279
Views
0
CrossRef citations to date
0
Altmetric
Perspective

Modeling the Dynamic Epigenome: From Histone Modifications Towards Self-Organizing Chromatin

, , , , &
Pages 205-219 | Published online: 27 Mar 2012

References

  • Reik W . Stability and flexibility of epigenetic gene regulation in mammalian development. Nature447 , 425–431 (2007).
  • Oakley EJ , ZantGV. Unraveling the complex regulation of stem cells: implications for aging and cancer. Leukemia21(4) , 612–621 (2007).
  • Bernstein BE , MeissnerA, LanderES. The mammalian epigenome. Cell128(4) , 669–681 (2007).
  • Felsenfeld G , GroudineM. Controlling the double helix. Nature421 , 448–453 (2003).
  • Kuzawa CW . Timescales of human adaptation: the role of epigenetic processes. Epigenomics3(2) , 221–234 (2011).
  • Luger K , MaderAW, RichmondRK, SargentDF, RichmondTJ. Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature389(6648) , 251–260 (1997).
  • Latham JA , DentSYR. Cross-regulation of histone modifications. Nat. Struct. Mol. Biol.14(11) , 1017–1024 (2007).
  • Probst AV , DunleavyE, AlmouzniG. Epigenetic inheritance during the cell cycle. Nat. Rev. Mol. Cell Biol.10(3) , 192–206 (2009).
  • Dodd IB , MicheelsenMA, SneppenK, ThonG. Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell129 , 813–822 (2007).
  • Szyf M . Implicatiions of a life-long dynamic epigenome. Epigenomics1(1) , 9–12 (2009).
  • Passarge E . Emil Heitz and the concept of heterochromatin: longitudinal chromosome differentiation was recognized fifty years ago. Am. J. Hum. Genet.31(2) , 106–115 (1979).
  • Stedman E , StedmanE. Cell specificity of histones. Nature166 , 780–781 (1950).
  • Allfrey VG , MirskyAE. Structural modifications of histones and their possible role in the regulation of RNA synthesis. Science144(3618) , 559 (1964).
  • Grunstein M . Histone function in transcription. Annu. Rev. Cell Biol.6 , 643–678 (1990).
  • Brownell JE , ZhouJ, RanalliT et al. Tetrahymena histone acetyltransferase A: a homolog to yeast Gcn5p linking histone acetylation to gene activation. Cell 84(6) , 843–851 (1996).
  • Turner BM . Defining an epigenetic code. Nat. Cell Biol.9(1) , 2–6 (2007).
  • Benecke A . Chromatin code, local non-equilibrium dynamics, and the emergence of transcription regulatory programs. Eur. Phys. J. E. Soft Matter19(3) , 353–366 (2006).
  • Prohaska SJ , StadlerPF, KrakauerDC. Innovation in gene regulation: the case of chromatin computation. J. Theor. Biol.265 , 27–44 (2010).
  • Sedighi M , SenguptaAM. Epigenetic chromatin silencing: bistability and front propagation. Phys. Biol.4(4) , 246 (2007).
  • Karlebach G , ShamirR. Modelling and analysis of gene regulatory networks. Nat. Rev. Mol. Cell Biol.9(10) , 770–780 (2008).
  • Rusche LN , KirchmaierAL, RineJ. Ordered nucleation and spreading of silenced chromatin in Saccharomyces cerevisiae. Mol. Biol. Cell13(7) , 2207–2222 (2002).
  • Schübeler D , FrancastelC, CimboraDM, ReikA, MartinDI, GroudineM. Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human β-globin locus. Genes Dev.14(8) , 940–950 (2000).
  • Vos DD , FrederiksF, TerweijM et al. Progressive methylation of ageing histones by Dot1 functions as a timer. EMBO Rep. 12(9) , 956–962 (2011).
  • Raghavan K , RuskinHJ, PerrinD, GoasmatF, BurnsJ. Computational micromodel for epigenetic mechanisms. PLoS ONE5(11) , e14031 (2010).
  • Segal E , WidomJ. What controls nucleosome positions? Trends Genet.25(8) , 335–343 (2009).
  • David-Rus D , MukhopadhyayS, LebowitzJL, SenguptaAM. Inheritance of epigenetic chromatin silencing. J. Theor. Biol.258(1) , 112–120 (2009).
