Age-associated epigenetic drift: implications, and a case of epigenetic thrift?

Abstract:

:It is now well established that the genomic landscape of DNA methylation (DNAm) gets altered as a function of age, a process we here call 'epigenetic drift'. The biological, functional, clinical and evolutionary significance of this epigenetic drift, however, remains unclear. We here provide a brief review of epigenetic drift, focusing on the potential implications for ageing, stem cell biology and disease risk prediction. It has been demonstrated that epigenetic drift affects most of the genome, suggesting a global deregulation of DNAm patterns with age. A component of this drift is tissue-specific, allowing remarkably accurate age-predictive models to be constructed. Another component is tissue-independent, targeting stem cell differentiation pathways and affecting stem cells, which may explain the observed decline of stem cell function with age. Age-associated increases in DNAm target developmental genes, overlapping those associated with environmental disease risk factors and with disease itself, notably cancer. In particular, cancers and precursor cancer lesions exhibit aggravated age DNAm signatures. Epigenetic drift is also influenced by genetic factors. Thus, drift emerges as a promising biomarker for premature or biological ageing, and could potentially be used in geriatrics for disease risk prediction. Finally, we propose, in the context of human evolution, that epigenetic drift may represent a case of epigenetic thrift, or bet-hedging. In summary, this review demonstrates the growing importance of the 'ageing epigenome', with potentially far-reaching implications for understanding the effect of age on stem cell function and differentiation, as well as for disease prevention.

journal_name

Hum Mol Genet

journal_title

Human molecular genetics

authors

Teschendorff AE,West J,Beck S

doi

10.1093/hmg/ddt375

subject

Has Abstract

pub_date

2013-10-15 00:00:00

pages

R7-R15

issue

R1

eissn

0964-6906

issn

1460-2083

pii

ddt375

journal_volume

22

pub_type

杂志文章,评审
  • Disruption of the neurexin 1 gene is associated with schizophrenia.

    abstract::Deletions within the neurexin 1 gene (NRXN1; 2p16.3) are associated with autism and have also been reported in two families with schizophrenia. We examined NRXN1, and the closely related NRXN2 and NRXN3 genes, for copy number variants (CNVs) in 2977 schizophrenia patients and 33 746 controls from seven European popula...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddn351

    authors: Rujescu D,Ingason A,Cichon S,Pietiläinen OP,Barnes MR,Toulopoulou T,Picchioni M,Vassos E,Ettinger U,Bramon E,Murray R,Ruggeri M,Tosato S,Bonetto C,Steinberg S,Sigurdsson E,Sigmundsson T,Petursson H,Gylfason A,Olason

    更新日期:2009-03-01 00:00:00

  • TOPORS, implicated in retinal degeneration, is a cilia-centrosomal protein.

    abstract::We recently reported that mutations in the widely expressed nuclear protein TOPORS (topoisomerase I-binding arginine/serine rich) are associated with autosomal dominant retinal degeneration. However, the precise localization and a functional role of TOPORS in the retina remain unknown. Here, we demonstrate that TOPORS...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddq543

    authors: Chakarova CF,Khanna H,Shah AZ,Patil SB,Sedmak T,Murga-Zamalloa CA,Papaioannou MG,Nagel-Wolfrum K,Lopez I,Munro P,Cheetham M,Koenekoop RK,Rios RM,Matter K,Wolfrum U,Swaroop A,Bhattacharya SS

    更新日期:2011-03-01 00:00:00

  • COPI transport complexes bind to specific RNAs in neuronal cells.

    abstract::Our fundamental understanding of how several thousand diverse RNAs are recognized in the soma, sorted, packaged, transported and localized within the cell is fragmentary. The COPa and COPb proteins of the coatomer protein I (COPI) vesicle complex were reported to interact with specific RNAs and represent a candidate R...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/dds480

    authors: Todd AG,Lin H,Ebert AD,Liu Y,Androphy EJ

    更新日期:2013-02-15 00:00:00

  • Arl3 and RP2 regulate the trafficking of ciliary tip kinesins.

    abstract::Ciliary trafficking defects are the underlying cause of many ciliopathies, including Retinitis Pigmentosa (RP). Anterograde intraflagellar transport (IFT) is mediated by kinesin motor proteins; however, the function of the homodimeric Kif17 motor in cilia is poorly understood, whereas Kif7 is known to play an importan...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx143

    authors: Schwarz N,Lane A,Jovanovic K,Parfitt DA,Aguila M,Thompson CL,da Cruz L,Coffey PJ,Chapple JP,Hardcastle AJ,Cheetham ME

