Effect of replication on epigenetic memory and consequences on gene transcription

Physical Biology

Volumn 12, Issue 2, 2015, Pages

  Zerihun, Mehari B ^a   Vaillant, Cédric ^a   Jost, Daniel ^b  

^a UNIVERSITÉ DE LYON   (France)

^b UNIV GRENOBLE ALPES   (France)

Author keywords

DNA replication; epigenetic marks; stability; stochastic modeling; transcriptional bursting

Indexed keywords

EUKARYOTA;

BIOLOGICAL MODEL; CELL CYCLE; CELL DIVISION; DNA REPLICATION; EUKARYOTE; GENETIC EPIGENESIS; GENETIC TRANSCRIPTION; GENETICS; MONTE CARLO METHOD; STATISTICS;

CELL CYCLE; CELL DIVISION; DNA REPLICATION; EPIGENESIS, GENETIC; EUKARYOTA; MODELS, GENETIC; MONTE CARLO METHOD; STOCHASTIC PROCESSES; TRANSCRIPTION, GENETIC;

EID: 84928804897     PISSN: 14783967     EISSN: 14783975     Source Type: Journal    
DOI: 10.1088/1478-3975/12/2/026007     Document Type: Article

References (51)

1. Holmberg J and Perlmann T 2012 Maintaining differentiated cellular identity Nat. Rev. Genetics 13 429-39
2. Allis C D, Jenuwein T and Reinberg D 2007 Epigenetics (New York: Cold Spring Harbor Laboratory)
3. Grewal S I S and Moazed D 2003 Heterochromatin and epigenetic control of gene expression Science 301 798-802
4. Kourazides T 2007 Chromatin modifications and their function Cell 128 693-705
5. Probst A V, Dunleavy H and Almouzni G 2009 Epigenetic inheritance during the cell cycle Nat. Rev. Mol. Cell Biol. 10 192-206
6. Lieberman-Aiden E et al 2009 Comprehensive mapping of long-range interactions reveals folding principles of the human genome Science 326 289-93
7. Sexton T, Yaffe E, Kenigsberg E, Bantignies F, Leblanc B, Hoichman M, Parrinello H, Tanay A and Cavalli G 2012 Three-dimensional folding and functional organization principles of the Drosophila genome Cell 148 458-72
8. Jost D, Carrivain P, Cavalli G and Vaillant C 2014 Modeling epigenome folding: formation and dynamics of topologically-associated chromatin domains Nucleic Acids Res. 42 9553-61
9. Kelemen J Z, Ratna P, Scherrer S and Becksei A 2010 Spatial epigenetic control of mono- and bistable gene expression PLoS Biol. 8 e1000332
10. Angel A, Song J, Dean C and Howard M 2011 A polycomb-based switch underlying quantitative epigenetic memory Nature 476 105-8
11. Hathaway N A, Bell O, Hodges C, Miller E L, Neel D S and Crabtree G R 2012 Dynamics and memory of heterochromatin in living cells Cell 149 1447-60
12. Mano Y, Kobayashi T J, Nakayama J-I, Uchida H and Oki M 2013 Single cell visualization of yeast gene expression shows correlation of epigenetic switching between multiple heterochromatic regions through multiple generations PLoS Biol. 11 e1001601
13. Yang H, Howard M and Dean C 2014 Antagonistic roles for H3K36me3 and H3K27me3 in the cold-induced epigenetic switch at arabidopsis FLC Curr. Biol. 24 1793-7
14. Shipony Z, Mukamel Z, Cohen N M, Landan G, Chomsky E, Zeliger S R, Fried Y C, Ainbinder E, Friedman N and Tanay A 2014 Dynamic and static maintenance of epigenetic memory in pluripotent and somatic cells Nature 513 115-9
15. Nagaraj V H, Mukhopadhyay S, Dayarian A and Sengupta A M 2014 Breaking an epigenetic switch: curious features of hysteresis in Saccharomyces cerevisiae telomeric silencing PLoS One 9 e113516
16. Dodson A E and Rine J 2015 Heritable capture of heterochromatin dynamics in Saccharomyces cerevisiae Elife 4 e05007
17. Dodd I A, Micheelsen M A, Sneppen K and Thon G 2007 Theoretical analysis of epigenetic cell memory by nucleosome modification Cell 129 813-22
18. David-Rus D, Mukhopadhyay S, Lebowitz J L and Sengupta A M 2009 Inheritance of epigenetic chromatin silencing J. Theor. Biol. 258 112-20
19. Mukhopadhyay S, Nagaraj V H and Sengupta A M 2010 Locus dependence in epigenetic chromatin silencing BioSystems 102 49-54
20. Micheelsen M M, Mitarai N, Sneppen K and Dodd I B 2010 Theory for stability and regulation of epigenetic landscapes Phys. Biol. 7 026010
21. Dodd I B and Sneppen K 2011 Barriers and silenciers; a theoretical toolkit for control and containment of nucleosome-based epigenetic states J. Mol. Biol. 414 624-37
