817
Views
10
CrossRef citations to date
0
Altmetric
Primary Research

Influence of the genomic sequence on the primary structure of chromatin

, &
Pages 29-68 | Received 17 Apr 2012, Accepted 30 Jun 2012, Published online: 28 Aug 2012

References

  • Adams CC and Workman JL. 1995. Binding of disparate transcriptional activators to nucleosomal DNA is inherently cooperative. Mol Cell Biol. 15:1405–1421.
  • Albert I Mavrich , T N , Tomsho LP Qi , J , Zanton , S J , Schuster , S C and Pugh , B F . 2007 . Translational and rotational settings of H2A.Z nucleosomes across the . Saccharomyces cerevisiae genome. Nature. , 446 : 572 – 576 .
  • Alberts B, Bray D, Lewis J, Raff M, Roberts K, Watson JD. 2002. Molecular biology of the cell. 4th ed. New-York: Garland Publishing.
  • Allan , J , Fraser , R , Owen-Hughes , T and Keszenman-Pereyra , D . 2012 . Micrococcal nuclease does not substantially bias nucleosome mapping . J Mol Biol. , 417 : 152 – 164 .
  • Angelov , D , Molla , A , Perche , P- Y , Hans , F , Cote , J , Khochbin , S , Bouvet , P and Dimitrov , S . 2003 . The histone variant macroH2A interferes with transcription factor binding and SWI/SNF nucleosome remodeling . Mol Cell. , 11 : 1033 – 1041 .
  • Anselmi , C , Bocchinfuso , G , Santis , P D , Savino , M and Scipioni , A . 2000 . A theoretical model for the prediction of sequence-dependent nucleosome thermodynamic stability . Biophys J. , 79 : 601 – 613 .
  • Arneodo , A , Vaillant , C , Audit , B , Argoul , F , d'Aubenton Carafa , Y and Thermes , C . 2011 . Multi-scale coding of genomic information: From DNA sequence to genome structure and function . Phys Rep. , 498 : 45 – 188 .
  • Audit , B , Thermes , C , Vaillant , C , d'Aubenton Carafa , Y , Muzy , J F and Arneodo , A . 2001 . Long-range correlations in genomic DNA: a signature of the nucleosomal structure . Phys Rev Lett. , 86 : 2471 – 2474 .
  • Audit , B , Vaillant , C , Arneodo , A , d'Aubenton Carafa , Y and Thermes , C . 2002 . Long-range correlations between DNA bending sites: relation to the structure and dynamics of nucleosomes . J Mol Biol. , 316 : 903 – 918 .
  • Audit , B , Vaillant , C , Arneodo , A , d'Aubenton-Carafa , Y and Thermes , C . 2004 . Wavelet analysis of DNA bending profiles reveals structural constraints on the evolution of genomic sequences . J Biol Phys. , 30 : 33 – 81 .
  • Bao , Y , White , C L and Luger , K . 2006 . Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure . J Mol Biol. , 361 : 617 – 624 .
  • Baxter , R . 1982 . Exactly solved models in statistical mechanics , London : Academic Press .
  • Bednar , J , Horowitz , R A , Grigoryev , S A , Carruthers , L M , Hansen , J C , Koster , A J and Woodcock , C L . 1998 . Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin . Proc Natl Acad Sci USA. , 95 : 14173 – 14178 .
  • Bernardi , G . 1989 . The isochore organization of the human genome . Annu Rev Genet. , 23 : 637 – 661 .
  • Bernardi , G . 1995 . The human genome: Organization and evolutionary history . Annu Rev Genet. , 29 : 445 – 476 .
  • Bernardi , G . 2000 . Isochores and the evolutionary genomics of vertebrates . Gene. , 241 : 3 – 17 .
  • Bernardi , G . 2001 . Misunderstandings about isochores . Part 1. Gene. , 276 : 3 – 13 .
  • Bernstein , B E , Liu , C L , Humphrey , E L , Perlstein , E O and Schreiber , S L . 2004 . Global nucleosome occupancy in yeast . Genome Biol. , 5 PR62
  • Blank , T A and Becker , P B . 1995 . Electrostatic mechanism of nucleosome spacing . J Mol Biol. , 252 : 305 – 313 .
  • Boeger , H , Griesenbeck , J and Kornberg , R D . 2008 . Nucleosome retention and the stochastic nature of promoter chromatin remodeling for transcription . Cell. , 133 : 716 – 726 .