    更新日期:2017-07-01 00:00:00

  • Fibulin-5 mutations: mechanisms of impaired elastic fiber formation in recessive cutis laxa.

    abstract::To elucidate the molecular mechanisms of impaired elastic fiber formation in recessive cutis laxa, we have investigated two disease-causing missense substitutions in fibulin-5, C217R and S227P. Pulse-chase immunoprecipitation experiments indicated that S227P mutant fibulin-5 was synthesized and secreted by skin fibrob...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddl414

    authors: Hu Q,Loeys BL,Coucke PJ,De Paepe A,Mecham RP,Choi J,Davis EC,Urban Z

    更新日期:2006-12-01 00:00:00

  • Characterization of molecular defects in xeroderma pigmentosum group F in relation to its clinically mild symptoms.

    abstract::Xeroderma pigmentosum (XP) complementation group F was first reported in Japan and most XP-F patients reported to date are Japanese. The clinical features of XP-F patients are rather mild, including late onset of skin cancer. Recently a cDNA that corrects the repair deficiency of cultured XP-F cells was isolated. The ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/7.6.969

    authors: Matsumura Y,Nishigori C,Yagi T,Imamura S,Takebe H

    更新日期:1998-06-01 00:00:00

  • Identification of a novel nuclear localization signal in Tbx1 that is deleted in DiGeorge syndrome patients harboring the 1223delC mutation.

    abstract::DiGeorge syndrome (DGS) is the most common human chromosomal deletion syndrome and is frequently associated with deletions on chromosome 22q11. Approximately 17% of patients with the phenotypic features of this syndrome have no detectable genomic deletion. Animal studies using mouse models have implicated Tbx1 as a cr...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi081

    authors: Stoller JZ,Epstein JA

    更新日期:2005-04-01 00:00:00

  • Imprinting analysis of three genes in the Prader-Willi/Angelman region: SNRPN, E6-associated protein, and PAR-2 (D15S225E).

    abstract::In order to identify genes in the Prader-Willi/Angelman syndrome critical region, radiolabeled cDNA probes from poly(A)+ RNA from mouse tissues were used to identify potential exon-containing genomic DNA fragments in cosmid or phage clones from appropriate yeast artificial chromosomes, and these fragments were subsequ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/3.2.309

    authors: Nakao M,Sutcliffe JS,Durtschi B,Mutirangura A,Ledbetter DH,Beaudet AL

    更新日期:1994-02-01 00:00:00

  • BRCA2 minor transcript lacking exons 4-7 supports viability in mice and may account for survival of humans with a pathogenic biallelic mutation.

    abstract::The breast cancer gene, BRCA2, is essential for viability, yet patients with Fanconi anemia-D1 subtype are born alive with biallelic mutations in this gene. The hypomorphic nature of the mutations is believed to support viability, but this is not always apparent. One such mutation is IVS7+2T>G, which causes premature ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddw066

    authors: Thirthagiri E,Klarmann KD,Shukla AK,Southon E,Biswas K,Martin BK,North SL,Magidson V,Burkett S,Haines DC,Noer K,Matthai R,Tessarollo L,Loncarek J,Keller JR,Sharan SK

    更新日期:2016-05-15 00:00:00

  • An embryonic-like methylation pattern of classical satellite DNA is observed in ICF syndrome.

    abstract::ICF syndrome has been described as the association of variable immunodeficiency, facial anomalies and centromeric heterochromatin instability. Since the chromosome rearrangements seen in cells of ICF patients are reminiscent of the chromosomal changes induced by the undermethylating agent 5-azacytidine in the late S-p...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/2.6.731

    authors: Jeanpierre M,Turleau C,Aurias A,Prieur M,Ledeist F,Fischer A,Viegas-Pequignot E

    更新日期:1993-06-01 00:00:00

  • Proximal deletions of the long arm of the Y chromosome suggest a critical region associated with a specific subset of characteristic Turner stigmata.

    abstract::Turner syndrome is a complex human disorder that generally associates a 45,X karyotype to a female phenotype presenting with gonadal dysgenesis, short stature and a number of characteristic somatic features. It has been hypothesized that this specific phenotype was the consequence of the haploinsufficiency of some X-l...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/4.9.1565

    authors: Barbaux S,Vilain E,Raoul O,Gilgenkrantz S,Jeandidier E,Chadenas D,Souleyreau N,Fellous M,McElreavey K

