Nucleosome-coupled expression differences in closely-related species

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Guan, Yuanfang ^a   Yao, Victoria ^a   Tsui, Kyle ^b,c   Gebbia, Marinella ^b,c   Dunham, Maitreya J ^d   Nislow, Corey ^b,c   Troyanskaya, Olga G ^a,e  

^a PRINCETON UNIVERSITY   (United States)

^b UNIVERSITY OF TORONTO   (Canada)

^c UNIVERSITY OF TORONTO   (Canada)

^d UNIVERSITY OF WASHINGTON   (United States)

^e Princeton University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; CELL CYCLE PROTEIN; FUNGAL PROTEIN; MBP1 PROTEIN, S CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEIN;

ARTICLE; BINDING SITE; CELL CYCLE G1 PHASE; CELL CYCLE REGULATION; CELL CYCLE S PHASE; CELL INTERACTION; CONTROLLED STUDY; DNA SEQUENCE; GENE EXPRESSION; GENE FUNCTION; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROMOTER REGION; SACCHAROMYCES BAYANUS; SACCHAROMYCES CEREVISIAE; SPECIES DIFFERENCE; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; SACCHAROMYCES;

SACCHAROMYCES BAYANUS;

CELL CYCLE PROTEINS; FUNGAL PROTEINS; GENE EXPRESSION REGULATION, FUNGAL; NUCLEOSOMES; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SPECIES SPECIFICITY; TRANSCRIPTION FACTORS;

EID: 80053356939     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-466     Document Type: Article

References (39)