  • Arya G , MaitraA, GrigoryevSA. A structural perspective on the where, how, why, and what of nucleosome positioning. J. Biomol. Struct. Dyn.27(6) , 803–820 (2010).
  • Misteli T . Beyond the sequence: cellular organization of genome function. Cell128(4) , 787–800 (2007).
  • Duan Z , AndronescuM, SchutzK et al. A three-dimensional model of the yeast genome. Nature 465(7296) , 363–367 (2010).
  • Vilar JMG , LeiblerS. DNA looping and physical constraints on transcription regulation. J. Mol. Biol.331 , 981–989 (2003).
  • Pirrotta V , GrossDS. Epigenetic silencing mechanisms in budding yeast and fruit fly: different paths, same destinations. Mol. Cell18(4) , 395–398 (2005).
  • Thomson JP , SkenePJ, SelfridgeJ et al. CpG islands influence chromatin structure via the CpG-binding protein Cfp1. Nature 464(7291) , 1082–1086 (2010).
  • Li B , CareyM, WorkmanJL. The role of chromatin during transcription. Cell128(4) , 707–719 (2007).
  • Dion MF , KaplanT, KimM, BuratowskiS, FriedmanN, RandoOJ. Dynamics of replication-independent histone turnover in budding yeast. Science315(5817) , 1405–1408 (2007).
  • Micheelsen MA , MitaraiN, SneppenK, DoddIB. Theory for the stability and regulation of epigenetic landscapes. Phys. Biol.7(2) , 026010 (2010).
  • Mukhopadhyay S , NagarajVH, SenguptaAM. Locus dependence in epigenetic chromatin silencing. Biosystems102(1) , 49–54 (2010).
  • Annunziato AT . Split decision: what happens to nucleosomes during DNA replication? J. Biol. Chem.280(13) , 12065–12068 (2005).
  • Sneppen K , MicheelsenMA, DoddIB. Ultrasensitive gene regulation by positive feedback loops in nucleosome modification. Mol. Sys. Biol.4 , 182 (2008).
  • Angel A , SongJ, DeanC, HowardM. A Polycomb-based switch underlying quantitative epigenetic memory. Nature476 , 105–108 (2011).
  • Park PJ . ChIP-seq: advantages and challenges of a maturing technology. Nat. Rev. Genet.10(10) , 669–680 (2009).
  • Mikkelsen TS , KuM, JaffeDB et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature 448(7153) , 553–560 (2007).
  • Wang Z , ZangC, RosenfeldJA et al. Combinatorial patterns of histone acetylations and methylations in the human genome. Nat. Genet. 40(7) , 897–903 (2008).
  • Cui K , ZangC, RohTY et al. Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell 4(1) , 80–93 (2009).
  • Bock C , LengauerT. Computational epigenetics. Bioinformatics24(1) , 1–10 (2008).
  • Ooi SKT , QiuC, BernsteinE et al. DNMT3L connects unmethylated lysine 4 of histone H3 to de novo methylation of DNA. Nature 448(7154) , 714–717 (2007).
  • Hashimoto H , VertinoPM, ChengX. Molecular coupling of DNA methylation and histone methylation. Epigenomics2(5) , 657–669 (2010).
  • Sontag LB , LorinczMC, Georg Luebeck E. Dynamics, stability and inheritance of somatic DNA methylation imprints. J. Theor. Biol.242(4) , 890–899 (2006).
  • Genereux DP , MinerBE, BergstromCT, LairdCD. A population-epigenetic model to infer site-specific methylation rates from double-stranded DNA methylation patterns. Proc. Natl Acad. Sci. USA102(16) , 5802–5807 (2005).
  • Meissner A , MikkelsenTS, GuH et al. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454(7205) , 766–770 (2008).
  • Reil T . Dynamics of gene expression in an artificial genome – implications for biological and artificial ontogeny. Lect. Notes Artif. Int.1674 , 457–466 (1999).
  • Binder H , WirthH, GalleJ. Gene expression density profiles characterize modes of genomic regulation: theory and experiment. J. Biotechnol.149(3) , 98–114 (2010).