  • Burcin , M , Arnold , R , Lutz , M , Kaiser , B , Runge , D , Lottspeich , F , Filippova , G N , Lobanenkov , V V and Renkawitz , R . 1997 . Negative protein 1, which is required for function of the chicken lysozyme gene silencer in conjunction with hormone receptors, is identical to the multivalent zinc finger repressor CTCF . Mol Cell Biol. , 17 : 1281 – 1288 .
  • Calladine , C R and Drew , H R . 1999 . Understanding DNA , San Diego : Academic Press .
  • Chereji , R V , Tolkunov , D , Locke , G and Morozov , A V . 2011 . Statistical mechanics of nucleosome ordering by chromatin-structure-induced two-body interactions . Phys Rev E: Stat Nonlin Soft Matter Phys. , 83 050903.
  • Chevereau G. 2010. Thermodynamique du positionnement des nucléosomes [Ph.D. thesis]. [Lyon (France)]: Université de Lyon-Ecole Normale Supérieure.
  • Chevereau , G , Palmeira , L , Thermes , C , Arneodo , A and Vaillant , C . 2009 . Thermodynamics of intragenic nucleosome ordering . Phys Rev Lett. , 103 188103.
  • Chung H-R, Dunkel I, Heise F, Linke C, Krobitsch S, Ehrenhofer-Murray AE, Sperling SR, Vingron M. 2010. The effect of micrococcal nuclease digestion on nucleosome positioning data. PLoS One. 5:e15754.
  • Clapier , C R and Cairns , B R . 2009 . The biology of chromatin remodeling complexes . Annu Rev Biochem. , 78 : 273 – 304 .
  • Davis , H T . 1990 . Density distribution functions of confined Tonks–Takahashi fluids . J Chem Phys. , 93 : 4339 – 4344 .
  • Dekker , J . 2008 . Mapping in vivo chromatin interactions in yeast suggests an extended chromatin fiber with regional variation in compaction . J Biol Chem. , 283 : 34532 – 34540 .
  • Deniz O, Flores O, Battistini F, Pérez A, Soler-Lòpez M, Orozco M. 2011. Physical properties of naked DNA influence nucleosome positioning and correlate with transcription start and termination sites in yeast. BMC Genomics. 12:489.
  • Depken , M and Schiessel , H . 2009 . Nucleosome shape dictates chromatin fiber structure . Biophys J. , 96 : 777 – 784 .
  • Dingwall , C , Lomonossoff , G P and Laskey , R A . 1981 . High sequence specificity of micrococcal nuclease . Nucleic Acids Res. , 9 : 2659 – 2673 .
  • Dong , F , Hansen , J C and van Holde , K E . 1990 . DNA and protein determinants of nucleosome positioning on sea urchin 5S rRNA gene sequencesin vitro . Proc Natl Acad Sci USA. , 87 : 5724 – 5728 .
  • Dorigo , B , Schalch , T , Kulangara , A , Duda , S , Schroeder , R R and Richmond , T J . 2004 . Nucleosome arrays reveal the two-start organization of the chromatin fibers . Science. , 306 : 1571 – 1573 .
  • Duret , L , Eyre-Walker , A and Galtier , N . 2006 . A new perspective on isochore evolution . Gene. , 385 : 71 – 74 .
  • Fan , X , Moqtaderi , Z , Jin , Y , Zhang , Y , Liu , X S and Struhl , K . 2010 . Nucleosome depletion at yeast terminators is not intrinsic and can occur by a transcriptional mechanism linked to 3’-end formation . Proc Natl Acad Sci USA. , 107 : 17945 – 17950 .
  • Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. 2008. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol. 4:e1000216.
  • Fire , A , Alcazar , R and Tan , F . 2006 . Unusual DNA structures associated with germline genetic activity in . Caenorhabditis elegans. Genetics. , 173 : 1259 – 1273 .
  • Floer , M , Wang , X , Prabhu , V , Berrozpe , G , Narayan , S , Spagna , D , Alvarez , D , Kendall , J , Krasnitz , A , Stepansky , A , Hicks , J , Bryant , G O and Ptashne , M . 2010 . A RSC/nucleosome complex determines chromatin architecture and facilitates activator binding . Cell. , 141 : 407 – 418 .
  • Fu Y, Sinha M, Peterson CL, Weng Z. 2008. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4:e1000138.
  • Gabrielian , A and Pongor , S . 1996 . Correlation of instrinsic DNA curvature with DNA property periodicity . FEBS Lett. , 393 : 65 – 68 .
