Chromatin and epigenetics: current biophysical views

Vladimir B. Teif; Andrey G. Cherstvy; Vladimir B. Teif; Andrey G. Cherstvy

doi:10.3934/biophy.2016.1.88

AIMS Biophysics

2016, Volume 3, Issue 1: 88-98. doi: 10.3934/biophy.2016.1.88

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Editorial Special Issues

Chromatin and epigenetics: current biophysical views

Vladimir B. Teif ^{1
,
,},
Andrey G. Cherstvy ^{2
,
,}

1.
School of Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
2.
Institute for Physics and Astronomy, University of Potsdam, 14476 Potsdam-Golm, Germany

Received: 18 February 2016 Accepted: 18 February 2016 Published: 23 February 2016

Recent advances in high-throughput sequencing experiments and their theoretical descriptions have determined fast dynamics of the “chromatin and epigenetics” field, with new concepts appearing at high rate. This field includes but is not limited to the study of DNA-protein-RNA interactions, chromatin packing properties at different scales, regulation of gene expression and protein trafficking in the cell nucleus, binding site search in the crowded chromatin environment and modulation of physical interactions by covalent chemical modifications of the binding partners. The current special issue does not pretend for the full coverage of the field, but it rather aims to capture its development and provide a snapshot of the most recent concepts and approaches. Eighteen open-access articles comprising this issue provide a delicate balance between current theoretical and experimental biophysical approaches to uncover chromatin structure and understand epigenetic regulation, allowing free flow of new ideas and preliminary results.
- chromatin,
- epigenetics,
- linker histones,
- nucleosome,
- DNA-protein binding,
- histone modifications,
- remodelers,
- topologically associated domains,
- DNA methylation,
- DNA supercoiling
Citation: Vladimir B. Teif, Andrey G. Cherstvy. Chromatin and epigenetics: current biophysical views[J]. AIMS Biophysics, 2016, 3(1): 88-98. doi: 10.3934/biophy.2016.1.88

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Abstract

Recent advances in high-throughput sequencing experiments and their theoretical descriptions have determined fast dynamics of the “chromatin and epigenetics” field, with new concepts appearing at high rate. This field includes but is not limited to the study of DNA-protein-RNA interactions, chromatin packing properties at different scales, regulation of gene expression and protein trafficking in the cell nucleus, binding site search in the crowded chromatin environment and modulation of physical interactions by covalent chemical modifications of the binding partners. The current special issue does not pretend for the full coverage of the field, but it rather aims to capture its development and provide a snapshot of the most recent concepts and approaches. Eighteen open-access articles comprising this issue provide a delicate balance between current theoretical and experimental biophysical approaches to uncover chromatin structure and understand epigenetic regulation, allowing free flow of new ideas and preliminary results.