    更新日期:1995-09-01 00:00:00

  • Mutations in congenital myasthenic syndromes reveal an epsilon subunit C-terminal cysteine, C470, crucial for maturation and surface expression of adult AChR.

    abstract::Many congenital myasthenic syndromes (CMS) are associated with mutations in the genes encoding the acetylcholine receptor (AChR), an oligomeric protein with the structure alpha(2)betadelta epsilon. AChR deficiency is frequently due to homozygous or heteroallelic mutations in the AChR epsilon subunit, most of which cau...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/11.24.3087

    authors: Ealing J,Webster R,Brownlow S,Abdelgany A,Oosterhuis H,Muntoni F,Vaux DJ,Vincent A,Beeson D

    更新日期:2002-11-15 00:00:00

  • Localization of a tumor suppressor gene in 11p15.5 using the G401 Wilms' tumor assay.

    abstract::Multiple studies have underscored the importance of loss of tumor suppressor genes in the development of human cancer. To identify these genes, we used somatic cell hybrids in a functional assay for tumor suppression in vivo. A tumor suppressor gene in 11p15.5 was detected by transferring single human chromosomes into...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/5.2.239

    authors: Reid LH,West A,Gioeli DG,Phillips KK,Kelleher KF,Araujo D,Stanbridge EJ,Dowdy SF,Gerhard DS,Weissman BE

    更新日期:1996-02-01 00:00:00

  • Transgenic mice expressing CUG-BP1 reproduce splicing mis-regulation observed in myotonic dystrophy.

    abstract::Myotonic dystrophy type I (DM1) is an RNA-mediated disease caused by a non-coding CTG repeat expansion. A key feature of the RNA-mediated pathogenesis model for DM is the disrupted splicing of specific pre-mRNA targets. A link has been established between splicing regulation by CUG-BP1, a member of the CELF family of ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi162

    authors: Ho TH,Bundman D,Armstrong DL,Cooper TA

    更新日期:2005-06-01 00:00:00

  • Hypermorphic and hypomorphic AARS alleles in patients with CMT2N expand clinical and molecular heterogeneities.

    abstract::Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes implicated in several dominant and recessive disease phenotypes. The canonical function of ARSs is to couple an amino acid to a cognate transfer RNA (tRNA). We identified three novel disease-associated missense mutations in the alanyl-tRNA synthetase...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddy290

    authors: Weterman MAJ,Kuo M,Kenter SB,Gordillo S,Karjosukarso DW,Takase R,Bronk M,Oprescu S,van Ruissen F,Witteveen RJW,Bienfait HME,Breuning M,Verhamme C,Hou YM,de Visser M,Antonellis A,Baas F

    更新日期:2018-12-01 00:00:00

  • Hay-Wells syndrome is caused by heterozygous missense mutations in the SAM domain of p63.

    abstract::Hay-Wells syndrome, also known as ankyloblepharon-ectodermal dysplasia-clefting (AEC) syndrome (OMIM 106260), is a rare autosomal dominant disorder characterized by congenital ectodermal dysplasia, including alopecia, scalp infections, dystrophic nails, hypodontia, ankyloblepharon and cleft lip and/or cleft palate. Th...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/10.3.221

    authors: McGrath JA,Duijf PH,Doetsch V,Irvine AD,de Waal R,Vanmolkot KR,Wessagowit V,Kelly A,Atherton DJ,Griffiths WA,Orlow SJ,van Haeringen A,Ausems MG,Yang A,McKeon F,Bamshad MA,Brunner HG,Hamel BC,van Bokhoven H

    更新日期:2001-02-01 00:00:00

  • Interaction of presenilins with FKBP38 promotes apoptosis by reducing mitochondrial Bcl-2.

    abstract::Presenilins 1 and 2 (PS1/2), causative molecules for familial Alzheimer's disease (FAD), are multipass transmembrane proteins localized predominantly in the endoplasmic reticulum (ER) and Golgi apparatus. Heteromeric protein complexes containing PS1/2 are thought to participate in several functions, including intramem...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi195

    authors: Wang HQ,Nakaya Y,Du Z,Yamane T,Shirane M,Kudo T,Takeda M,Takebayashi K,Noda Y,Nakayama KI,Nishimura M