  • Garcia , J F , Dumesic , P A , Hartley , P D , El-Samad , H and Madhani , H D . 2010 . Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions . Genes Dev. , 24 : 1758 – 1771 .
  • Giaquinta , P . 2008 . Entropy and ordering of hard rods in one dimension . Entropy. , 10 : 248 – 260 .
  • Gkikopoulos , T , Schofield , P , Singh , V , Pinskaya , M , Mellor , J , Smolle , M , Workman , J L , Barton , G J and Owen-Hughes , T . 2011 . A role for Snf2-related nucleosome-spacing enzymes in genome-wide nucleosome organization . Science. , 333 : 1758 – 1760 .
  • Goodsell , D S and Dickerson , R E . 1994 . Bending and curvature calculations in B-DNA . Nucleic Acids Res. , 22 : 5497 – 5503 .
  • Hall , M A , Shundrovsky , A , Bai , L , Fulbright , R M , Lis , J T and Wang , M D . 2009 . High-resolution dynamic mapping of histone-DNA interactions in a nucleosome . Nat Struct Mol Biol. , 16 : 124 – 129 .
  • Hamiche , A , Kang , J G , Dennis , C , Xiao , H and Wu , C . 2001 . Histone tails modulate nucleosome mobility and regulate ATP-dependent nucleosome sliding by NURF . Proc Natl Acad Sci USA. , 98 : 14316 – 14321 .
  • Hansen , J and McDonald , I . 2006 . Theory of simple liquids , London : Academic Press .
  • Hartley , P D and Madhani , H D . 2009 . Mechanisms that specify promoter nucleosome location and identity . Cell. , 137 : 445 – 458 .
  • Hörz , W and Altenburger , W . 1981 . Sequence specific cleavage of DNA by micrococcal nuclease . Nucleic Acids Res. , 9 : 2643 – 2658 .
  • Ioshikhes , I , Bolshoy , A , Derenshteyn , K , Borodovsky , M and Trifonov , E N . 1996 . Nucleosome DNA sequence pattern revealed by multiple alignment of experimentally mapped sequences . J Mol Biol. , 262 : 129 – 139 .
  • Ioshikhes , I P , Albert , I , Zanton , S J and Pugh , B F . 2006 . Nucleosome positions predicted through comparative genomics . Nat Genet. , 38 : 1210 – 1215 .
  • Iyer , V and Struhl , K . 1995 . Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure . EMBO J. , 14 : 2570 – 2579 .
  • Johnson , S M , Tan , F J , McCullough , H L , Riordan , D P and Fire , A Z . 2006 . Flexibility and constraint in the nucleosome core landscape of . Caenorhabditis elegans chromatin. Genome Res. , 16 : 1505 – 1516 .
  • Kaplan , N , Moore , I K , Fondufe-Mittendorf , Y , Gossett , A J , Tillo , D , Field , Y , LeProust , E M , Hughes , T R , Lieb , J D , Widom , J and Segal , E . 2009 . The DNA-encoded nucleosome organization of a eukaryotic genome . Nature. , 458 : 362 – 366 .
  • Kenigsberg E, Bar A, Segal E, Tanay A. 2010. Widespread compensatory evolution conserves DNA-encoded nucleosome organization in yeast. PLoS Comput Biol. 6:e1001039.
  • Kepper , N , Foethke , D , Stehr , R , Wedemann , G and Rippe , K . 2008 . Nucleosome geometry and internucleosomal interactions control the chromatin fiber conformation . Biophys J. , 95 : 3692 – 3705 .
  • Klenova EM, Nicolas RH, Paterson HF, Carne AF, Heath CM, Goodwin GH, Neiman PE, Lobanenkov VV. 1993. CTCF, a conserved nuclear factor required for optimal transcriptional activity of the chicken c-myc gene, is an 11-Zn-finger protein differentially expressed in multiple forms. Mol Cell Biol. 13:7612–7624.
  • Koerber , R T , Rhee , H S , Jiang , C and Pugh , B F . 2009 . Interaction of transcriptional regulators with specific nucleosomes across the . Saccharomyces genomes. Mol Cell. , 35 : 889 – 902 .
  • Kornberg , R D and Lorch , Y . 1999 . Twenty-five years of the nucleosome, fundamental particle of the eukaryote chromosomes . Cell. , 98 : 285 – 294 .
  • Kornberg , R D and Stryer , L . 1988 . Statistical distributions of nucleosomes: nonrandom locations by a stochastic mechanism . Nucleic Acids Res. , 16 : 6677 – 6690 .
