Skip to main content
SpringerLink
Log in

Genome Regulation Is All Non-local: Maps and Functions

  • Chapter
  • First Online:
The Map and the Territory

Part of the book series: The Frontiers Collection ((FRONTCOLL))

  • 1769 Accesses

Abstract

In this chapter, we try to envision genomes both as macroscopic entities that living systems carry in the form of genetic information as well as relevant nitty-gritty details of the mechanisms that help maintain genome stability. The human genome contains approximately 6 billion bases of DNA, extending approximately to 2 m of DNA in a cell.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 109.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book
USD 139.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • B.R. Adams, S.E. Golding, R.R. Rao, K. Valerie, Dynamic dependence on ATR and ATM for double-strand break repair in human embryonic stem cells and neural descendants. PLoS ONE 5(4), e10001 (2010a)

    Article  ADS  Google Scholar 

  • B.R. Adams, A.J. Hawkins, L.F. Povirk, K. Valerie, ATM-independent, high-fidelity nonhomologous end joining predominates in human embryonic stem cells. Aging (Albany NY) 2(9), 582–596 (2010b)

    Article  Google Scholar 

  • A. Aguilar-Mahecha, B.F. Hales, B. Robaire, Expression of stress response genes in germ cells during spermatogenesis. Biol. Reprod. 65(1), 119–127 (2001)

    Article  Google Scholar 

  • A. Armesilla-Diaz, P. Bragado, I. Del Valle, E. Cuevas, I. Lazaro, C. Martin, J.C. Cigudosa, A. Silva, p53 regulates the self-renewal and differentiation of neural precursors. Neuroscience 158(4), 1378–1389 (2009a)

    Article  Google Scholar 

  • A. Armesilla-Diaz, G. Elvira, A. Silva, p53 regulates the proliferation, differentiation and spontaneous transformation of mesenchymal stem cells. Exp. Cell Res. 315(20), 3598–3610 (2009b)

    Article  Google Scholar 

  • A. Bancaud, S. Huet, N. Daigle, J. Mozziconacci, J. Beaudouin, J. Ellenberg, Molecular crowding affects diffusion and binding of nuclear proteins in heterochromatin and reveals the fractal organization of chromatin. EMBO J. 28, 3785–3798 (2009)

    Article  Google Scholar 

  • T.S. Barton, B. Robaire, B.F. Hales, DNA damage recognition in the rat zygote following chronic paternal cyclophosphamide exposure. Toxicol. Sci. 100(2), 495–503 (2007)

    Article  Google Scholar 

  • K.A. Becker, P.N. Ghule, J.A. Therrien, J.B. Lian, J.L. Stein, A.J. van Wijnen, G.S. Stein, Self-renewal of human embryonic stem cells is supported by a shortened G1 cell cycle phase. J. Cell. Physiol. 209(3), 883–893 (2006)

    Article  Google Scholar 

  • W.A. Bickmore, The spatial organization of the human genome. Annu. Rev. Genomics Hum. Genet. 14, 67–84 (2013)

    Article  Google Scholar 

  • A.N. Bogomazova, M.A. Lagarkova, L.V. Tskhovrebova, M.V. Shutova, S.L. Kiselev, Error-prone nonhomologous end joining repair operates in human pluripotent stem cells during late G2. Aging (Albany NY) 3(6), 584–596 (2011)

    Article  Google Scholar 

  • A.L. Bredemeyer, B.A. Helmink, C.L. Innes, B. Calderon, L.M. McGinnis, G.K. Mahowald, E.J. Gapud, L.M. Walker, J.B. Collins, B.K. Weaver, L. Mandik-Nayak, R.D. Schreiber, P.M. Allen, M.J. May, R.S. Paules, C.H. Bassing, B.P. Sleckman, DNA double-strand breaks activate a multi-functional genetic program in developing lymphocytes. Nature 456(7223), 819–823 (2008)

    Article  ADS  Google Scholar 

  • J. Carroll, P. Marangos, The DNA damage response in mammalian oocytes. Front. Genet. 4, 117 (2013)

    Article  Google Scholar 

  • S. Chakraborty, I. Mehta, M. Kulashreshtha, B.J. Rao, Quantitative analysis of chromosome localization in the nucleus. Methods Mol. Biol. 1228, 223–233 (2015). https://doi.org/10.1007/978-1-4939-1680-1_17