References

[1]	Knight K (2015) A comparative perspective on epigenetics. J Exp Biol 218: 1–5. doi: 10.1242/jeb.118075
[2]	Hoppeler HH (2015) Epigenetics in comparative physiology. J Exp Biol 218: 6–6. doi: 10.1242/jeb.117754
[3]	Chen X, Qi Y, Sung ZR (2015) Special issue on plant epigenetics. Molecular Plant 7: 453.
[4]	Gutierrez C, Puchta H (2015) Chromatin and development: a special issue. Plant J 83: 1–3.
[5]	Meissner A (2012) What can epigenomics do for you? Genome Biology 13: 420. doi: 10.1186/gb-2012-13-10-420
[6]	Attar N (2012) The allure of the epigenome. Genome Biology 13: 419. doi: 10.1186/gb-2012-13-10-419
[7]	Tyler J (2015) Special Issue "Chromatin dynamics". Genes. MDPI, Basel, Switzerland. Available from: http://www.mdpi.com/journal/genes/special_issues/chromatin_dynamics.
[8]	Muñoz-Cánoves P, Di Croce L (2015) Special Issue: Epigenetics. FEBS J 282: 1569–1570. doi: 10.1111/febs.13281
[9]	Everaers R, Schiessel H (2015) The physics of chromatin. J Phys Condens Matter 27: 060301.
[10]	Biscotti MA, Olmo E, Heslop-Harrison JS (2015) Repetitive DNA in eukaryotic genomes. Chromosome Res 23: 415–420. doi: 10.1007/s10577-015-9499-z
[11]	Imhof A, Rappsilber J (2016) A Focus on Chromatin Proteomics. Proteomics 16: 379–380.
[12]	Zhou HX, Rivas G, Minton AP (2008) Macromolecular crowding and confinement: biochemical, biophysical, and potential physiological consequences. Annu Rev Biophys 37: 375–397. doi: 10.1146/annurev.biophys.37.032807.125817
[13]	Zimmerman SB, Minton AP (1993) Macromolecular crowding: biochemical, biophysical, and physiological consequences. Annu Rev Biophys Biomol Struct 22: 27–65. doi: 10.1146/annurev.bb.22.060193.000331
[14]	Schubert T, Längst G (2015) Studying epigenetic interactions using MicroScale Thermophoresis (MST). AIMS Biophysics 2: 370–380. doi: 10.3934/biophy.2015.3.370
[15]	Bereznyak E, Gladkovskaya N, Dukhopelnykov E, et al. (2015) Thermal analysis of ligand-DNA interaction: determination of binding parameters. AIMS Biophysics 2: 423–440. doi: 10.3934/biophy.2015.4.423
[16]	Mast CB, Schink S, Gerland U, et al. (2013) Escalation of polymerization in a thermal gradient. Proc Natl Acad Sci U S A 110: 8030–8035.
[17]	Teif VB, Erdel F, Beshnova DA, et al. (2013) Taking into account nucleosomes for predicting gene expression. Methods 62: 26–38. doi: 10.1016/j.ymeth.2013.03.011
[18]	Weingarten-Gabbay S, Segal E (2014) The grammar of transcriptional regulation. Hum Genet 133: 701–711. doi: 10.1007/s00439-013-1413-1
[19]	Yanao T, Sano T, Yoshikawa K (2015) Chiral selection in wrapping, crossover, and braiding of DNA mediated by asymmetric bend-writhe elasticity. AIMS Biophysics 2: 666–694.
[20]	Luger K, Mader AW, Richmond RK, et al. (1997) Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature 389: 251–260.
[21]	Lee DJ, Cortini R, Korte AP, et al. (2013) Chiral effects in dual-DNA braiding. Soft Matter 9: 9833–9848.
[22]	Langowski J (2006) Polymer chain models of DNA and chromatin. Eur Phys J E Soft Matter 19: 241–249. doi: 10.1140/epje/i2005-10067-9
[23]	Stehr R, Kepper N, Rippe K, et al. (2008) The effect of internucleosomal interaction on folding of the chromatin fiber. Biophys J 95: 3677–3691. doi: 10.1529/biophysj.107.120543
[24]	Wedemann G, Langowski J (2002) Computer simulation of the 30-nanometer chromatin fiber. Biophys J 82: 2847–2859. doi: 10.1016/S0006-3495(02)75627-0
[25]	Schiessel H (2003) The physics of chromatin. J Phys Condens Matter 15: R699. doi: 10.1088/0953-8984/15/19/203
[26]	Mergell B, Everaers R, Schiessel H (2004) Nucleosome interactions in chromatin: fiber stiffening and hairpin formation. Phys Rev E Stat Nonlin Soft Matter Phys 70: 011915.
[27]	Marti-Renom MA, Mirny LA (2011) Bridging the resolution gap in structural modeling of 3D genome organization. PLoS Comput Biol 7: e1002125.
[28]	Norouzi D, Katebi A, Cui F, et al. (2015) Topological diversity of chromatin fibers: Interplay between nucleosome repeat length, DNA linking number and the level of transcription. AIMS Biophysics 2: 613–629.