  • Lam , F H , Steger , D J and O'Shea , E K . 2008 . Chromatin decouples promoter threshold from dynamic range . Nature. , 453 : 246 – 250 .
  • Lander , E S . 2001 . Initial sequencing and analysis of the human genomes . Nature. , 409 : 860 – 921 .
  • Längst , G , Bonte , E J , Corona , D F and Becker , P B . 1999 . Nucleosome movement by CHRAC and ISWI without disruption or trans-displacement of the histone octamer . Cell. , 97 : 843 – 852 .
  • Lantermann , A B , Straub , T , Strålfors , A , Yuan , G- C , Ekwall , K and Korber , P . 2010 . Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae . Nat Struct Mol Biol. , 17 : 251 – 257 .
  • Lee , C- K , Shibata , Y , Rao , B , Strahl , B D and Lieb , J D . 2004 . Evidence for nucleosome depletion at active regulatory regions genome-wide . Nat Genet. , 36 : 900 – 905 .
  • Lee JT. 2003. Molecular links between X-inactivation and autosomal imprinting: X-inactivation as a driving force for the evolution of imprinting? Curr Biol. 13:R242–R254.
  • Lee , W , Tillo , D , Bray , N , Morse , R H , Davis , R W , Hughes , T R and Nislow , C . 2007 . A high-resolution atlas of nucleosome occupancy in yeast . Nat Genet. , 39 : 1235 – 1244 .
  • Lesne , A and Victor , J- M . 2006 . Chromatin fiber functional organization: some plausible models . Eur Phys J E Soft Matter. , 19 : 279 – 290 .
  • Li , B , Carey , M and Workman , JL . 2007 . The role of chromatin during transcription . Cell. , 128 : 707 – 719 .
  • Li , W , Bernaola-Galván , P , Carpena , P and Oliver , JL . 2003 . Isochores merit the prefix iso . Comput Biol Chem. , 27 : 5 – 10 .
  • Lieb , E and Mattis , D . 1966 . Mathematical physics in one dimension , London : Academic Press .
  • Lionnet , T , Dawid , A , Bigot , S , Barre , F- X , Saleh , O A , Heslot , F , Allemand , J- F , Bensimon , D and Croquette , V . 2006 . DNA mechanics as a tool to probe helicase and translocase activity . Nucleic Acids Res. , 34 : 4232 – 4244 .
  • Lorch , Y , Zhang , M and Kornberg , R D . 1999 . Histone octamer transfer by a chromatin-remodeling complex . Cell. , 96 : 389 – 392 .
  • Lowary , P T and Widom , J . 1997 . Nucleosome packaging and nucleosome positioning of genomic DNA . Proc Natl Acad Sci USA. , 94 : 1183 – 1188 .
  • Lowary , P T and Widom , J . 1998 . New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning . J Mol Biol. , 276 : 19 – 42 .
  • Luger , K , Mäder , A W , Richmond , R K , Sargent , D F and Richmond , T J . 1997 . Crystal structure of the nucleosome core particle at 2.8 \r A resolution . Nature. , 389 : 251 – 260 .
  • Mavrich , T N , Ioshikhes , I P , Venters , B J , Jiang , C , Tomsho , L P , Qi , J , Schuster , S C , Albert , I and Pugh , B F . 2008a . A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome . Genome Res. , 18 : 1073 – 1083 .
  • Mavrich , T N , Jiang , C , Ioshikhes , I P , Li , X , Venters , B J , Zanton , S J , Tomsho , L P , Qi , J , Glaser , R L , Schuster , S C , Gilmour , D S , Albert , I and Pugh , B F . 2008b . Nucleosome organization in the Drosophila . genome. Nature. , 453 : 358 – 362 .
  • Mergell , B and Everaers , R . Schiessel H. 2004. Nucleosome interactions in chromatin: fiber stiffening hairpin formation . Phys Rev E: Stat Nonlin Soft Matter Phys. , 70 011915.
  • Miele , V , Vaillant , C , d'Aubenton Carafa , Y , Thermes , C and Grange , T . 2008 . DNA physical properties determine nucleosome occupancy from yeast to fly . Nucleic Acids Res. , 36 : 3746 – 3756 .
  • Milani , P , Chevereau , G , Vaillant , C , Audit , B , Haftek-Terreau , Z , Marilley , M , Bouvet , P , Argoul , F and Arneodo , A . 2009 . Nucleosome positioning by genomic excluding-energy barriers . Proc Natl Acad Sci USA. , 106 : 22257 – 22262 .