  • D. Chen, K.Z. Pan, J.E. Palter, P. Kapahi, Longevity determined by developmental arrest genes in Caenorhabditis elegans. Aging Cell 6(4), 525–533 (2007)

    Article  Google Scholar 

  • K.K. Chiruvella, R. Sebastian, S. Sharma, A.A. Karande, B. Choudhary, S.C. Raghavan, Time-dependent predominance of nonhomologous DNA end-joining pathways during embryonic development in mice. J. Mol. Biol. 417(3), 197–211 (2012)

    Article  Google Scholar 

  • V.M. Craddock, A.R. Henderson, S. Gash, Repair and replication of DNA in rat brain and liver during foetal and post-natal development, in relation to nitroso-alkyl-urea induced carcinogenesis. J. Cancer Res. Clin. Oncol. 108(1), 30–35 (1984)

    Article  Google Scholar 

  • T. Cremer, C. Cremer, Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat. Rev. Genet. 2, 292–301 (2001)

    Article  Google Scholar 

  • T. Cremer, M. Cremer, Chromosome territories. Cold Spring Harb. Perspect. Biol. 2, a003889 (2010)

    Article  Google Scholar 

  • B. de Laval, P. Pawlikowska, D. Barbieri, C. Besnard-Guerin, A. Cico, R. Kumar, M. Gaudry, V. Baud, F. Porteu, Thrombopoietin promotes NHEJ DNA repair in hematopoietic stem cells through specific activation of Erk and NF-kappaB pathways and their target IEX-1. Blood, 2014 Jan 23, vol. 123(4), pp. 509–519 (2013). https://doi.org/10.1182/blood-2013-07-515874. Epub 2013 Nov 1

  • B. de Laval, P. Pawlikowska, L. Petit-Cocault, C. Bilhou-Nabera, G. Aubin-Houzelstein, M. Souyri, F. Pouzoulet, M. Gaudry, F. Porteu, Thrombopoietin-increased DNA-PK-dependent DNA repair limits hematopoietic stem and progenitor cell mutagenesis in response to DNA damage. Cell Stem Cell 12(1), 37–48 (2013)

    Article  Google Scholar 

  • A. Derijck, G. van der Heijden, M. Giele, M. Philippens, P. de Boer, DNA double-strand break repair in parental chromatin of mouse zygotes, the first cell cycle as an origin of de novo mutation. Hum. Mol. Genet. 17(13), 1922–1937 (2008)

    Article  Google Scholar 

  • J.A. Desmarais, M.J. Hoffmann, G. Bingham, M.E. Gagou, M. Meuth, P.W. Andrews, Human embryonic stem cells fail to activate CHK1 and commit to apoptosis in response to DNA replication stress. Stem Cells 30(7), 1385–1393 (2012)

    Article  Google Scholar 

  • D.G. Eickbush, J. Ye, X. Zhang, W.D. Burke, T.H. Eickbush, Epigenetic regulation of retrotransposons within the nucleolus of Drosophila. Mol. Cell. Biol. 28(20), 6452–6461 (2008)

    Article  Google Scholar 

  • M.A. Ermolaeva, A. Segref, A. Dakhovnik, H.L. Ou, J.I. Schneider, O. Utermohlen, T. Hoppe, B. Schumacher, DNA damage in germ cells induces an innate immune response that triggers systemic stress resistance. Nature 501(7467), 416–420 (2013)

    Article  ADS  Google Scholar 

  • R. Ertsey, C.J. Chapin, J.A. Kitterman, L.M. Scavo, Ontogeny of poly(ADP-ribose) polymerase-1 in lung and developmental implications. Am. J. Respir. Cell Mol. Biol. 30(6), 853–861 (2004)

    Article  Google Scholar 

  • T.M. Filion, M. Qiao, P.N. Ghule, M. Mandeville, A.J. van Wijnen, J.L. Stein, J.B. Lian, D.C. Altieri, G.S. Stein, Survival responses of human embryonic stem cells to DNA damage. J. Cell. Physiol. 220(3), 586–592 (2009)

    Article  Google Scholar 

  • P. Fortini, C. Ferretti, E. Dogliotti, The response to DNA damage during differentiation: pathways and consequences. Mutat. Res. 743–744, 160–168 (2013)

    Article  Google Scholar 

  • P. Fortini, C. Ferretti, B. Pascucci, L. Narciso, D. Pajalunga, E.M. Puggioni, R. Castino, C. Isidoro, M. Crescenzi, E. Dogliotti, DNA damage response by single-strand breaks in terminally differentiated muscle cells and the control of muscle integrity. Cell Death Differ. 19(11), 1741–1749 (2012)

