|
|
|
Insights into DNA signals for nucleosome positioning |
| DAI Zhiming, DAI Xianhua, FENG Jihua, XIANG Qian, DENG Yangyang, WANG Jiang |
| Department of Electronic Engineering, Sun Yat-sen University |
|
|
|
|
Abstract The nucleosome is the fundamental unit of eukaryotic genomes. Its positioning in the promoter region plays a central role in regulating gene transcription. Experimental evidence suggests that the genomic DNA sequence is one impor
|
|
Issue Date: 05 December 2008
|
|
| 1 |
Kornberg R D, Lorch Y . Twenty-five years of thenucleosome, fundamental particle of the eukaryote chromosome. Cell, 1999, 98(3): 285–294. doi:10.1016/S0092-8674(00)81958-3
|
| 2 |
Khorasanizadeh S . Thenucleosome: from genomic organization to genomic regulation. Cell, 2004, 116(2): 259–272. doi:10.1016/S0092-8674(04)00044-3
|
| 3 |
Luger K, Hansen J C . Nucleosome and chromatinfiber dynamics. Current Opinion in StructuralBiology, 2005, 15(2): 188–196. doi:10.1016/j.sbi.2005.03.006
|
| 4 |
Richmond T J, Davey C A . The structure of DNA in thenucleosome core. Nature, 2003, 423(6936): 145–150. doi:10.1038/nature01595
|
| 5 |
Yuan G C, Liu Y J, Dion M F, et al.. Genome-scale identification of nucleosome positionsin S. cerevisiae. Science, 2005, 309(5734): 626–630. doi:10.1126/science.1112178
|
| 6 |
Albert I, Mavrich T N, Tomsho L P, et al.. Translational and rotational settings of H2A.Znucleosomes across the Saccharomyces cerevisiae genome. Nature, 2007, 446(7135): 572–576. doi:10.1038/nature05632
|
| 7 |
Ozsolak F, Song J S, Liu X S, et al.. High-throughput mapping of the chromatin structureof human promoters. Nature Biotechnology, 2007, 25(2): 244–248. doi:10.1038/nbt1279
|
| 8 |
Lee W, Tillo D, Bray N, et al.. A high-resolution atlas of nucleosome occupancyin yeast. Nature Genetics, 2007, 39(10): 1235–1244. doi:10.1038/ng2117
|
| 9 |
Wyrick J J, Holstege F C P, Jennings E G, et al.. Chromosomal landscape of nucleosome-dependentgene expression and silencing in yeast. Nature, 1999, 402(6760): 418–421. doi:10.1038/46567
|
| 10 |
Flaus A, Owen-Hughes T . Mechanisms for ATP-dependentchromatin remodelling. Current Opinionin Genetics and Development, 2001, 11(2): 148–154. doi:10.1016/S0959-437X(00)00172-6
|
| 11 |
Strahl B D, Allis C D . The language of covalenthistone modifications. Nature, 2000, 403(6765): 41–45. doi:10.1038/47412
|
| 12 |
Jenuwein T, Allis C D . Translating the histone code. Science, 2001, 293(5532): 1074–1080. doi:10.1126/science.1063127
|
| 13 |
Henikoff S, Ahmad K . Assembly of variant histonesinto chromatin. Annual Review of Cell andDevelopmental Biology, 2005, 21: 133–153. doi:10.1146/annurev.cellbio.21.012704.133518
|
| 14 |
Widom J . Roleof DNA sequence in nucleosome stability and dynamics. Quarterly Reviews of Biophysics, 2001, 34(3): 269–324. doi:10.1017/S0033583501003699
|
| 15 |
Davey C, Pennings S, Meersseman G, et al.. Periodicity of strong nucleosome positioningsites around the chicken adult globin gene may encode regularly spacedchromatin. Proceedings of the NationalAcademy of Sciences of the United States of America, 1995, 92(24): 11210–11214. doi:10.1073/pnas.92.24.11210