    更新日期:2005-07-01 00:00:00

  • Spinal muscular atrophy: mechanisms and therapeutic strategies.

    abstract::Spinal muscular atrophy (SMA) is an autosomal recessive neurodegenerative disorder and a leading genetic cause of infantile mortality. SMA is caused by mutation or deletion of Survival Motor Neuron-1 (SMN1). The clinical features of the disease are caused by specific degeneration of alpha-motor neurons in the spinal c...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,评审

    doi:10.1093/hmg/ddq147

    authors: Lorson CL,Rindt H,Shababi M

    更新日期:2010-04-15 00:00:00

  • Genome-wide expression profiling of lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways.

    abstract::Autism is a heterogeneous condition that is likely to result from the combined effects of multiple genetic factors interacting with environmental factors. Given its complexity, the study of autism associated with Mendelian single gene disorders or known chromosomal etiologies provides an important perspective. We used...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddm116

    authors: Nishimura Y,Martin CL,Vazquez-Lopez A,Spence SJ,Alvarez-Retuerto AI,Sigman M,Steindler C,Pellegrini S,Schanen NC,Warren ST,Geschwind DH

    更新日期:2007-07-15 00:00:00

  • Homozygous EEF1A2 mutation causes dilated cardiomyopathy, failure to thrive, global developmental delay, epilepsy and early death.

    abstract::Eukaryotic elongation factor 1A (EEF1A), is encoded by two distinct isoforms, EEF1A1 and EEF1A2; whereas EEF1A1 is expressed almost ubiquitously, EEF1A2 expression is limited such that it is only detectable in skeletal muscle, heart, brain and spinal cord. Currently, the role of EEF1A2 in normal cardiac development an...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddx239

    authors: Cao S,Smith LL,Padilla-Lopez SR,Guida BS,Blume E,Shi J,Morton SU,Brownstein CA,Beggs AH,Kruer MC,Agrawal PB

    更新日期:2017-09-15 00:00:00

  • Hypoxic drive caused type 3 neovascularization in a preclinical model of exudative age-related macular degeneration.

    abstract::Hypoxia associated with the high metabolic demand of rods has been implicated in the pathology of age-related macular degeneration (AMD), the most common cause of adult blindness in the developed world. The majority of AMD-associated severe vision loss cases are due to exudative AMD, characterized by neovascularizatio...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddz159

    authors: Zhang L,Cui X,Han Y,Park KS,Gao X,Zhang X,Yuan Z,Hu Y,Hsu CW,Li X,Bassuk AG,Mahajan VB,Wang NK,Tsang SH

    更新日期:2019-10-15 00:00:00

  • Genome-wide association study identifies a novel susceptibility gene for serum TSH levels in Chinese populations.

    abstract::Thyroid-stimulating hormone (TSH) is a sensitive indicator of thyroid function. High and low TSH levels reflect hypothyroidism and hyperthyroidism, respectively. Even within the normal range, small differences in TSH levels, on the order of 0.5-1.0 mU/l, are associated with significant differences in blood pressure, B...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddu250

    authors: Zhan M,Chen G,Pan CM,Gu ZH,Zhao SX,Liu W,Wang HN,Ye XP,Xie HJ,Yu SS,Liang J,Gao GQ,Yuan GY,Zhang XM,Zuo CL,Su B,Huang W,Ning G,Chen SJ,Chen JL,Song HD,China Consortium for Genetics of Autoimmune Thyroid Disease.

    更新日期:2014-10-15 00:00:00

  • Progress and challenges in viral vector manufacturing.

    abstract::Promising results in several clinical studies have emphasized the potential of gene therapy to address important medical needs and initiated a surge of investments in drug development and commercialization. This enthusiasm is driven by positive data in clinical trials including gene replacement for Hemophilia B, X-lin...

    journal_title:Human molecular genetics

    pub_type: 杂志文章,评审

    doi:10.1093/hmg/ddv451

    authors: van der Loo JC,Wright JF

    更新日期:2016-04-15 00:00:00

  • Batten disease: evaluation of CLN3 mutations on protein localization and function.