    Article  Google Scholar 

  • S. Francia, F. Michelini, A. Saxena, D. Tang, M. de Hoon, V. Anelli, M. Mione, P. Carninci, F. d’Adda di Fagagna, Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature 488(7410), 231–235 (2012)

    Article  ADS  Google Scholar 

  • E.C. Friedberg, A. Aguilera, M. Gellert, P.C. Hanawalt, J.B. Hays, A.R. Lehmann, T. Lindahl, N. Lowndes, A. Sarasin, R.D. Wood, DNA repair: from molecular mechanism to human disease. DNA Repair (Amst) 5(8), 986–996 (2006)

    Article  Google Scholar 

  • E.C. Friedberg, L.B. Meira, Database of mouse strains carrying targeted mutations in genes affecting biological responses to DNA damage Version 7. DNA Repair (Amst) 5(2), 189–209 (2006)

    Article  Google Scholar 

  • G. Frosina, The bright and the dark sides of DNA repair in stem cells. J. Biomed. Biotechnol. 2010, 845396 (2010)

    Article  Google Scholar 

  • C. Giachino, L. Orlando, V. Turinetto, Maintenance of genomic stability in mouse embryonic stem cells: relevance in aging and disease. Int. J. Mol. Sci. 14(2), 2617–2636 (2013)

    Article  Google Scholar 

  • R.D. Goldman, D.K. Shumaker, M.R. Erdos, M. Eriksson, A.E. Goldman, L.B. Gordon, Y. Gruenbaum, S. Khuon, M. Mendez, R. Varga, F.S. Collins, Accumulation of mutant lamin A causes progressive changes in nuclear architecture in Hutchinson-Gilford progeria syndrome. Proc. Natl. Acad. Sci. USA 101(24), 8963–8968 (2004)

    Article  ADS  Google Scholar 

  • L.W.E. Gong, S.Y. Lin, Chromatin Remodeling in DNA Damage Response and Human Aging. Licensee InTech, 2013

    Google Scholar 

  • B. Hamilton, Y. Dong, M. Shindo, W. Liu, I. Odell, G. Ruvkun, S.S. Lee, A systematic RNAi screen for longevity genes in C. elegans. Genes Dev. 19(13), 1544–1555 (2005)

    Article  Google Scholar 

  • S. Han, A. Brunet, Histone methylation makes its mark on longevity. Trends Cell Biol. 22(1), 42–49 (2012)

    Article  Google Scholar 

  • M. Hansen, S. Taubert, D. Crawford, N. Libina, S.J. Lee, C. Kenyon, Lifespan extension by conditions that inhibit translation in Caenorhabditis elegans. Aging Cell 6(1), 95–110 (2007)

    Article  Google Scholar 

  • D. Harman, Aging: a theory based on free radical and radiation chemistry. J. Gerontol. 11(3), 298–300 (1956)

    Article  Google Scholar 

  • D. Harman, Free radical theory of aging. Triangle 12(4), 153–158 (1973)

    Google Scholar 

  • J. Hendrey, D. Lin, M. Dziadek, Developmental analysis of the Hba(th-J) mouse mutation: effects on mouse peri-implantation development and identification of two candidate genes. Dev. Biol. 172(1), 253–263 (1995)

    Article  Google Scholar 

  • B.S. Heyer, A. MacAuley, O. Behrendtsen, Z. Werb, Hypersensitivity to DNA damage leads to increased apoptosis during early mouse development. Genes Dev. 14(16), 2072–2084 (2000)

    Google Scholar 

  • P.H. Hsu, P.C. Hanawalt, T. Nouspikel, Nucleotide excision repair phenotype of human acute myeloid leukemia cell lines at various stages of differentiation. Mutat. Res. 614(1–2), 3–15 (2007)

    Article  Google Scholar 

  • T. Hirano, Philos. Trans. R. Soc. Lond. B Biol. Sci. 360(1455), 507–514 (2005). SMC proteins and chromosome mechanics: from bacteria to humans

    Google Scholar 

  • S.M. Ishita, M. Kulashreshtha, S. Chakraborty, U. Kolthur-Seetharam, B.J. Rao, Chromosome territories reposition during DNA damage-repair response. Genome Biol. 14(12), R135 (2013)