[29]	Korolev N, Allahverdi A, Lyubartsev AP, et al. (2012) The polyelectrolyte properties of chromatin. Soft Matter 8: 9322–9333.
[30]	Korolev N, Fan Y, Lyubartsev AP, et al. (2012) Modelling chromatin structure and dynamics: status and prospects. Curr Opin Struct Biol 22: 151–159. doi: 10.1016/j.sbi.2012.01.006
[31]	Kunze KK, Netz RR (2002) Complexes of semiflexible polyelectrolytes and charged spheres as models for salt-modulated nucleosomal structures. Phys Rev E Stat Nonlin Soft Matter Phys 66: 011918. doi: 10.1103/PhysRevE.66.011918
[32]	Sun J, Zhang Q, Schlick T (2005) Electrostatic mechanism of nucleosomal array folding revealed by computer simulation. Proc Natl Acad Sci U S A 102: 8180–8185.
[33]	Bohinc K, Lue L (2016) On the electrostatics of DNA in chromatin. AIMS Biophysics 3: 75–87.
[34]	Vijayanathan V, Thomas T, Shirahata A, et al. (2001) DNA condensation by polyamines: a laser light scattering study of structural effects. Biochemistry 40: 13644–13651. doi: 10.1021/bi010993t
[35]	Deng H, Bloomfield VA, Benevides JM, et al. (2000) Structural basis of polyamine-DNA recognition: spermidine and spermine interactions with genomic B-DNAs of different GC content probed by Raman spectroscopy. Nucleic Acids Res 28: 3379–3385. doi: 10.1093/nar/28.17.3379
[36]	Segal E, Widom J (2009) What controls nucleosome positions? Trends Genet 25: 335–343. doi: 10.1016/j.tig.2009.06.002
[37]	Lowary PT, Widom J (1997) Nucleosome packaging and nucleosome positioning of genomic DNA. Proc Natl Acad Sci U S A 94: 1183–1188. doi: 10.1073/pnas.94.4.1183
[38]	Kaplan N, Moore IK, Fondufe-Mittendorf Y, et al. (2009) The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 458: 362–366. doi: 10.1038/nature07667
[39]	Trifonov EN (1980) Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res 8: 4041–4053. doi: 10.1093/nar/8.17.4041
[40]	Trifonov EN (2015) Columnar structure of SV40 minichromosome. AIMS Biophysics 2: 274–283. doi: 10.3934/biophy.2015.3.274
[41]	Trifonov EN, Nibhani R (2015) Review fifteen years of search for strong nucleosomes. Biopolymers 103: 432–437.
[42]	Li G, Levitus M, Bustamante C, et al. (2005) Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol 12: 46–53.
[43]	Singh RP, Brysbaert G, Lensink MF, et al. (2015) Kinetic proofreading of chromatin remodeling: from gene activation to gene repression and back. AIMS Biophysics 2: 398–411. doi: 10.3934/biophy.2015.4.398
[44]	Racki LR, Yang JG, Naber N, et al. (2009) The chromatin remodeller ACF acts as a dimeric motor to space nucleosomes. Nature 462: 1016. doi: 10.1038/nature08621
[45]	Blosser TR, Yang JG, Stone MD, et al. (2009) Dynamics of nucleosome remodelling by individual ACF complexes. Nature 462: 1022–1027.
[46]	Blossey R, Schiessel H (2011) The dynamics of the nucleosome: thermal effects, external forces and ATP. FEBS J 278: 3619–3632.
[47]	Clapier CR, Cairns BR (2009) The biology of chromatin remodeling complexes. Annu Rev Biochem 78: 273–304.
[48]	Moshkin YM (2015) Chromatin—a global buffer for eukaryotic gene control. AIMS Biophysics 2: 531–554. doi: 10.3934/biophy.2015.4.531
[49]	Jacob F, Monod J (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3: 318–356. doi: 10.1016/S0022-2836(61)80072-7
[50]	Mirny LA (2010) Nucleosome-mediated cooperativity between transcription factors. Proc Natl Acad Sci U S A 107: 22534–22539.
[51]	Cremer T, Cremer C (2001) Chromosome territories, nuclear architecture and gene regulation in mammalian cells. Nat Rev Genet 2: 292–301.
[52]	Fudenberg G, Mirny LA (2012) Higher-order chromatin structure: bridging physics and biology. Curr Opin Genet Dev 22: 115–124.
[53]	Babu D, Fullwood MJ (2015) 3D genome organization in health and disease: emerging opportunities in cancer translational medicine. Nucleus 6: 382–393. doi: 10.1080/19491034.2015.1106676
[54]	Nichols MH, Corces VG (2015) A CTCF Code for 3D Genome Architecture. Cell 162: 703–705.
[55]	Genomics PE (2015) Inching toward the 3D genome. Science 347: 10. doi: 10.1126/science.347.6217.10
