Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E: Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput Biol. 2008, 4: e1000216-10.1371/journal.pcbi.1000216.
Article
PubMed Central
PubMed
Google Scholar
Shivaswamy S, Bhinge A, Zhao Y, Jones S, Hirst M, Iyer VR: Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation. PLoS Biol. 2008, 6: e65-10.1371/journal.pbio.0060065.
Article
PubMed Central
PubMed
Google Scholar
Jiang C, Pugh BF: Nucleosome positioning and gene regulation: advances through genomics. Nature Rev Genet. 2009, 10: 161-172.
Article
CAS
PubMed
Google Scholar
Guan Y, Yao V, Tsui K, Gebbia M, Dunham MJ, Nislow C, Troyanskaya OG: Nucleosome-coupled expression differences in closely-related species. BMC Genomics. 2011, 12: 466-10.1186/1471-2164-12-466.
Article
PubMed Central
CAS
PubMed
Google Scholar
Segal E, Fondufe-Mittendorf Y, Chen L, Thastrom A, Field Y, Moore IK, Wang JP, Widom J: A genomic code for nucleosome positioning. Nature. 2006, 442: 772-778. 10.1038/nature04979.
Article
PubMed Central
CAS
PubMed
Google Scholar
Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E: The DNA-encoded nucleosome organization of a eukaryotic genome. Nature. 2009, 458: 362-366. 10.1038/nature07667.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yuan GC, Liu JS: Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput Biol. 2008, 4: e13-10.1371/journal.pcbi.0040013.
Article
PubMed Central
PubMed
Google Scholar
Rapoport AE, Frenkel ZM, Trifonov EN: Nucleosome positioning pattern derived from oligonucleotide compositions of genomic sequences. J Biomol Struct Dynam. 2011, 28: 567-574. 10.1080/07391102.2011.10531243.
Article
CAS
Google Scholar
Sandman K, Reeve JN: Archaeal histones and the origin of the histone fold. Curr Opin Microbiol. 2006, 9: 520-525. 10.1016/j.mib.2006.08.003.
Article
CAS
PubMed
Google Scholar
Cubonova L, Sandman K, Hallam SJ, Delong EF, Reeve JN: Histones in Crenarchaea. J Bacteriol. 2005, 187: 5482-5485. 10.1128/JB.187.15.5482-5485.2005.
Article
PubMed Central
CAS
PubMed
Google Scholar
Friedrich-Jahn U, Aigner J, Langst G, Reeve JN, Huber H: Nanoarchaeal origin of histone H3?. J Bacteriol. 2009, 191: 1092-1096. 10.1128/JB.01431-08.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bailey KA, Pereira SL, Widom J, Reeve JN: Archaeal histone selection of nucleosome positioning sequences and the procaryotic origin of histone-dependent genome evolution. J Mol Biol. 2000, 303: 25-34. 10.1006/jmbi.2000.4128.
Article
CAS
PubMed
Google Scholar
Cubonova L, Katano M, Kanai T, Atomi H, Reeve JN, Santangelo TJ: An archaeal histone is required for transformation of Thermococcus kodakarensis. J Bacteriol. 2012, 194: 6864-6874. 10.1128/JB.01523-12.
Article
PubMed Central
CAS
Google Scholar
Sandman K, Krzycki JA, Dobrinski B, Lurz R, Reeve JN: HMf, a DNA-binding protein isolated from the hyperthermophilic archaeon Methanothermus fervidus, is most closely related to histones. Proc Natl Acad Sci USA. 1990, 87: 5788-5791. 10.1073/pnas.87.15.5788.
Article
PubMed Central
CAS
PubMed
Google Scholar
Samson R, Reeve JN: DNA binding proteins and chromatin. Archaea: Molecular and Cellular Biology. Edited by: Cavicchioli R. 2007, Washington, DC: ASM Press, 110-119.
Chapter
Google Scholar
Pereira SL, Grayling RA, Lurz R, Reeve JN: Archaeal nucleosomes. Proc Natl Acad Sci USA. 1997, 94: 12633-12637. 10.1073/pnas.94.23.12633.
Article
PubMed Central
CAS
PubMed
Google Scholar
Bailey KA, Marc F, Sandman K, Reeve JN: Both DNA and histone fold sequences contribute to archaeal nucleosome stability. J Biol Chem. 2002, 277: 9293-9301. 10.1074/jbc.M110029200.
Article
CAS
PubMed
Google Scholar
Marc F, Sandman K, Lurz R, Reeve JN: Archaeal histone tetramerization determines DNA affinity and the direction of DNA supercoiling. J Biol Chem. 2002, 277: 30879-30886. 10.1074/jbc.M203674200.