  • Miller , J A and Widom , J . 2003 . Collaborative competition mechanism for gene activation in vivo . Mol Cell Biol. , 23 : 1623 – 1632 .
  • Mito , Y , Henikoff , J G and Henikoff , S . 2007 . Histone replacement marks the boundaries of cis-regulatory domains . Science. , 315 : 1408 – 1411 .
  • Möbius W, Gerland U. 2010. Quantitative test of the barrier nucleosome model for statistical positioning of nucleosomes up- and downstream of transcription start sites. PLoS Comput Biol. 6:e1000891.
  • Montel , F , Fontaine , E , St-Jean , P , Castelnovo , M and Faivre-Moskalenko , C . 2007 . Atomic force microscopy imaging of SWI/SNF action: mapping the nucleosome remodeling and sliding . Biophys J. , 93 : 566 – 578 .
  • Moreira , J M and Holmberg , S . 1999 . Transcriptional repression of the yeast CHA1 gene requires the chromatin-remodeling complex RSC . EMBO J. , 18 : 2836 – 2844 .
  • Morozov , A V , Fortney , K , Gaykalova , D A , Studitsky , V M , Widom , J and Siggia , E D . 2009 . Using DNA mechanics to predict in vitro nucleosome positions and formation energies . Nucleic Acids Res. , 37 : 4707 – 4722 .
  • Morse , R H . 2007 . Transcription factor access to promoter elements . J Cell Biochem. , 102 : 560 – 570 .
  • Moshkin , Y M , Chalkley , G E , Kan , T W , Reddy , B A , Ozgur , Z , van Ijcken , WF J , Dekkers , DH W , Demmers , J A , Travers , A A and Verrijzer , C P . 2012 . Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner . Mol Cell Biol. , 32 : 675 – 688 .
  • Mouchiroud , D and Bernardi , G . 1993 . Compositional properties of coding sequences and mammalian phylogeny . J Mol Evol. , 37 : 109 – 116 .
  • Moukhtar , J , Faivre-Moskalenko , C , Milani , P , Audit , B , Vaillant , C , Fontaine , E , Mongelard , F , Lavorel , G , St-Jean , P , Bouvet , P , Argoul , F and Arneodo , A . 2010 . Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments . J Phys Chem B. , 114 : 5125 – 5143 .
  • Moukhtar , J , Fontaine , E , Faivre-Moskalenko , C and Arneodo , A . 2007 . Probing persistence in DNA curvature properties with atomic force microscopy . Phys Rev Lett. , 98 178101.
  • Moukhtar , J , Vaillant , C , Audit , B and Arneodo , A . 2009 . Generalized wormlike chain model for long-range correlated heteropolymers . Europhys Lett. , 86 48001.
  • Moukhtar , J , Vaillant , C , Audit , B and Arneodo , A . 2011 . Revisiting polymer statistical physics to account for the presence of long-range-correlated structural disorder in 2D DNA chains . Eur Phys J E: Soft Matter. , 34 : 119
  • Noll , M and Kornberg , R D . 1977 . Action of micrococcal nuclease on chromatin and the location of histone H1 . J Mol Biol. , 109 : 393 – 404 .
  • Ohlsson , R , Bartkuhn , M and Renkawitz , R . 2010 . CTCF shapes chromatin by multiple mechanisms: the impact of 20 years of CTCF research on understanding the workings of chromatin . Chromosoma. , 119 : 351 – 360 .
  • Ozsolak , F , Song , J S , Liu , X S and Fisher , D E . 2007 . High-throughput mapping of the chromatin structure of human promoters . Nat Biotechnol. , 25 : 244 – 248 .
  • Payen , C , Fischer , G , Marck , C , Proux , C , Sherman , D J , Coppée , J- Y , Johnston , M , Dujon , B and Neuvéglise , C . 2009 . Unusual composition of a yeast chromosome arm is associated with its delayed replication . Genome Res. , 19 : 1710 – 1721 .
  • Peckham , H E , Thurman , R E , Fu , Y , Stamatoyannopoulos , J A , Noble , W S , Struhl , K and Weng , Z . 2007 . Nucleosome positioning signals in genomic DNA . Genome Res. , 17 : 1170 – 1177 .
  • Percus , J K . 1976 . Equilibrium state of a classical fluid of hard rods in an external field . J Stat Phys. , 15 : 505 – 511 .