[56]	Rao SS, Huntley MH, Durand NC, et al. (2014) A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159: 1665–1680.
[57]	Mizuguchi T, Fudenberg G, Mehta S, et al. (2014) Cohesin-dependent globules and heterochromatin shape 3D genome architecture in S. pombe. Nature 516: 432–435.
[58]	Bianchi A, Lanzuolo C (2015) Into the chromatin world: Role of nuclear architecture in epigenome regulation. AIMS Biophysics 2: 585–612. doi: 10.3934/biophy.2015.4.585
[59]	Caré BR, Emeriau P-E, Cortini R, et al. (2015) Chromatin epigenomic domain folding: size matters. AIMS Biophysics 2: 517–530. doi: 10.3934/biophy.2015.4.517
[60]	Jost D, Carrivain P, Cavalli G, et al. (2014) Modeling epigenome folding: formation and dynamics of topologically associated chromatin domains. Nucleic Acids Res 42: 9553–9561. doi: 10.1093/nar/gku698
[61]	Moscalets AP, Nazarov LI, Tamm MV (2015) Towards a robust algorithm to determine topological domains from colocalization data. AIMS Biophysics 2: 503–516. doi: 10.3934/biophy.2015.4.503
[62]	Lifshitz IM, Grosberg AY, Khokhlov AR (1978) Some problems of the statistical physics of polymer chains with volume interaction. Rev Modern Phys 50: 683 doi: 10.1103/RevModPhys.50.683
[63]	Hansen JC (2002) Conformational dynamics of the chromatin fiber in solution: determinants, mechanisms, and functions. Annu Rev Biophys Biomol Struct 31: 361–392.
[64]	Rosa A, Everaers R (2008) Structure and dynamics of interphase chromosomes. PLoS Comput Biol 4: e1000153. doi: 10.1371/journal.pcbi.1000153
[65]	Lebeaupin T, Sellou H, Timinszky G, et al. (2015) Chromatin dynamics at DNA breaks: what, how and why? AIMS Biophysics 2: 458–475.
[66]	Mirny LA (2011) The fractal globule as a model of chromatin architecture in the cell. Chromosome Res 19: 37–51.
[67]	Grant DJ, Shakes LA, Wolf HM, et al. (2015) Exploring function of conserved non-coding DNA in its chromosomal context. AIMS Biophysics 2: 773–793. doi: 10.3934/biophy.2015.4.773
[68]	McFadden EJ, Hargrove AE (2016) Biochemical Methods to Investigate lncRNA and the Influence of lncRNA:protein Complexes on Chromatin. Biochemistry.
[69]	Hamilton MJ, Young MD, Sauer S, et al. (2015) The interplay of long non-coding RNAs and MYC in cancer. AIMS Biophysics 2: 794–809.
[70]	Strahl BD, Allis CD (2000) The language of covalent histone modifications. Nature 403: 41–45. doi: 10.1038/47412
[71]	Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16: 6–21. doi: 10.1101/gad.947102
[72]	Lawrence M, Daujat S, Schneider R (2016) Lateral Thinking: How Histone Modifications Regulate Gene Expression. Trends Genet 32: 42–56. doi: 10.1016/j.tig.2015.10.007
[73]	Chen QY, Costa M, Sun H (2015) Structure and function of histone acetyltransferase MOF. AIMS Biophysics 2: 555–569. doi: 10.3934/biophy.2015.4.555
[74]	Venkatasubramani AV, McLaughlin K, Blanco GR, et al. (2015) Pilot RNAi screening using mammalian cell-based system identifies novel putative silencing factors including Kat5/Tip60. AIMS Biophysics 2: 570–584. doi: 10.3934/biophy.2015.4.570
[75]	Mandrioli M, Manicardi GC (2015) Cytosine methylation in insects: new routes for the comprehension of insect complexity. AIMS Biophysics 2: 412–422. doi: 10.3934/biophy.2015.4.412
[76]	Kim JM, Kim K, Punj V, et al. (2015) Linker histone H1.2 establishes chromatin compaction and gene silencing through recognition of H3K27me3. Sci Rep 5: 16714.
[77]	Sun J, Wei HM, Xu J, et al. (2015) Histone H1-mediated epigenetic regulation controls germline stem cell self-renewal by modulating H4K16 acetylation. Nat Commun 6: 8856. doi: 10.1038/ncomms9856
[78]	Thorslund T, Ripplinger A, Hoffmann S, et al. (2015) Histone H1 couples initiation and amplification of ubiquitin signalling after DNA damage. Nature 527: 389–393. doi: 10.1038/nature15401
[79]	Parseghian MH (2015) What is the role of histone H1 heterogeneity? A functional model emerges from a 50 year mystery. AIMS Biophysics 2: 724–772.

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