  • de Wit E , van Steensel B. Chromatin domains in higher eukaryotes: insights from genome-wide mapping studies. Chromosoma118(1) , 25–36 (2009).
  • Bushey AM , DormanER, CorcesVG. Chromatin insulators: regulatory mechanisms and epigenetic inheritance. Mol. Cell32(1) , 1–9 (2008).
  • Struhl K . Histone acetylation and transcriptional regulatory mechanisms. Genes Dev.12(5) , 599–606 (1998).
  • Arya G , SchlickT. Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model. Proc. Natl Acad. Sci. USA103(44) , 16236–16241 (2006).
  • Razin SV , GavrilovAA, PichuginA, LipinskiM, IarovaiaOV, VassetzkyYS. Transcription factories in the context of the nuclear and genome organization. Nucleic Acids Res.39(21) , 9085–9092 (2011).
  • Chambeyron S , BickmoreWA. Does looping and clustering in the nucleus regulate gene expression? Curr. Opin. Cell Biol.16(3) , 256–262 (2004).
  • Deng W , BlobelGA. Do chromatin loops provide epigenetic gene expression states? Curr. Opin. Genet. Dev.20 , 548–554 (2010).
  • Vernimmen D , GobbiMD, Sloane-StanleyJA, WoodWG, HiggsDR. Long-range chromosomal interactions regulate the timing of the transition between poised and active gene expression. EMBO J.26(8) , 2041–2051 (2007).
  • Junier I , MartinO, KepesF. Spatial and topological organization of DNA chains induced by gene co-localization. PLoS Comput. Biol.6(2) , e1000678 (2010).
  • Fraga MF , BallestarE, PazMF et al. Epigenetic differences arise during the lifetime of monozygotic twins. Proc. Natl Acad. Sci. USA 102(30) , 10604–10609 (2005).
  • Cooney CA . Are somatic cells inherently deficient in methylation metabolism? A proposed mechanism for DNA methylation loss, senescence and aging. Growth Dev. Aging57(4) , 261–273 (1993).
  • Hayashi Y , SendaT, SanoN, HorikoshiM. Theoretical framework for the histone modification network: modifications in the unstructured histone tails form a robust scale-free network. Genes Cells14(7) , 789–806 (2009).
  • Liu L , RandoTA. Manifestations and mechanisms of stem cell aging. J. Cell Biol.193(2) , 257–266 (2011).
  • Pollina EA , BrunetA. Epigenetic regulation of aging stem cells. Oncogene30(28) , 3105–3126 (2011).
  • Ordovas JM , SmithCE. Epigenetics and cardiovascular disease. Nat. Rev. Cardiol.7(9) , 510–519 (2010).
  • Penner MR , RothTL, ChawlaMK et al. Age-related changes in Arc transcription and DNA methylation within the hippocampus. Neurobiol. Aging 32(12) , 2198–2210 (2010).
  • Rakyan VK , DownTA, MaslauS et al. Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains. Genome Res. 20(4) , 434–439 (2010).
  • Rodríguez-Paredes M , EstellerM. Cancer epigenetics reaches mainstream oncology. Nat. Med.17(3) , 330–339 (2011).
  • Teschendorff AE , MenonU, Gentry-MaharajA et al. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res. 20(4) , 440–446 (2010).
  • Galle J , HoffmannM, AustG. From single cells to tissue architecture-a bottom-up approach to modelling the spatiotemporal organisation of complex multi-cellular systems. J. Math. Biol.58(1–2) , 261–283 (2009).
  • Galle J , AustG, SchallerG, BeyerT, DrasdoD. Individual cell-based models of the spatial-temporal organization of multicellular systems – achievements and limitations. Cytometry A69(7) , 704–710 (2006).
  • Thorne BC , BaileyAM, DesimoneDW, PeirceSM. Agent-based modeling of multicell morphogenic processes during development. Birth Defects Res. C Embryo Today81(4) , 344–353 (2007).

▪ Website

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.