Article
CAS
PubMed
Google Scholar
Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Hughes TR, Lieb JD, Widom J, Segal E: Nucleosome sequence preferences influence in vivo nucleosome organization. Nat Struct Mol Biol. 2010, 17: 918-920. 10.1038/nsmb0810-918. author reply 920–922
Article
PubMed Central
CAS
PubMed
Google Scholar
Gaffney DJ, McVicker G, Pai AA, Fondufe-Mittendorf YN, Lewellen N, Michelini K, Widom J, Gilad Y, Pritchard JK: Controls of nucleosome positioning in the human genome. PLoS Genet. 2012, 8: e1003036-10.1371/journal.pgen.1003036.
Article
PubMed Central
CAS
PubMed
Google Scholar
Brogaard K, Xi L, Wang JP, Widom J: A map of nucleosome positions in yeast at base-pair resolution. Nature. 2012, 486: 496-501.
PubMed Central
CAS
PubMed
Google Scholar
Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C: A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet. 2007, 39: 1235-1244. 10.1038/ng2117.
Article
CAS
PubMed
Google Scholar
Segal E, Widom J: Poly(dA:dT) tracts: major determinants of nucleosome organization. Curr Opin Struct Biol. 2009, 19: 65-71. 10.1016/j.sbi.2009.01.004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Iyer V, Struhl K: Poly(dA:dT), a ubiquitous promoter element that stimulates transcription via its intrinsic DNA structure. EMBO J. 1995, 14: 2570-2579.
PubMed Central
CAS
PubMed
Google Scholar
Lascaris RF, Groot E, Hoen PB, Mager WH, Planta RJ: Different roles for abf1p and a T-rich promoter element in nucleosome organization of the yeast RPS28A gene. Nucl Acids Res. 2000, 28: 1390-1396. 10.1093/nar/28.6.1390.
Article
PubMed Central
CAS
PubMed
Google Scholar
Morohashi N, Yamamoto Y, Kuwana S, Morita W, Shindo H, Mitchell AP, Shimizu M: Effect of sequence-directed nucleosome disruption on cell-type-specific repression by alpha2/Mcm1 in the yeast genome. Euk Cell. 2006, 5: 1925-1933. 10.1128/EC.00105-06.
Article
CAS
Google Scholar
Bao Y, White CL, Luger K: Nucleosome core particles containing a poly(dA.dT) sequence element exhibit a locally distorted DNA structure. J Mol Biol. 2006, 361: 617-624. 10.1016/j.jmb.2006.06.051.
Article
CAS
PubMed
Google Scholar
Struhl K: Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl Acad Sci USA. 1985, 82: 8419-8423. 10.1073/pnas.82.24.8419.
Article
PubMed Central
CAS
PubMed
Google Scholar
Nelson HC, Finch JT, Luisi BF, Klug A: The structure of an oligo(dA)-oligo(dT) tract and its biological implications. Nature. 1987, 330: 221-226. 10.1038/330221a0.
Article
CAS
PubMed
Google Scholar
Suter B, Schnappauf G, Thoma F: Poly(dA.dT) sequences exist as rigid DNA structures in nucleosome-free yeast promoters in vivo. Nucl Acids Res. 2000, 28: 4083-4089. 10.1093/nar/28.21.4083.
Article
PubMed Central
CAS
PubMed
Google Scholar
Anderson JD, Widom J: Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. Mol Cell Biol. 2001, 21: 3830-3839. 10.1128/MCB.21.11.3830-3839.2001.
Article
PubMed Central
CAS
PubMed
Google Scholar
Sekinger EA, Moqtaderi Z, Struhl K: Intrinsic histone-DNA interactions and low nucleosome density are important for preferential accessibility of promoter regions in yeast. Mol Cell. 2005, 18: 735-748. 10.1016/j.molcel.2005.05.003.
Article
CAS
PubMed
Google Scholar
Ioshikhes IP, Albert I, Zanton SJ, Pugh BF: Nucleosome positions predicted through comparative genomics. Nat Genet. 2006, 38: 1210-1215. 10.1038/ng1878.
Article
CAS
PubMed
Google Scholar
Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T: Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res. 2005, 15: 352-363. 10.1101/gr.3003105.
Article
PubMed Central
CAS
PubMed
Google Scholar
Grohmann D, Werner F: Recent advances in the understanding of archaeal transcription. Curr Opin Microbiol. 2011, 14: 328-334. 10.1016/j.mib.2011.04.012.