1. 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(10):1235-1244. 10.1038/ng2117, 17873876.
2. Olins AL, Olins DE. Spheroid chromatin units (v bodies). Science 1974, 183(4122):330-332. 10.1126/science.183.4122.330, 4128918.
3. Kornberg RD. Chromatin structure: a repeating unit of histones and DNA. Science 1974, 184(139):868-871. 10.1126/science.184.4139.868, 4825889.
4. Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL. Global nucleosome occupancy in yeast. Genome Biol 2004, 5(9):R62. 10.1186/gb-2004-5-9-r62, 522869, 15345046.
5. Ozsolak F, Song JS, Liu XS, Fisher DE. High-throughput mapping of the chromatin structure of human promoters. Nat Biotechnol 2007, 25(2):244-248. 10.1038/nbt1279, 17220878.
6. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome. Cell 2008, 132(5):887-898. 10.1016/j.cell.2008.02.022, 18329373.
7. 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(7104):772-778. 10.1038/nature04979, 2623244, 16862119.
8. 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(5734):626-630. 10.1126/science.1112178, 15961632.
9. Owen-Hughes T, Workman JL. Experimental analysis of chromatin function in transcription control. Crit Rev Eukaryot Gene Expr 1994, 4(4):403-441.
10. Liu X, Lee CK, Granek JA, Clarke ND, Lieb JD. Whole-genome comparison of Leu3 binding in vitro and in vivo reveals the importance of nucleosome occupancy in target site selection. Genome Res 2006, 16(12):1517-1528. 10.1101/gr.5655606, 1665635, 17053089.
11. Morohashi N, Nakajima K, Kurihara D, Mukai Y, Mitchell AP, Shimizu M. A nucleosome positioned by alpha2/Mcm1 prevents Hap1 activator binding in vivo. Biochem Biophys Res Commun 2007, 364(3):583-588. 10.1016/j.bbrc.2007.10.037, 2131697, 17959145.
12. 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(6):735-748. 10.1016/j.molcel.2005.05.003, 15949447.
13. Badis G, Chan ET, van Bakel H, Pena-Castillo L, Tillo D, Tsui K, Carlson CD, Gossett AJ, Hasinoff MJ, Warren CL, et al. A library of yeast transcription factor motifs reveals a widespread function for Rsc3 in targeting nucleosome exclusion at promoters. Mol Cell 2008, 32(6):878-887. 10.1016/j.molcel.2008.11.020, 2743730, 19111667.
14. Zawadzki KA, Morozov AV, Broach JR. Chromatin-dependent transcription factor accessibility rather than nucleosome remodeling predominates during global transcriptional restructuring in Saccharomyces cerevisiae. Mol Biol Cell 2009, 20(15):3503-3513. 10.1091/mbc.E09-02-0111, 2719568, 19494041.
15. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. The DNA-encoded nucleosome organization of a eukaryotic genome. Nature 2009, 458(7236):362-366. 10.1038/nature07667, 2658732, 19092803.
16. 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(3):e65. 10.1371/journal.pbio.0060065, 2267817, 18351804.
17. Bai L, Charvin G, Siggia ED, Cross FR. Nucleosome-depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle. Dev Cell 2010, 18(4):544-555. 10.1016/j.devcel.2010.02.007, 2867244, 20412770.
18. Tsankov AM, Thompson DA, Socha A, Regev A, Rando OJ. The role of nucleosome positioning in the evolution of gene regulation. PLoS Biol 2010, 8(7):e1000414. 10.1371/journal.pbio.1000414, 2897762, 20625544.
19. Washietl S, Machne R, Goldman N. Evolutionary footprints of nucleosome positions in yeast. Trends Genet 2008, 24(12):583-587. 10.1016/j.tig.2008.09.003, 18951646.
20. Zhang Y, Shin H, Song JS, Lei Y, Liu XS. Identifying positioned nucleosomes with epigenetic marks in human from ChIP-Seq. BMC Genomics 2008, 9:537. 10.1186/1471-2164-9-537, 2596141, 19014516.
21. Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen BA, Johnston M. Finding functional features in Saccharomyces genomes by phylogenetic footprinting. Science 2003, 301(5629):71-76. 10.1126/science.1084337, 12775844.
22. Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. Nucleosome positions predicted through comparative genomics. Nat Genet 2006, 38(10):1210-1215. 10.1038/ng1878, 16964265.
23. Elemento O, Slonim N, Tavazoie S. A universal framework for regulatory element discovery across all genomes and data types. Mol Cell 2007, 28(2):337-350. 10.1016/j.molcel.2007.09.027, 2900317, 17964271.
24. Mahony S, Benos PV. STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res 2007, (35 Web Server):W253-258.
25. Hughes JD, Estep PW, Tavazoie S, Church GM. Computational identification of cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae. J Mol Biol 2000, 296(5):1205-1214. 10.1006/jmbi.2000.3519, 10698627.
26. Koch C, Moll T, Neuberg M, Ahorn H, Nasmyth K. A role for the transcription factors Mbp1 and Swi4 in progression from G1 to S phase. Science 1993, 261(5128):1551-1557. 10.1126/science.8372350, 8372350.
27. Pramila T, Wu W, Miles S, Noble WS, Breeden LL. The Forkhead transcription factor Hcm1 regulates chromosome segregation genes and fills the S-phase gap in the transcriptional circuitry of the cell cycle. Genes Dev 2006, 20(16):2266-2278. 10.1101/gad.1450606, 1553209, 16912276.
28. Mahony S, Auron PE, Benos PV. DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol 2007, 3(3):e61. 10.1371/journal.pcbi.0030061, 1848003, 17397256.
29. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, Macisaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. Transcriptional regulatory code of a eukaryotic genome. Nature 2004, 431(7004):99-104. 10.1038/nature02800, 3006441, 15343339.
30. Doniger SW, Fay JC. Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol 2007, 3(5):e99. 10.1371/journal.pcbi.0030099, 1876492, 17530920.
31. Martin OC, DeSevo CG, Guo BZ, Koshland DE, Dunham MJ, Zheng Y. Telomere behavior in a hybrid yeast. Cell Res 2009, 19(7):910-912. 10.1038/cr.2009.65, 19506581.
32. Hogan GJ, Lee CK, Lieb JD. Cell cycle-specified fluctuation of nucleosome occupancy at gene promoters. PLoS Genet 2006, 2(9):e158. 10.1371/journal.pgen.0020158, 1570381, 17002501.
33. Tirosh I, Weinberger A, Bezalel D, Kaganovich M, Barkai N. On the relation between promoter divergence and gene expression evolution. Mol Syst Biol 2008, 4:159. 2238714, 18197176.
34. Li H, Ruan J, Durbin R. Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 2008, 18(11):1851-1858. 10.1101/gr.078212.108, 2577856, 18714091.
35. Guan Y, Dunham M, Caudy A, Troyanskaya O. Systematic planning of genome-scale experiments in poorly studied species. PLoS Comput Biol 2010, 6(3):e1000698. 10.1371/journal.pcbi.1000698, 2832676, 20221257.
36. Troyanskaya O, Cantor M, Sherlock G, Brown P, Hastie T, Tibshirani R, Botstein D, Altman RB. Missing value estimation methods for DNA microarrays. Bioinformatics 2001, 17(6):520-525. 10.1093/bioinformatics/17.6.520, 11395428.
37. Byrne KP, Wolfe KH. Visualizing syntenic relationships among the hemiascomycetes with the Yeast Gene Order Browser. Nucleic Acids Res 2006, (34 Database):D452-455.
38. Zhu G, Spellman PT, Volpe T, Brown PO, Botstein D, Davis TN, Futcher B. Two yeast forkhead genes regulate the cell cycle and pseudohyphal growth. Nature 2000, 406(6791):90-94. 10.1038/35017581, 10894548.
39. Clifton P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R, Cohen AB, Johnston M. Finding functional features in Saccharomyces Genome by phylogenetic footprinting. Science 2003, 301(5629):71-6. 10.1126/science.1084337, 12775844.