    Google Scholar 

  • T. Iyama, D.M. Wilson 3rd, DNA repair mechanisms in dividing and non-dividing cells. DNA Repair (Amst) 12(8), 620–636 (2013)

    Article  Google Scholar 

  • P. Jacquet, Developmental defects and genomic instability after x-irradiation of wild-type and genetically modified mouse pre-implantation and early post-implantation embryos. J. Radiol. Prot. 32(4), R13–R36 (2012)

    Article  Google Scholar 

  • S. Jaroudi, S. SenGupta, DNA repair in mammalian embryos. Mutat. Res. 635(1), 53–77 (2007)

    Article  Google Scholar 

  • A. Jurisicova, K.E. Latham, R.F. Casper, R.F. Casper, S.L. Varmuza, Expression and regulation of genes associated with cell death during murine preimplantation embryo development. Mol. Reprod. Dev. 51(3), 243–253 (1998)

    Article  Google Scholar 

  • J. Kanungo, R.S. Cameron, Y. Takeda, J.A. Hardin, DNA-dependent protein phosphorylation activity in Xenopus is coupled to a Ku-like protein. Biol. Bull. 193(2), 147–152 (1997)

    Article  Google Scholar 

  • J. Kenyon, S.L. Gerson, The role of DNA damage repair in aging of adult stem cells. Nucleic Acids Res. 35(22), 7557–7565 (2007)

    Article  Google Scholar 

  • C. Khan, S. Muliyil, C. Ayyub, B.J. Rao, The initiator caspase Dronc plays a non-apoptotic role in promoting DNA damage signalling in D. melanogaster. J. Cell Sci. 130(18), 2984–2995 (2017). https://doi.org/10.1242/jcs.200782. Epub 2017 Jul 27

  • T.B. Kirkwood, Evolution of ageing. Nature 270(5635), 301–304 (1977)

    Article  ADS  Google Scholar 

  • T.B. Kirkwood, Systems biology of ageing and longevity. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366(1561), 64–70 (2011)

    Article  Google Scholar 

  • J. Kristian, T. Kanno, K. Shirahige, C. Sjögren, The maintenance of chromosome structure: positioning and functioning of SMC complexes. Nat. Rev. Mol. Cell Biol. 15, 601–614 (2014)

    Google Scholar 

  • I.I. Kruman, Why do neurons enter the cell cycle? Cell Cycle 3(6), 769–773 (2004)

    Article  Google Scholar 

  • A. Kulkarni, D.R. McNeill, M. Gleichmann, M.P. Mattson, D.M. Wilson 3rd, XRCC1 protects against the lethality of induced oxidative DNA damage in nondividing neural cells. Nucleic Acids Res. 36(15), 5111–5121 (2008)

    Article  Google Scholar 

  • A. Lal, Y. Pan, F. Navarro, D.M. Dykxhoorn, L. Moreau, E. Meire, Z. Bentwich, J. Lieberman, D. Chowdhury, miR-24-mediated downregulation of H2AX suppresses DNA repair in terminally differentiated blood cells. Nat. Struct. Mol. Biol. 16(5), 492–498 (2009)

    Article  Google Scholar 

  • K. Larson, S.J. Yan, A. Tsurumi, J. Liu, J. Zhou, K. Gaur, D. Guo, T.H. Eickbush, W.X. Li, Heterochromatin formation promotes longevity and represses ribosomal RNA synthesis. PLoS Genet. 8(1), e1002473 (2012)

    Article  Google Scholar 

  • H.M. Lee, Z. Hu, H. Ma, G.H. Greeley Jr., C. Wang, E.W. Englander, Developmental changes in expression and subcellular localization of the DNA repair glycosylase, MYH, in the rat brain. J. Neurochem. 88(2), 394–400 (2004)

    Article  Google Scholar 

  • Y. Lee, S. Katyal, Y. Li, S.F. El-Khamisy, H.R. Russell, K.W. Caldecott, P.J. McKinnon, The genesis of cerebellar interneurons and the prevention of neural DNA damage require XRCC1. Nat. Neurosci. 12(8), 973–980 (2009)

    Article  Google Scholar 

  • E. Lieberman-Aiden, N.L. van Berkum, L. Williams, M. Imakaev, T. Ragoczy, A. Telling, I. Amit, B.R. Lajoie, P.J. Sabo, M.O. Dorschner et al., Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326, 289–293 (2009)

    Article  ADS  Google Scholar 

  • G.A. Lisa, The fractal geometry of life. Riv. Biol. 102, 29–59 (2009)

