Nucleosome fragility reveals novel functional states of chromatin and poises genes for activation

Genome Research

Volumn 21, Issue 5, 2011, Pages 718-724

  Xi, Yuanxin ^a   Yao, Jianhui ^a   Chen, Rui ^a   Li, Wei ^a   He, Xiangwei ^a  

^a BAYLOR COLLEGE OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

NUCLEASE;

ARTICLE; CHROMATIN; GENE ACTIVATION; GENE REPLICATION; GENE SEQUENCE; GENE STRUCTURE; GENE TRANSLOCATION; GENETIC TRANSCRIPTION; HIGH THROUGHPUT SCREENING; NONHUMAN; NUCLEOSOME; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL;

CHROMATIN; DNA REPLICATION; GENE EXPRESSION REGULATION, FUNGAL; GENES, FUNGAL; GENOME, FUNGAL; HEAT-SHOCK RESPONSE; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MICROCOCCAL NUCLEASE; NUCLEOSOMES; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; TRANSCRIPTION, GENETIC; UP-REGULATION;

EID: 79955559703     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.117101.110     Document Type: Article

References (24)

1. Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. 2007. Translational and rotational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature 446: 572-576. (Pubitemid 46514724)
2. Bjorklund S, Gustafsson CM. 2005. The yeast Mediator complex and its regulation. Trends Biochem Sci 30: 240-244. (Pubitemid 40693866)
3. Cairns BR. 2009. The logic of chromatin architecture and remodelling at promoters. Nature 461: 193-198.
4. Casamassimi A, Napoli C. 2007. Mediator complexes and eukaryotic transcription regulation: An overview. Biochimie 89: 1439-1446. (Pubitemid 350122855)
5. Causton HC, Ren B, Koh SS, Harbison CT, Kanin E, Jennings EG, Lee TI, True HL, Lander ES, Young RA. 2001. Remodeling of yeast genome expression in response to environmental changes. Mol Biol Cell 12: 323-337. (Pubitemid 33051578)
6. 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. doi: 10.1371/journal.pcbi.1000216.
7. Gasch AP, Spellman PT, Kao CM, Carmel-Harel O, Eisen MB, Storz G, Botstein D, Brown PO. 2000. Genomic expression programs in the response of yeast cells to environmental changes. Mol Biol Cell 11: 4241-4257.
8. Goh WS, Orlov Y, Li J, Clarke ND. 2010. Blurring of high-resolution data shows that the effect of intrinsic nucleosome occupancy on transcription factor binding is mostly regional, not local. PLoS Comput Biol 6: e1000649. doi: 10.1371/journal.pcbi.1000649.
9. Hahn JS, Hu Z, Thiele DJ, Iyer VR. 2004. Genome-wide analysis of the biology of stress responses through heat shock transcription factor. Mol Cell Biol 24: 5249-5256. (Pubitemid 38738160)
10. Jin C, Felsenfeld G. 2007. Nucleosome stability mediated by histone variants H3.3 and H2A.Z. Genes Dev 21: 1519-1529. (Pubitemid 46955724)
11. Jin C, Zang C, Wei G, Cui K, Peng W, Zhao K, Felsenfeld G. 2009. H3.3/ H2A.Z double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nat Genet 41: 941-945.
12. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, et al. 2009. The DNAencoded nucleosome organization of a eukaryotic genome. Nature 458: 362-366.
13. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. 2007. A high-resolution atlas of nucleosome occupancy in yeast. Nat Genet 39: 1235-1244. (Pubitemid 47482684)
14. Li G, Levitus M, Bustamante C, Widom J. 2005. Rapid spontaneous accessibility of nucleosomal DNA. Nat Struct Mol Biol 12: 46-53. (Pubitemid 40082916)
15. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. 1997. Crystal structure of the nucleosome core particle at 2.8 Å resolution. Nature 389: 251-260. (Pubitemid 27406632)
16. Mavrich TN, Ioshikhes IP, Venters BJ, Jiang C, Tomsho LP, Qi J, Schuster SC, Albert I, Pugh BF. 2008a. A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome. Genome Res 18: 1073-1083. (Pubitemid 351931158)
17. Mavrich TN, Jiang C, Ioshikhes IP, LiX, Venters BJ, Zanton SJ, Tomsho LP,Qi J, Glaser RL, Schuster SC, et al. 2008b. Nucleosome organization in the Drosophila genome. Nature 453: 358-362. (Pubitemid 351693129)
18. Nagalakshmi U,Wang Z,Waern K, Shou C, Raha D, Gerstein M, Snyder M. 2008. The transcriptional landscape of the yeast genome defined by RNA sequencing. Science 320: 1344-1349. (Pubitemid 351929471)
19. Noll M, Kornberg RD. 1977. Action of micrococcal nuclease on chromatin and the location of histone H1. J Mol Biol 109: 393-404. (Pubitemid 8034998)
20. Shivaswamy S, Iyer VR. 2008. Stress-dependent dynamics of global chromatin remodeling in yeast: Dual role for SWI/SNF in the heat shock stress response. Mol Cell Biol 28: 2221-2234. (Pubitemid 351429969)
21. Tirosh I, Barkai N. 2008. Two strategies for gene regulation by promoter nucleosomes. Genome Res 18: 1084-1091. (Pubitemid 351931159)
22. Weiner A, Hughes A, Yassour M, Rando OJ, Friedman N. 2010. Highresolution nucleosome mapping reveals transcription-dependent promoter packaging. Genome Res 20: 90-100.
23. Workman JL, Kingston RE. 1998. Alteration of nucleosome structure as amechanismof transcriptional regulation. Annu Rev Biochem67: 545-579. (Pubitemid 28411138)
24. Yuan GC, Liu YJ, Dion MF, Slack MD,Wu LF, Altschuler SJ, Rando OJ. 2005. Genome-scale identification of nucleosome positions in S. cerevisiae. Science 309: 626-630. (Pubitemid 41033649)