  • Percus , J K . 1982 . One-dimensional classical fluid with nearest-neighbor interaction in arbitrary external field . J Stat Phys. , 28 : 67
  • Peterson , C L and Workman , J L . 2000 . Promoter targeting and chromatin remodeling by the SWI/SNF complex . Curr Opin Genet Dev. , 10 : 187 – 192 .
  • Piasecki , J and Peliti , L . 1993 . Harmonic properties of hard-spheres crystals: a one-demensional study . J Phys A: Math Gen. , 26 : 4819 – 4825 .
  • Polach , K J and Widom , J . 1996 . A model for the cooperative binding of eukaryotic regulatory proteins to nucleosomal target sites . J Mol Biol. , 258 : 800 – 812 .
  • Pusarla , R- H , Vinayachandran , V and Bhargava , P . 2007 . Nucleosome positioning in relation to nucleosome spacing and DNA sequence-specific binding of a protein . FEBS J. , 274 : 2396 – 2410 .
  • Radman-Livaja , M and Rando , O J . 2010 . Nucleosome positioning: how is it established, and why does it matter? . Dev Biol. , 339 : 258 – 266 .
  • Rando , O J and Ahmad , K . 2007 . Rules and regulation in the primary structure of chromatin . Curr Opin Cell Biol. , 19 : 250 – 256 .
  • Raveh-Sadka , T , Levo , M and Segal , E . 2009 . Incorporating nucleosomes into thermodynamic models of transcription regulation . Genome Res. , 19 : 1480 – 1496 .
  • Rayleigh Lord (1891). On the virial of a system of hard colliding bodies. Nature London. 45:80–82.
  • Richard , G- F , Kerrest , A and Dujon , B . 2008 . Comparative genomics and molecular dynamics of DNA repeats in eukaryotes . Microbiol Mol Biol Rev. , 72 : 686 – 727 .
  • Richmond , T J and Davey , C A . 2003 . The structure of DNA in the nucleosome core . Nature. , 423 : 145 – 150 .
  • Riposo , J and Mozziconacci , J . 2012 . Nucleosome positioning and nucleosome stacking: two faces of the same coin . Mol Biosyst. , 8 : 1172 – 1178 .
  • Rippe , K , Schrader , A , Riede , P , Strohner , R , Lehmann , E and Längst , G . 2007 . DNA sequence- and conformation-directed positioning of nucleosomes by chromatin-remodeling complexes . Proc Natl Acad Sci USA. , 104 : 15635 – 15640 .
  • Robinson , P , Fairall , L , Huynh , V and Rhodes , D . 2006 . EM measurements define the dimensions of the “30-nm” chromatin fibre: evidence for a compact, interdigitated structures . Proc Natl Acad Sci USA. , 103 : 6506 – 6511 .
  • Robledo , A and Rowlinson , J . 1986 . The distribution of hard rods on a line of finite length . Mol Phys. , 58 : 711 – 721 .
  • Salsburg , Z W , Kirkwood , J and Zwanzig , R . 1953 . Molecular distribution functions in a one-dimensional fluid . J Chem Phys. , 21 : 1098
  • Santis , P D , Morosetti , S and Scipioni , A . 2010 . Prediction of nucleosome positioning in genomes: limits and perspectives of physical and bioinformatic approaches . J Biomol Struct Dyn. , 27 : 747 – 764 .
  • Satchwell , S C , Drew , H R and Travers , A A . 1986 . Sequence periodicities in chicken nucleosome core DNA . J Mol Biol. , 191 : 659 – 675 .
  • Schones , D E , Cui , K , Cuddapah , S , Roh , T- Y , Barski , A , Wang , Z , Wei , G and Zhao , K . 2008 . Dynamic regulation of nucleosome positioning in the human genome . Cell. , 132 : 887 – 898 .
  • Segal , E , Fondufe-Mittendorf , Y , Chen , L , Thåström , A , Field , Y , Moore , I K , Wang , J-P Z and Widom , J . 2006 . A genomic code for nucleosome positioning . Nature. , 442 : 772 – 778 .
  • Segal , E and Widom , J . 2009a . Poly(dA:dT) tracts: major determinants of nucleosome organization . Curr Opin Struct Biol. , 19 : 65 – 71 .
  • Segal , E and Widom , J . 2009b . From DNA sequence to transcriptional behaviour: a quantitative approach . Nat Rev Genet. , 10 : 443 – 456 .
  • Segal , E and Widom , J . 2009c . What control nucleosome positions? . Trends Genet. , 25 : 335 – 343 .
