2,460
Views
8
CrossRef citations to date
0
Altmetric
Short Communication

The Histone Modification H3K4me3 is Altered at the ANK1 Locus in Alzheimer's Disease Brain

ORCID Icon, , , , , , , & ORCID Icon show all
Article: FSO665 | Received 15 Aug 2020, Accepted 04 Nov 2020, Published online: 09 Feb 2021

References

  • PrinceM , AndersW , MaëlennG , Gemma-ClaireA , Yu-TzuW , MatthewP. World Alzheimer Report 2015 - The Global Impact of Dementia, an analysis of prevalence, incidence, cost and trends. Alzheimer's Dis. Int.1–87 (2015).
  • SmithRG , LunnonK. DNA modifications and Alzheimer's disease. Adv. Exp. Med. Biol.978, 303–319 (2017).
  • LunnonK , MillJ. Epigenetic studies in Alzheimer's disease: current findings, caveats, and considerations for future studies. Am. J. Med. Genet. B Neuropsychiatr. Genet.162B(8), 789–799 (2013).
  • RoubroeksJaY , SmithRG , VanDen Hove DLA , LunnonK. Epigenetics and DNA methylomic profiling in Alzheimer's disease and other neurodegenerative diseases. J. Neurochem.143(2), 158–170 (2017).
  • SmithAR , SmithRG , PishvaEet al.Parallel profiling of DNA methylation and hydroxymethylation highlights neuropathology-associated epigenetic variation in Alzheimer's disease. Clin. Epigenetics11(1), 52 (2019).
  • SmithRG , HannonE , DeJager PLet al.Elevated DNA methylation across a 48-kb region spanning the HOXA gene cluster is associated with Alzheimer's disease neuropathology. Alzheimers Dement.14(12), 1580–1588 (2018).
  • LunnonK , SmithR , HannonEet al.Methylomic profiling implicates cortical deregulation of ANK1 in Alzheimer's disease. Nat. Neurosci.17(9), 1164–1170 (2014).
  • DeJager PL , SrivastavaG , LunnonKet al.Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat. Neurosci.17(9), 1156–1163 (2014).
  • LardenoijeR , RoubroeksJaY , PishvaEet al.Alzheimer's disease-associated (hydroxy)methylomic changes in the brain and blood. Clin. Epigenetics11(1), 164 (2019).
  • SmithRG , PishvaE , ShirebyGet al.Meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex. bioRxiv doi:10.1101/2020.02.28.9578942020.2002.2028.957894 (2020).
  • SmithAR , SmithRG , BurrageJet al.A cross-brain regions study of ANK1 DNA methylation in different neurodegenerative diseases. Neurobiol. Aging74, 70–76 (2019).
  • CedarH , BergmanY. Linking DNA methylation and histone modification: patterns and paradigms. Nat. Rev. Genet.10(5), 295–304 (2009).
  • Sadakierska-ChudyA , FilipM. A comprehensive view of the epigenetic landscape. Part II: histone post-translational modification, nucleosome level, and chromatin regulation by ncRNAs. Neurotox Res.27, 172–197 (2015).
  • Santos-RosaH , SchneiderR , BannisterAJet al.Active genes are tri-methylated at K4 of histone H3. Nature419(6905), 407–411 (2002).
  • BarskiA , CuddapahS , CuiKet al.High-resolution profiling of histone methylations in the human genome. Cell129(4), 823–837 (2007).
  • BoyerLA , PlathK , ZeitlingerJet al.Polycomb complexes repress developmental regulators in murine embryonic stem cells. Nature441(7091), 349–353 (2006).
  • LeeTI , JennerRG , BoyerLAet al.Control of developmental regulators by polycomb in human embryonic stem cells. Cell125(2), 301–313 (2006).
  • KouzaridesT. Chromatin modifications and their function. Cell128 (2007).
  • BernsteinBE , KamalM , Lindblad-TohKet al.Genomic maps and comparative analysis of histone modifications in human and mouse. Cell120(2), 169–181 (2005).
  • KimHS , KimEM , KimNJet al.Inhibition of histone deacetylation enhances the neurotoxicity induced by the c-terminal fragments of amyloid precursor protein. J. Neurosci. Res.75(1), 117–124 (2004).
  • GuanJ-S , HaggartySJ , GiacomettiEet al.HDAC2 negatively regulates memory formation and synaptic plasticity. Nature459, 55 (2009).
