion in cell biology.

[133]  G. Romanov,et al.  Methylation of reiterated sequences in mammalian DNAs. Effects of the tissue type, age, malignancy and hormonal induction. , 1981, Biochimica et biophysica acta.

[134]  D. Mccormick Sequence the Human Genome , 1986, Bio/Technology.

[135]  Manel Esteller,et al.  Role of the RB1 family in stabilizing histone methylation at constitutive heterochromatin , 2005, Nature Cell Biology.

[136]  P. Klatt,et al.  Suv4-20h deficiency results in telomere elongation and derepression of telomere recombination , 2007, The Journal of cell biology.

[137]  J. Workman,et al.  Function and Selectivity of Bromodomains in Anchoring Chromatin-Modifying Complexes to Promoter Nucleosomes , 2002, Cell.

[138]  Ali Shilatifard,et al.  Chromatin modifications by methylation and ubiquitination: implications in the regulation of gene expression. , 2006, Annual review of biochemistry.

[139]  S. Baylin,et al.  Double Strand Breaks Can Initiate Gene Silencing and SIRT1-Dependent Onset of DNA Methylation in an Exogenous Promoter CpG Island , 2008, PLoS genetics.

[140]  M. Serrano,et al.  Polycomb Mediated Epigenetic Silencing and Replication Timing at the INK4a/ARF Locus during Senescence , 2009, PloS one.

[141]  T. Jenuwein,et al.  Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component , 2002, Nature Genetics.