  • Shivaswamy , S , Bhinge , A , Zhao , Y , Jones , S , Hirst , M and Iyer , V R . 2008 . Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation . PLoS Biol. , 6 : e65
  • Shlyakhtenko , L S , Lushnikov , A Y and Lyubchenko , Y L . 2009 . Dynamics of nucleosomes revealed by time-lapse atomic force microscopy . Biochemistry. , 48 : 7842 – 7848 .
  • Solis , F J , Bash , R , Yodh , J , Lindsay , S M and Lohr , D . 2004 . A statistical thermodynamic model applied to experimental AFM population and location data is able to quantify DNA-histone binding strength and internucleosomal interaction differences between acetylated and unacetylated nucleosomal arrays . Biophys J. , 87 : 3372 – 3387 .
  • Strick , T R , Dessinges , M N , Charvin , G , Dekker , N H , Allemand , J F , Bensimon , D and Croquette , V . 2003 . Stretching of macromolecules and proteins . Rep Prog Phys. , 66 : 1 – 45 .
  • Suter , B , Schnappauf , G and Thoma , F . 2000 . Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promotersinvivo . Nucleic Acids Res. , 28 : 4083 – 4089 .
  • Takahashi H. 1942. A simple method for treating the statistical mechanics of one-dimensional substances. Proc Phys Math Soc Jpn. 24:60.
  • Teif , V B and Rippe , K . 2009 . Predicting nucleosome positions on the DNA: combining intrinsic sequence preferences and remodeler activities . Nucleic Acids Res. , 37 : 5641 – 5655 .
  • Thåström , A , Bingham , L M and Widom , J . 2004 . Nucleosomal locations of dominant DNA sequence motifs for histone-DNA interactions and nucleosome positioning . J Mol Biol. , 338 : 695 – 709 .
  • Thåström , A , Lowary , P T , Widlund , H R , Cao , H , Kubista , M and Widom , J . 1999 . Sequence motifs and free energies of selected natural and non-natural nucleosome positioning DNA sequences . J Mol Biol. , 288 : 213 – 229 .
  • Tillo , D and Hughes , T R . 2009 . G+C content dominates intrinsic nucleosome occupancy . BMC Bioinforma. , 10 : 442
  • Tirosh , I and Barkai , N . 2008 . Two strategies for gene regulation by promoter nucleosomes . Genome Res. , 18 : 1084 – 1091 .
  • Tolkunov , D and Morozov , A V . 2010 . Genomic studies and computational predictions of nucleosome positions and formation energies . Adv Protein Chem Struct Biol. , 79 : 1 – 57 .
  • Tolstorukov , M Y , Colasanti , A V , McCandlish , D M , Olson , W K and Zhurkin , V B . 2007 . A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning . J Mol Biol. , 371 : 725 – 738 .
  • Tonks , L . 1936 . The complete equation of state of one, two and three-dimensional gases of hard elastic spheres . Phys Rev. , 50 : 955 – 963 .
  • Travers , A . 1999 . An engine for nucleosome remodeling . Cell. , 96 : 311 – 314 .
  • Tsankov , A , Yanagisawa , Y , Rhind , N , Regev , A and Rando , O J . 2011 . Evolutionary divergence of intrinsic and trans-regulated nucleosome positioning sequences reveals plastic rules for chromatin organization . Genome Res. , 21 : 1851 – 1862 .
  • Tsankov , A M , Thompson , D A , Socha , A , Regev , A and Rando , O J . 2010 . The role of nucleosome positioning in the evolution of gene regulation . PLoS Biol. , 8 : e1000414
  • Tsukiyama , T and Wu , C . 1997 . Chromatin remodeling and transcription . Curr Opin Genet Dev. , 7 : 182 – 191 .
  • Vaillant , C , Audit , B and Arneodo , A . 2005 . Thermodynamics of DNA loops with long-range correlated structural disorder . Phys Rev Lett. , 95 : 068101
  • Vaillant , C , Audit , B and Arneodo , A . 2007 . Experiments confirm the influence of genome long-range correlations on nucleosome positioning . Phys Rev Lett. , 99 : 218103
  • Vaillant , C , Audit , B , Thermes , C and Arnéodo , A . 2006 . Formation and positioning of nucleosomes: effect of sequence-dependent long-range correlated structural disorder . Eur Phys J E: Soft Matter , 19 : 263 – 277 .