    abstract::Juvenile neuronal ceroid lipofuscinosis (JNCL), Batten disease, is an autosomal recessive lysosomal storage disease associated with mutations in CLN3. CLN3 has no known homology to other proteins and a function has not yet been described. The predominant mutation in CLN3 is a 1.02 kb genomic deletion that accounts for...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/9.5.735

    authors: Haskell RE,Carr CJ,Pearce DA,Bennett MJ,Davidson BL

    更新日期:2000-03-22 00:00:00

  • Increased tumour risk for BWS patients correlates with aberrant H19 and not KCNQ1OT1 methylation: occurrence of KCNQ1OT1 hypomethylation in familial cases of BWS.

    abstract::Beckwith-Wiedemann syndrome (BWS) is an overgrowth malformation syndrome that maps to human chromosome 11p15.5, a region that harbours a number of imprinted genes. We studied the methylation status of H19 and KCNQ1OT1 (LIT1/KvDMR1) in a large series of BWS patients. Different patient groups were identified: group I pa...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/10.5.467

    authors: Bliek J,Maas SM,Ruijter JM,Hennekam RC,Alders M,Westerveld A,Mannens MM

    更新日期:2001-03-01 00:00:00

  • AF-6 is a positive modulator of the PINK1/parkin pathway and is deficient in Parkinson's disease.

    abstract::Parkin E3 ubiquitin-ligase activity and its role in mitochondria homeostasis are thought to play a role in Parkinson's disease (PD). We now report that AF-6 is a novel parkin interacting protein that modulates parkin ubiquitin-ligase activity and mitochondrial roles. Parkin interacts with the AF-6 PDZ region through i...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt058

    authors: Haskin J,Szargel R,Shani V,Mekies LN,Rott R,Lim GG,Lim KL,Bandopadhyay R,Wolosker H,Engelender S

    更新日期:2013-05-15 00:00:00

  • Rapid evolution of primate antiviral enzyme APOBEC3G.

    abstract::Human cytidine deaminase APOBEC3G and the virion infectivity factor (vif) of the human immunodeficiency virus (HIV) are a pair of antagonistic molecules. In the absence of vif, APOBEC3G induces a high rate of dC to dU mutations in the nascent reverse transcripts of HIV that leads to the degradation of the HIV genome. ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddh183

    authors: Zhang J,Webb DM

    更新日期:2004-08-15 00:00:00

  • Loss of hierarchical imprinting regulation at the Prader-Willi/Angelman syndrome locus in human iPSCs.

    abstract::The human chr15q11-q13 imprinted cluster is linked to several disorders, including Prader-Willi (PWS) and Angelman (AS) syndromes. Recently, disease modeling approaches based on induced pluripotent stem cells (iPSCs) have been used to study these syndromes. A concern regarding the use of these cells for imprinted dise...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddy274

    authors: Pólvora-Brandão D,Joaquim M,Godinho I,Aprile D,Álvaro AR,Onofre I,Raposo AC,Pereira de Almeida L,Duarte ST,da Rocha ST

    更新日期:2018-12-01 00:00:00

  • Epigenetic regulation of COL15A1 in smooth muscle cell replicative aging and atherosclerosis.

    abstract::Smooth muscle cell (SMC) proliferation is a hallmark of vascular injury and disease. Global hypomethylation occurs during SMC proliferation in culture and in vivo during neointimal formation. Regardless of the programmed or stochastic nature of hypomethylation, identifying these changes is important in understanding v...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddt365

    authors: Connelly JJ,Cherepanova OA,Doss JF,Karaoli T,Lillard TS,Markunas CA,Nelson S,Wang T,Ellis PD,Langford CF,Haynes C,Seo DM,Goldschmidt-Clermont PJ,Shah SH,Kraus WE,Hauser ER,Gregory SG

    更新日期:2013-12-20 00:00:00

  • Allelic association of the human homologue of the mouse modifier Ptprj with breast cancer.

    abstract::Human homologues of mouse cancer modifier genes may play a role in cancer risk and prognosis. A proportion of the familial risk of common cancers may be attributable to variants in such genes, each contributing to a small effect. The protein tyrosine phosphatase receptor type J (PTPRJ) has been recently identified as ...

    journal_title:Human molecular genetics

    pub_type: 杂志文章

    doi:10.1093/hmg/ddi237

    authors: Lesueur F,Pharoah PD,Laing S,Ahmed S,Jordan C,Smith PL,Luben R,Wareham NJ,Easton DF,Dunning AM,Ponder BA

    更新日期:2005-08-15 00:00:00