    Google Scholar 

  • E. Lukasova, Z. Koristek, M. Klabusay, V. Ondrej, S. Grigoryev, A. Bacikova, M. Rezacova, M. Falk, J. Vavrova, V. Kohutova, S. Kozubek, Granulocyte maturation determines ability to release chromatin NETs and loss of DNA damage response; these properties are absent in immature AML granulocytes. Biochim. Biophys. Acta 1833(3), 767–779 (2013)

    Article  Google Scholar 

  • P.K. Mandal, C. Blanpain, D.J. Rossi, DNA damage response in adult stem cells: pathways and consequences. Nat. Rev. Mol. Cell Biol. 12(3), 198–202 (2011)

    Article  Google Scholar 

  • B.B. Mandelbrot, Stochastic models for the Earth’s relief, the shape and the fractal dimension of the coastlines, and the number-area rule for islands. Proc. Natl. Acad. Sci. USA 72, 3825–3828 (1975)

    Article  ADS  MathSciNet  Google Scholar 

  • C. Mantel, Y. Guo, M.R. Lee, M.K. Kim, M.K. Han, H. Shibayama, S. Fukuda, M.C. Yoder, L.M. Pelus, K.S. Kim, H.E. Broxmeyer, Checkpoint-apoptosis uncoupling in human and mouse embryonic stem cells: a source of karyotpic instability. Blood 109(10), 4518–4527 (2007)

    Article  Google Scholar 

  • C. Marietta, F. Palombo, P. Gallinari, J. Jiricny, P.J. Brooks, Expression of long-patch and short-patch DNA mismatch repair proteins in the embryonic and adult mammalian brain. Brain Res. Mol. Brain Res. 53(1–2), 317–320 (1998)

    Article  Google Scholar 

  • K. Marinoglou, The role of the DNA damage response kinase ataxia telangiectasia mutated in neuroprotection. Yale J. Biol. Med. 85(4), 469–480 (2012)

    Google Scholar 

  • A. Meulle, B. Salles, D. Daviaud, P. Valet, C. Muller, Positive regulation of DNA double strand break repair activity during differentiation of long life span cells: the example of adipogenesis. PLoS ONE 3(10), e3345 (2008)

    Article  ADS  Google Scholar 

  • T. Misteli, Higher-order genome organization in human disease. Cold Spring Harb. Perspect. Biol. 2, a000794 (2010)

    Article  Google Scholar 

  • O. Momcilovic, S. Choi, S. Varum, C. Bakkenist, G. Schatten, C. Navara, Ionizing radiation induces ataxia telangiectasia mutated-dependent checkpoint signaling and G(2) but not G(1) cell cycle arrest in pluripotent human embryonic stem cells. Stem Cells 27(8), 1822–1835 (2009)

    Article  Google Scholar 

  • O. Momcilovic, L. Knobloch, J. Fornsaglio, S. Varum, C. Easley, G. Schatten, DNA damage responses in human induced pluripotent stem cells and embryonic stem cells. PLoS ONE 5(10), e13410 (2010)

    Article  ADS  Google Scholar 

  • R. Mudhasani, Z. Zhu, G. Hutvagner, C.M. Eischen, S. Lyle, L.L. Hall, J.B. Lawrence, A.N. Imbalzano, S.N. Jones, Loss of miRNA biogenesis induces p19Arf-p53 signaling and senescence in primary cells. J. Cell Biol. 181(7), 1055–1063 (2008)

    Article  Google Scholar 

  • K. Mugdha, I.S. Mehta, P. Kumar, B.J. Rao, Chromosome territory relocation during DNA repair requires nuclear myosin1β recruitment to chromatin mediated by Υ-H2AX signaling. Nucleic Acids Research 2016 Jun 30. pii: gkw573

    Google Scholar 

  • P. Nagaria, C. Robert, F.V. Rassool, DNA double-strand break response in stem cells: mechanisms to maintain genomic integrity. Biochimica et Biophysica Acta (BBA)—Gen. Subj. 1830(2), 2345–2353 (2013)

    Google Scholar 

  • L. Narciso, P. Fortini, D. Pajalunga, A. Franchitto, P. Liu, P. Degan, M. Frechet, B. Demple, M. Crescenzi, E. Dogliotti, Terminally differentiated muscle cells are defective in base excision DNA repair and hypersensitive to oxygen injury. Proc. Natl. Acad. Sci. USA 104(43), 17010–17015 (2007)