  • Vaillant , C , Palmeira , L , Chevereau , G , Audit , B , d'Aubenton Carafa , Y , Thermes , C and Arneodo , A . 2010 . A novel strategy of transcription regulation by intragenic nucleosome ordering . Genome Res. , 20 : 59 – 67 .
  • Valouev , A , Ichikawa , J , Tonthat , T , Stuart , J , Ranade , S , Peckham , H , Zeng , K , Malek , J A , Costa , G , McKernan , K , Sidow , A , Fire , A and Johnson , S M . 2008 . A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. . Genome Res. , 18 : 1051 – 1063 .
  • Valouev , A , Johnson , S M , Boyd , S D , Smith , C L , Fire , A Z and Sidow , A . 2011 . Determinants of nucleosome organization in primary human cells . Nature. , 474 : 516 – 520 .
  • van Holde , K E . 1988 . Chromatin , New York : Springer-Verlag .
  • Vanderlick , T K , Scriven , L E and Davis , H T . 1986 . Solution of Percus equation for the density of hard-rods in an external-field . Phys Rev A. , 34 : 5130 – 5131 .
  • Vashee , S , Melcher , K , Ding , W V , Johnston , S A and Kodadek , T . 1998 . Evidence for two modes of cooperative DNA binding in vivo that do not involve direct protein–protein interactions . Curr Biol. , 8 : 452 – 458 .
  • Wang , M D , Schnitzer , M J , Yin , H , Landick , R , Gelles , J and Block , S M . 1998 . Force and velocity measured for single molecules of RNA polymerase . Science. , 282 : 902 – 907 .
  • Wang , X , Bai , L , Bryant , G O and Ptashne , M . 2011a . Nucleosomes and the accessibility problem . Trends Genet. , 27 : 487 – 492 .
  • Wang , X , Bryant , G O , Floer , M , Spagna , D and Ptashne , M . 2011b . An effect of DNA sequence on nucleosome occupancy and removal . Nat Struct Mol Biol. , 18 : 507 – 509 .
  • Weiner , A , Hughes , A , Yassour , M , Rando , O J and Friedman , N . 2010 . High-resolution nucleosome mapping reveals transcription-dependent promoter packaging . Genome Res. , 20 : 90 – 100 .
  • Whitehouse , I , Flaus , A , Cairns , B R , White , M F , Workman , J L and Owen-Hughes , T . 1999 . Nucleosome mobilization catalysed by the yeast SWI/SNF complex . Nature. , 400 : 784 – 787 .
  • Whitehouse , I , Rando , O J , Delrow , J and Tsukiyama , T . 2007 . Chromatin remodelling at promoters suppresses antisense transcription . Nature. , 450 : 1031 – 1035 .
  • Whitehouse , I and Tsukiyama , T . 2006 . Antagonistic forces that position nucleosomes . in vivo. Nat Struct Mol Biol. , 13 : 633 – 640 .
  • Widom , J . 1996 . Short-range order in two eukaryotic genomes: relation to chromosome structure . J Mol Biol. , 259 : 579 – 588 .
  • Widom , J . 2001 . Role of DNA sequence in nucleosome stability and dynamics . Q Rev Biophys. , 34 : 269 – 324 .
  • Wolffe , A P . 1998 . Chromatin Structure and Function , 3 , London : Academic Press .
  • Woodcock , C L , Skoultchi , A I and Fan , Y . 2006 . Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length . Chromosome Res. , 14 : 17 – 25 .
  • Yuan , G- C and Liu , J S . 2008 . Genomic sequence is highly predictive of local nucleosome depletion . PLoS Comput Biol. , 4 : e13
  • Yuan , G- C , Liu , Y- J , Dion , M F , Slack , M D , Wu , L F , Altschuler , S J and Rando , O J . 2005 . Genome-scale identification of nucleosome positions in S. cerevisiae . Science. , 309 : 626 – 630 .
  • Zhang , Y , Moqtaderi , Z , Rattner , B P , Euskirchen , G , Snyder , M , Kadonaga , J T , Liu , X S and Struhl , K . 2009 . Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo . Nat Struct Mol Biol. , 16 : 847 – 852 .
  • Zhang , Z and Pugh , B F . 2011 . High-resolution genome-wide mapping of the primary structure of chromatin . Cell. , 144 : 175 – 186 .
  • Zhang , Z , Wippo , C J , Wal , M , Ward , E , Korber , P and Pugh , B F . 2011 . A packing mechanism for nucleosome organization reconstituted across a eukaryotic genome . Science. , 332 : 977 – 980 .

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.