  • KleinHU , MccabeC , GjoneskaEet al.Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains. Nat. Neurosci.22(1), 37–46 (2019).
  • MarziSJ , LeungSK , RibarskaTet al.A histone acetylome-wide association study of Alzheimer's disease identifies disease-associated H3K27ac differences in the entorhinal cortex. Nat. Neurosci.21(11), 1618–1627 (2018).
  • YocumAO , SteinerLA , SeidelNEet al.A tissue-specific chromatin loop activates the erythroid ankyrin-1 promoter. Blood120(17), 3586–3593 (2012).
  • UntergasserA , CutcutacheI , KoressaarTet al.Primer3–new capabilities and interfaces. Nucleic Acids Res.40(15), (2012).
  • TaberlayPhillippa C , KellyTheresa K , LiuC-Cet al.Polycomb-repressed genes have permissive enhancers that initiate reprogramming. Cell147(6), 1283–1294 (2011).
  • Vienna RDCT. R Foundation for Statistical Computing (2012).
  • HarikumarA , MeshorerE. Chromatin remodeling and bivalent histone modifications in embryonic stem cells. EMBO Rep.16(12), 1609–1619 (2015).
  • BalasubramanianD , Akhtar-ZaidiB , SongLet al.H3K4me3 inversely correlates with DNA methylation at a large class of non-CpG-island-containing start sites. Genome Med.4(5), 47 (2012).
  • MastroeniD , SekarS , NolzJet al.ANK1 is up-regulated in laser captured microglia in Alzheimer's brain; the importance of addressing cellular heterogeneity. PloS one12(7), e0177814 (2017).
  • GolebiewskaA , AtkinsonSP , LakoM , ArmstrongL. Epigenetic landscaping during hESC differentiation to neural cells. Stem cells (Dayton, Ohio)27(6), 1298–1308 (2009).
  • PanG , TianS , NieJet al.Whole-genome analysis of histone H3 lysine 4 and lysine 27 methylation in human embryonic stem cells. Cell Stem Cell1(3), 299–312 (2007).
  • KondoY. Epigenetic cross-talk between DNA methylation and histone modifications in human cancers. Yonsei Med. J.50(4), 455–463 (2009).
  • NanX , NgHH , JohnsonCAet al.Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature393(6683), 386–389 (1998).
  • ChiP , AllisCD , WangGG. Covalent histone modifications–miswritten, misinterpreted and mis-erased in human cancers. Nat. Rev. Cancer10(7), 457–469 (2010).
  • JinB , LiY , RobertsonKD. DNA methylation: superior or subordinate in the epigenetic hierarchy?Genes Cancer2(6), 607–617 (2011).
  • MaunakeaAK , NagarajanRP , BilenkyMet al.Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature466(7303), 253–257 (2010).
  • SpiersH , HannonE , SchalkwykLC , BrayNJ , MillJ. 5-hydroxymethylcytosine is highly dynamic across human fetal brain development. BMC Genomics18(1), 738 (2017).
  • MunzelM , GlobischD , BrucklTet al.Quantification of the sixth DNA base hydroxymethylcytosine in the brain. Angew Chem. Int. Ed. Engl.49(31), 5375–5377 (2010).
  • KriaucionisS , HeintzN. The nuclear DNA base 5-hydroxymethylcytosine is present in Purkinje neurons and the brain. Science324(5929), 929–930 (2009).
  • SzulwachKE , LiX , LiYet al.Integrating 5-hydroxymethylcytosine into the epigenomic landscape of human embryonic stem cells. PLoS Genet.7(6), e1002154 (2011).
  • WeberM , HellmannI , StadlerMBet al.Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat. Genet.39(4), 457–466 (2007).
  • OoiSK , QiuC , BernsteinEet al.DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature448(7154), 714–717 (2007).
  • RoseNR , KloseRJ. Understanding the relationship between DNA methylation and histone lysine methylation. Biochim. Biophys. Acta1839(12), 1362–1372 (2014).
  • OtaniJ , NankumoT , AritaK , InamotoS , AriyoshiM , ShirakawaM. Structural basis for recognition of H3K4 methylation status by the DNA methyltransferase 3A ATRX-DNMT3-DNMT3L domain. EMBO Rep.10(11), 1235–1241 (2009).
  • KarlićR , ChungH-R , LasserreJ , VlahovičekK , VingronM. Histone modification levels are predictive for gene expression. Proc. Natl Acad. Sci. USA107(7), 2926–2931 (2010).