    Article  ADS  Google Scholar 

  • T. Nouspikel, DNA repair in differentiated cells: some new answers to old questions. Neuroscience 145(4), 1213–1221 (2007)

    Article  Google Scholar 

  • T. Nouspikel, DNA repair in mammalian cells: Nucleotide excision repair: variations on versatility. Cell. Mol. Life Sci. 66(6), 994–1009 (2009a)

    Article  Google Scholar 

  • T. Nouspikel, DNA repair in mammalian cells: So DNA repair really is that important? Cell. Mol. Life Sci. 66(6), 965–967 (2009b)

    Article  Google Scholar 

  • T. Nouspikel, P.C. Hanawalt, Terminally differentiated human neurons repair transcribed genes but display attenuated global DNA repair and modulation of repair gene expression. Mol. Cell. Biol. 20(5), 1562–1570 (2000)

    Article  Google Scholar 

  • T. Nouspikel, P.C. Hanawalt, DNA repair in terminally differentiated cells. DNA Repair (Amst) 1(1), 59–75 (2002a)

    Article  Google Scholar 

  • T. Nouspikel, P.C. Hanawalt, DNA repair in terminally differentiated cells. DNA Repair 1(1), 59–75 (2002b)

    Article  Google Scholar 

  • T. Nouspikel, P.C. Hanawalt, Impaired nucleotide excision repair upon macrophage differentiation is corrected by E1 ubiquitin-activating enzyme. Proc. Natl. Acad. Sci. USA 103(44), 16188–16193 (2006)

    Article  ADS  Google Scholar 

  • T.P. Nouspikel, N. Hyka-Nouspikel, P.C. Hanawalt, Transcription domain-associated repair in human cells. Mol. Cell. Biol. 26(23), 8722–8730 (2006)

    Article  Google Scholar 

  • L. Oliver, E. Hue, Q. Sery, A. Lafargue, C. Pecqueur, F. Paris, F.M. Vallette, Differentiation-related response to DNA breaks in human mesenchymal stem cells. Stem Cells 31(4), 800–807 (2013)

    Article  Google Scholar 

  • T.R. Ozolins, B.F. Hales, Oxidative stress regulates the expression and activity of transcription factor activator protein-1 in rat conceptus. J. Pharmacol. Exp. Ther. 280(2), 1085–1093 (1997)

    Google Scholar 

  • B.F. Pachkowski, K.Z. Guyton, B. Sonawane, DNA repair during in utero development: a review of the current state of knowledge, research needs, and potential application in risk assessment. Mutat. Res. 728(1–2), 35–46 (2011)

    Article  Google Scholar 

  • S. Pampfer, C. Streffer, Increased chromosome aberration levels in cells from mouse fetuses after zygote X-irradiation. Int. J. Radiat. Biol. 55(1), 85–92 (1989)

    Article  Google Scholar 

  • K.Z. Pan, J.E. Palter, A.N. Rogers, A. Olsen, D. Chen, G.J. Lithgow, P. Kapahi, Inhibition of mRNA translation extends lifespan in Caenorhabditis elegans. Aging Cell 6(1), 111–119 (2007)

    Article  Google Scholar 

  • G. Pegoraro, N. Kubben, U. Wickert, H. Gohler, K. Hoffmann, T. Misteli, Ageing-related chromatin defects through loss of the NURD complex. Nat. Cell Biol. 11(10), 1261–1267 (2009)

    Article  Google Scholar 

  • G. Pegoraro, T. Misteli, The central role of chromatin maintenance in aging. Aging (Albany NY) 1(12), 1017–1022 (2009)

    Article  Google Scholar 

  • P. Ramos-Espinosa, E. Rojas, M. Valverde, Differential DNA damage response to UV and hydrogen peroxide depending of differentiation stage in a neuroblastoma model. Neurotoxicology 33(5), 1086–1095 (2012)

    Article  Google Scholar 

  • E. Rass, G. Chandramouly, S. Zha, F.W. Alt, A. Xie, Ataxia telangiectasia mutated (ATM) is dispensable for endonuclease I-SceI-induced homologous recombination in mouse embryonic stem cells. J. Biol. Chem. 288(10), 7086–7095 (2013)

    Article  Google Scholar 

  • L.L. Richardson, C. Pedigo, M. Ann Handel, Expression of deoxyribonucleic acid repair enzymes during spermatogenesis in mice. Biol. Reprod. 62(3), 789–796 (2000)