Article
CAS
PubMed
Google Scholar
Santangelo TJ, Reeve JN: Archaeal RNA polymerase is sensitive to intrinsic termination directed by transcribed and remote sequences. J Mol Biol. 2006, 355: 196-210. 10.1016/j.jmb.2005.10.062.
Article
CAS
PubMed
Google Scholar
Nishida H, Kondo S, Matsumoto T, Suzuki Y, Yoshikawa H, Taylor TD, Sugiyama J: Characteristics of nucleosomes and linker DNA regions on the genome of the basidiomycete Mixia osmundae revealed by mono- and dinucleosome mapping. Open Biol. 2012, 2: 120043-10.1098/rsob.120043.
Article
PubMed Central
PubMed
Google Scholar
Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z: Nucleosome positioning signals in genomic DNA. Genome Res. 2007, 17: 1170-1177. 10.1101/gr.6101007.
Article
PubMed Central
CAS
PubMed
Google Scholar
Archaeal Genome Browser. http://archaea.ucsc.edu,
Santangelo TJ, Cubonova L, Matsumi R, Atomi H, Imanaka T, Reeve JN: Polarity in archaeal operon transcription in Thermococcus kodakaraensis. J Bacteriol. 2008, 190: 2244-2248. 10.1128/JB.01811-07.
Article
PubMed Central
CAS
PubMed
Google Scholar
Smith DR, Doucette-Stamm LA, Deloughery C, Lee H, Dubois J, Aldredge T, Bashirzadeh R, Blakely D, Cook R, Gilbert K, Harrison D, Hoang L, Keagle P, Lumm W, Pothier B, Qiu D, Spadafora R, Vicaire R, Wang Y, Wierzbowski J, Gibson R, Jiwani N, Caruso A, Bush D, Reeve JN: Complete genome sequence of Methanobacterium thermoautotrophicum ΔH: functional analysis and comparative genomics. J Bacteriol. 1997, 179: 7135-7155.
PubMed Central
CAS
PubMed
Google Scholar
UCSC Genome Browser on Thermococcus kodakarensis May 2004 Assembly (therKoda1). 2004, http://archaea.ucsc.edu/lists/therKoda1/refSeq-list.html, May Assembly (therKoda1),
Gupta S, Dennis J, Thurman RE, Kingston R, Stamatoyannopoulos JA, Noble WS: Predicting human nucleosome occupancy from primary sequence. PLoS Comput Biol. 2008, 4: e1000134-10.1371/journal.pcbi.1000134.
Article
PubMed Central
PubMed
Google Scholar
Zhang Y, Moqtaderi Z, Rattner BP, Euskirchen G, Snyder M, Kadonaga JT, Liu XS, Struhl K: Intrinsic histone-DNA interactions are not the major determinant of nucleosome positions in vivo. Nat Struct Mol Biol. 2009, 16: 847-852. 10.1038/nsmb.1636.
Article
PubMed Central
CAS
PubMed
Google Scholar
Ioshikhes I, Hosid S, Pugh BF: Variety of genomic DNA patterns for nucleosome positioning. Genome Res. 2011, 21: 1863-1871. 10.1101/gr.116228.110.
Article
PubMed Central
CAS
PubMed
Google Scholar
Tillo D, Hughes TR: G + C content dominates intrinsic nucleosome occupancy. BMC Bioinforma. 2009, 10: 442-10.1186/1471-2105-10-442.
Article
Google Scholar
Visnapuu ML, Greene EC: Single-molecule imaging of DNA curtains reveals intrinsic energy landscapes for nucleosome deposition. Nat Struct Mol Biol. 2009, 16: 1056-1062. 10.1038/nsmb.1655.
Article
PubMed Central
CAS
PubMed
Google Scholar
Lankas F, Sponer J, Langowski J, Cheatham TE: DNA basepair step deformability inferred from molecular dynamics simulations. Biophys J. 2003, 85: 2872-2883. 10.1016/S0006-3495(03)74710-9.
Article
PubMed Central
CAS
PubMed
Google Scholar
Luger K, Mäder AW, Richmond RK, Sargent DF, Richmond TJ: Crystal structure of the nucleosome core particle at 2.8 A resolution. Nature. 1997, 389: 251-260. 10.1038/38444.
Article
CAS
PubMed
Google Scholar
Luger K, Mader A, Sargent DF, Richmond TJ: The atomic structure of the nucleosome core particle. J Biomol Struct Dyn. 2000, 17 (Suppl 1): 185-188.
Article
PubMed
Google Scholar
Decanniere K, Babu AM, Sandman K, Reeve JN, Heinemann U: Crystal structures of recombinant histones HMfA and HMfB from the hyperthermophilic archaeon Methanothermus fervidus. J Mol Biol. 2000, 303: 35-47. 10.1006/jmbi.2000.4104.