22. Becskei A, Scherrer S, Kelemen J Z and Murray A E 2011 Modeling of chromosomal epigenetic silencing processes Transcription 2 173-8
23. Satake A and Iwasa Y 2012 A stochastic model of chromatin modification: cell population coding winter memory in plants J. Theor. Biol. 302 6-17
24. Sneppen K and Dodd I B 2012 A simple histone code opens many paths to epigenetics PLoS Comput. Biol. 8 e1002643
25. Binder H, Steiner L, Przybilla J, Rohlf T, Prohaska S and Galle J 2013 Transcriptional regulation by histones modifications: toward a theory of chromatin re-organization during stem cell differentiation Phys. Biol. 10 026006
26. Dayarian A and Sengupta A M 2013 Titration and hysteresis in epigenetic chromatin silencing Phys. Biol. 10 036005
27. Arnold C, Stadler P F and Prohaska S J 2013 Chromatin computation: epigenetic inheritance as a pattern reconstruction problem J. Theor. Biol. 336 61-74
28. Schwammle V and Jensen O N 2013 A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types PLoS One 8 e73818
29. Mukhopadhyay S and Sengupta A M 2013 The role of multiple marks in epigenetic silencing and the emergence of a stable bivalent chromatin state PLoS Comput. Biol. 9 e1003121
30. Haerter J O, Lovkvist C, Dodd I B and Sneppen K 2013 Collaboration between CpG sites is needed for stable somatic inheritance of DNA methylation states Nucleic Acids Res. 42 2235-44
31. Jost D 2014 Bifurcation in epigenetics: implications to development, proliferation and diseases Phys. Rev. E 89 010701
32. Zhang H, Tian X-J, Mukhopadhyay A, Kim K S and Xing J 2014 Statistical mechanics model for the dynamics of collective epigenetic histone modification Phys. Rev. Lett. 112 068101
33. Xu M, Long C, Chen X, Huang C, Chen S and Zhu B 2010 Partitioning of histone h3-h4 tetramers during DNA replication-dependent chromatin assembly Science 328 94-8
34. Alabert C and Groth A 2012 Chromatin replication and epigenome maintenance Nat. Rev. Mol. Cell Biol. 13 153-67
35. Kuang Z, Cai L, Zhang X, Ji H, Tu B P and Boeke J D 2014 High-temporal-resolution view of transcription and chromatin states across distinct metabolic states in budding yeast Nat. Struct. Mol. Biol. 21 854-63
36. Maeshima K, Kaizu K, Tamura S, Nozaki T, Kokubo T and Takahashi K 2015 The physical size of transcription factors is key to transcriptional regulation in chromatin domains J. Phys.: Condens. Matter 27 064116
37. Castel S E and Martienssen R A 2013 RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond Nat. Rev. Genetics 14 100-12
38. Gillespie D T 1977 Exact stochastic simulation of coupled chemical reactions J. Phys. Chem. 81 2340-61
39. Deal R G, Henikoff J G and Henikoff S 2010 Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones Science 328 1161-4
40. Budirahardja Y and Gonczy P 2009 Coupling the cell cycle to development Development 136 2861-72
41. Sharma S, Kelly T K and Jones P A 2010 Epigenetics in cancer Carcinogenesis 31 27-36
42. Pujadas E and Feinberg A P 2012 Regulated noise in the epigenetic landscape of development and disease Cell 148 1123-31
43. Sarkies P and Sale J E 2012 Cellular epigenetic stability and cancer Trends Genetics 28 118-27
44. Bayne E H et al 2010 Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity Cell 140 666-77
45. Moazed D 2011 Mechanisms for the inheritance of chromatin states Cell 146 510-8
46. Madhani H D 2013 The frustrated gene: origins of eukaryotic gene expression Cell 115 144-9
47. Youk H, Raj A and van Oudenaarden A 2010 Imaging single mRNA molecules in yeast Methods Enzymol. 470 429-46
48. Hayashi-Takanaka Y et al 2011 Tracking histone modifications in single cells using Fab-based live endogenous modification labeling Nucleic Acids Res. 39 6475-88
49. Kaufman P D and Rando O J 2010 Chromatin as a potential carrier of heritable information Curr. Opin. Cell Biol. 22 284-90
50. Eaton M L, Prinz J A, MacAlpine H K, Tretyakov G, Kharchenko P V and MacAlpine D M 2011 Chromatin signatures of the Drosophila replication program Genome Res. 21 164-74
51. Comoglio D and Paro R 2014 Combinatorial modeling of chromatin features quantitatively predicts DNA replication timing in Drosophila PLoS Comput. Biol. 10 e1003419