    Article  Google Scholar 

  • B. Riis, L. Risom, S. Loft, H.E. Poulsen, Increased rOGG1 expression in regenerating rat liver tissue without a corresponding increase in incision activity. DNA Repair (Amst) 1(5), 419–424 (2002)

    Article  Google Scholar 

  • P.M. Rodrigues, P. Grigaravicius, M. Remus, G.R. Cavalheiro, A.L. Gomes, M.R. Martins, L. Frappart, D. Reuss, P.J. McKinnon, A. von Deimling, R.A. Martins, P.O. Frappart, Nbn and atm cooperate in a tissue and developmental stage-specific manner to prevent double strand breaks and apoptosis in developing brain and eye. PLoS ONE 8(7), e69209 (2013)

    Article  ADS  Google Scholar 

  • S.L. Rulten, K.W. Caldecott, DNA strand break repair and neurodegeneration. DNA Repair (Amst) 12(8), 558–567 (2013)

    Article  Google Scholar 

  • N.F.* Sarosh, I.S. Mehta, B.J. Rao*, Spatial arrangement of chromosomes in human interphase nuclei is self-organized by inter-chromosomal systemic couplings. Nat. Sci. Rep. 6, 36819 (2016). https://doi.org/10.1038/srep36819

  • P. Scaffidi, T. Misteli, Reversal of the cellular phenotype in the premature aging disease Hutchinson-Gilford progeria syndrome. Nat. Med. 11(4), 440–445 (2005)

    Article  Google Scholar 

  • P. Scaffidi, T. Misteli, Lamin A-dependent nuclear defects in human aging. Science 312(5776), 1059–1063 (2006)

    Article  ADS  Google Scholar 

  • S. Schmetsdorf, E. Arnold, M. Holzer, T. Arendt, U. Gartner, A putative role for cell cycle-related proteins in microtubule-based neuroplasticity. Eur. J. Neurosci. 29(6), 1096–1107 (2009)

    Article  Google Scholar 

  • L. Schneider, M. Fumagalli, F. d’Adda di Fagagna, Terminally differentiated astrocytes lack DNA damage response signaling and are radioresistant but retain DNA repair proficiency. Cell Death Differ. 19(4), 582–591 (2012)

    Article  Google Scholar 

  • N. Schuler, C.E. Rube, Accumulation of DNA damage-induced chromatin alterations in tissue-specific stem cells: the driving force of aging? PLoS ONE 8(5), e63932 (2013)

    Article  ADS  Google Scholar 

  • E.I. Schwartz, L.B. Smilenov, M.A. Price, T. Osredkar, R.A. Baker, S. Ghosh, F.D. Shi, T.L. Vollmer, A. Lencinas, D.M. Stearns, M. Gorospe, II. Kruman, Cell cycle activation in postmitotic neurons is essential for DNA repair. Cell Cycle 6(3), 318–329 (2007)

    Google Scholar 

  • M.H. Sherman, A.I. Kuraishy, C. Deshpande, J.S. Hong, N.A. Cacalano, R.A. Gatti, J.P. Manis, M.A. Damore, M. Pellegrini, M.A. Teitell, AID-induced genotoxic stress promotes B cell differentiation in the germinal center via ATM and LKB1 signaling. Mol. Cell 39(6), 873–885 (2010)

    Article  Google Scholar 

  • D.K. Shumaker, T. Dechat, A. Kohlmaier, S.A. Adam, M.R. Bozovsky, M.R. Erdos, M. Eriksson, A.E. Goldman, S. Khuon, F.S. Collins, T. Jenuwein, R.D. Goldman, Mutant nuclear lamin A leads to progressive alterations of epigenetic control in premature aging. Proc. Natl. Acad. Sci. USA 103(23), 8703–8708 (2006)

    Article  ADS  Google Scholar 

  • M. Simonatto, L. Giordani, F. Marullo, G.C. Minetti, P.L. Puri, L. Latella, Coordination of cell cycle, DNA repair and muscle gene expression in myoblasts exposed to genotoxic stress. Cell Cycle. 10(14), 2355–2363 (2011)

    Article  Google Scholar 

  • M. Simonatto, F. Marullo, F. Chiacchiera, A. Musaro, J.Y. Wang, L. Latella, P.L. Puri, DNA damage-activated ABL-MyoD signaling contributes to DNA repair in skeletal myoblasts. Cell Death Differ. 20(12), 1664–1674 (2013)