Article
CAS
PubMed
Google Scholar
Soares DJ, Sandman K, Reeve JN: Mutational analysis of archaeal histone-DNA interactions. J Mol Biol. 2000, 297: 39-47. 10.1006/jmbi.2000.3546.
Article
CAS
PubMed
Google Scholar
French SL, Santangelo TJ, Beyer AL, Reeve JN: Transcription and translation are coupled in Archaea. Mol Biol Evol. 2007, 24: 893-895. 10.1093/molbev/msm007.
Article
CAS
PubMed
Google Scholar
Wilkinson SP, Ouhammouch M, Geiduschek EP: Transcriptional activation in the context of repression mediated by archaeal histones. Proc Natl Acad Sci USA. 2010, 107: 6777-6781. 10.1073/pnas.1002360107.
Article
PubMed Central
CAS
PubMed
Google Scholar
Xie Y, Reeve JN: Transcription by an archaeal RNA polymerase is slowed but not blocked by an archaeal nucleosome. J Bacteriol. 2004, 186: 3492-3498. 10.1128/JB.186.11.3492-3498.2004.
Article
PubMed Central
CAS
PubMed
Google Scholar
Yuan GC, Liu YJ, Dion MF, Slack MD, Wu LF, Altschuler SJ, Rando OJ: Genome-scale identification of nucleosome positions in S. cerevisiae. Science. 2005, 309: 626-630. 10.1126/science.1112178.
Article
CAS
PubMed
Google Scholar
Ammar R, Torti D, Tsui K, Gebbia M, Durbic T, Bader GD, Giaever G, Nislow C: Chromatin is an ancient innovation conserved between Archaea and Eukarya. Elife. 2012, 1: e00078-10.7554/eLife.00078.
Article
PubMed Central
PubMed
Google Scholar
Hartman AL, Norais C, Badger JH, Delmas S, Haldenby S, Madupu R, Robinson J, Khouri H, Ren Q, Lowe TM, Maupin-Furlow J, Pohlschroder M, Daniels C, Pfeiffer F, Allers T, Eisen JA: The complete genome sequence of Haloferax volcanii DS2, a model archaeon. PLoS One. 2010, 5: e9605-10.1371/journal.pone.0009605.
Article
PubMed Central
PubMed
Google Scholar
Mavrich TN, Jiang C, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glaser RL, Schuster SC, Gilmour DS, Albert I, Pugh BF: Nucleosome organization in the Drosophila genome. Nature. 2008, 453: 358-362. 10.1038/nature06929.
Article
PubMed Central
CAS
PubMed
Google Scholar
Field Y, Fondufe-Mittendorf Y, Moore IK, Mieczkowski P, Kaplan N, Lubling Y, Lieb JD, Widom J, Segal E: Gene expression divergence in yeast is coupled to evolution of DNA-encoded nucleosome organization. Nat Genet. 2009, 41: 438-445. 10.1038/ng.324.
Article
PubMed Central
CAS
PubMed
Google Scholar
Rapoport AE, Trivonof EF: “Anticipated” nucleosome positioning pattern in prokaryotes. Gene. 2011, 488: 41-45. 10.1016/j.gene.2011.08.002.
Article
CAS
PubMed
Google Scholar
Reeve JN: Archaeal chromatin and transcription. Mol Microbiol. 2003, 48: 587-598. 10.1046/j.1365-2958.2003.03439.x.
Article
CAS
PubMed
Google Scholar
Feng HP, Scherl DS, Widom J: Lifetime of the histone octamer studied by continuous-flow quasielastic light scattering: test of a model for nucleosome transcription. Biochemistry. 1993, 32: 7824-7831. 10.1021/bi00081a030.
Article
CAS
PubMed
Google Scholar
Applied Biosystems protocol for SOLiD sequencing. http://tools.invitrogen.com/content/sfs/manuals/SOLiD4_Library_Preparation_man.pdf,
Brogaard KR, Xi L, Wang JP, Widom J: A chemical approach to mapping nucleosomes at base pair resolution in yeast. Meth Enzymol. 2012, 513: 315-334.
Article
CAS
PubMed
Google Scholar
Genome-database of Methanobacterium thermoautotrophicum and Thermococcus kodakarensis sequenced nucleosomal reads. 2012, http://ncode.northwestern.edu,
UCSC Genome Browser on Methanobacterium thermoautotrophicum Aug 1997 Assembly (methTher1). 1997, http://archaea.ucsc.edu/lists/methTher1/refSeq-list.html, Aug Assembly (methTher1),