    Article  Google Scholar 

  • P. Sykora, D.M. Wilson 3rd, V.A. Bohr, Base excision repair in the mammalian brain: Implication for age related neurodegeneration. Mech. Ageing Dev. 134(10), 440–448 (2013a)

    Article  Google Scholar 

  • P. Sykora, J.L. Yang, L.K. Ferrarelli, J. Tian, T. Tadokoro, A. Kulkarni, L. Weissman, G. Keijzers, D.M. Wilson 3rd, M.P. Mattson, V.A. Bohr, Modulation of DNA base excision repair during neuronal differentiation. Neurobiol. Aging 34(7), 1717–1727 (2013b)

    Article  Google Scholar 

  • A. Tedeschi, S. Di Giovanni, The non-apoptotic role of p53 in neuronal biology: enlightening the dark side of the moon. EMBO Rep. 10(6), 576–583 (2009)

    Article  Google Scholar 

  • C. Thamrin, G. Stern, U. Frey, Fractals for physicians. Paediatr. Respir. Rev. 11, 123–131 (2010)

    Article  Google Scholar 

  • E.D. Tichy, R. Pillai, L. Deng, L. Liang, J. Tischfield, S.J. Schwemberger, G.F. Babcock, P.J. Stambrook, Mouse embryonic stem cells, but not somatic cells, predominantly use homologous recombination to repair double-strand DNA breaks. Stem Cells Dev. 19(11), 1699–1711 (2010)

    Article  Google Scholar 

  • A. Tomashevski, D.R. Webster, P. Grammas, M. Gorospe, I.I. Kruman, Cyclin-C-dependent cell-cycle entry is required for activation of non-homologous end joining DNA repair in postmitotic neurons. Cell Death Differ. 17(7), 1189–1198 (2010)

    Article  Google Scholar 

  • R.K. Vinson, B.F. Hales, Expression of base excision, mismatch, and recombination repair genes in the organogenesis-stage rat conceptus and effects of exposure to a genotoxic teratogen, 4-hydroperoxycyclophosphamide. Teratology 64(6), 283–291 (2001a)

    Article  Google Scholar 

  • R.K. Vinson, B.F. Hales, Nucleotide excision repair gene expression in the rat conceptus during organogenesis. Mutat. Res. 486(2), 113–123 (2001b)

    Article  Google Scholar 

  • R.K. Vinson, B.F. Hales, DNA repair during organogenesis. Mutat. Res. 509(1–2), 79–91 (2002)

    Article  Google Scholar 

  • D. Wells, M.G. Bermudez, N. Steuerwald, A.R. Thornhill, D.L. Walker, H. Malter, J.D. Delhanty, J. Cohen, Expression of genes regulating chromosome segregation, the cell cycle and apoptosis during human preimplantation development. Hum. Reprod. 20(5), 1339–1348 (2005)

    Article  Google Scholar 

  • G. Xu, G. Spivak, D.L. Mitchell, T. Mori, J.R. McCarrey, C.A. McMahan, R.B. Walter, P.C. Hanawalt, C.A. Walter, Nucleotide excision repair activity varies among murine spermatogenic cell types. Biol. Reprod. 73(1), 123–130 (2005)

    Article  Google Scholar 

  • P. Zheng, R.D. Schramm, K.E. Latham, Developmental regulation and in vitro culture effects on expression of DNA repair and cell cycle checkpoint control genes in rhesus monkey oocytes and embryos. Biol. Reprod. 72(6), 1359–1369 (2005)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Tata Institute of Fundamental Research, Homi Bhabha Road, Mumbai, 400005, India

    Basuthkar J. Rao

Authors
  1. Basuthkar J. Rao
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Basuthkar J. Rao .

Editor information

Editors and Affiliations

  1. R. N. Podar School, Mumbai, India

    Shyam Wuppuluri

  2. Advanced Studies Research Group, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil

    Francisco Antonio Doria

Rights and permissions

Reprints and permissions

Copyright information

© 2018 Springer International Publishing AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

Rao, B.J. (2018). Genome Regulation Is All Non-local: Maps and Functions. In: Wuppuluri, S., Doria, F. (eds) The Map and the Territory. The Frontiers Collection. Springer, Cham. https://doi.org/10.1007/978-3-319-72478-2_28

Download citation

Publish with us

Policies and ethics

Search

Navigation