|
| 16 |
Roychoudhury M, Sitlani A, Lapham J, et al.. Global structure and mechanical properties ofa 10-bp nucleosome positioning motif. Proceedingsof the National Academy of Sciences of the United States of America, 2000, 97(25): 13608–13613. doi:10.1073/pnas.250476297
|
| 17 |
Satchwell S C, Drew H R, Travers A A . Sequence periodicities in chicken nucleosome core DNA. Journal of Molecular Biology, 1986, 191(4): 659–675. doi:10.1016/0022-2836(86)90452-3
|
| 18 |
Segal E, Fondufe-Mittendorf Y, Chen L, et al.. A genomic code for nucleosomepositioning. Nature, 2006, 442(7104): 772–778. doi:10.1038/nature04979
|
| 19 |
Ioshikhes I P, Albert I, Zanton S J, et al.. Nucleosome positions predicted through comparativegenomics. Nature Genetics, 2006, 38(10): 1210–1215. doi:10.1038/ng1878
|
| 20 |
Wang J Z, Widom J . Improved alignment of nucleosomeDNA sequences using a mixture model. NucleicAcids Research, 2005, 33(21): 6743–6755. doi:10.1093/nar/gki977
|
| 21 |
Levitsky V G . RECON: a program for prediction of nucleosome formation potential. Nucleic Acids Research, 2004, 32: W346–349. doi:10.1093/nar/gkh482
|
| 22 |
Cao H, Widlund H R, Simonsson T, et al.. TGGA repeats impair nucleosome formation. Journal of Molecular Biology, 1998, 281(2): 253–260. doi:10.1006/jmbi.1998.1925
|
| 23 |
Baldi P, Brunak S, Chauvin Y, et al.. Naturally occurring nucleosome positioning signalsin human exons and introns. Journal ofMolecular Biology, l996, 263(4): 503–510. doi:10.1006/jmbi.1996.0592
|
| 24 |
Godde J S, Wolffe A P . Nucleosome assembly on CTGtriplet repeats. Journal of BiologicalChemistry, 1996, 271(25): 15222–15229. doi:10.1074/jbc.271.25.15222
|
| 25 |
Luger K, Mäder A W, Richmond R K, et al.. Crystal structure of the nucleosome core particleat 2.8 A resolution. Nature, 1997, 389(6648): 251–260. doi:10.1038/38444
|
| 26 |
Johnson S M, Tan F J, McCullough H L, et al.. Flexibility and constraint in the nucleosomecore landscape of Caenorhabditis elegans chromatin. Genome Research, 2006, 16(12): 1505–1516. doi:10.1101/gr.5560806
|
| 27 |
Mavrich T N, Jiang C, Ioshikhes I P, et al.. Nucleosome organization in the Drosophila genome. Nature, 2008, 453(7193): 358–362. doi:10.1038/nature06929
|
| 28 |
Widlund H R, Cao H, Simonsson S, et al.. Identification and characterization of genomicnucleosome-positioning sequences. Journalof Molecular Biology, 1997, 267(4): 807–817. doi:10.1006/jmbi.1997.0916
|
| 29 |
Yuan G C, Liu J S . Genomic sequence is highlypredictive of local nucleosome depletion. PLoS Computational Biology, 2008, 4(1): e13. . doi: doi:10.1371/journal.pcbi.0040013 . doi: 10.1371/journal.pcbi.0040013
|
| 30 |
Peckham H E, Thurman R E, Fu Y, et al.. Nucleosome positioning signals in genomic DNA. Genome Research, 2007, 17(8): 1170–1177. doi:10.1101/gr.6101007
|
| 31 |
Redon C, Pilch D, Rogakou E, et al.. Histone H2A variants H2AX and H2AZ. Current Opinion in Genetics and Development, 2002, 12(2): 162–169. doi:10.1016/S0959-437X(02)00282-4
|
|
Viewed |
|
|
|
Full text
|
|
|
|
|
Abstract
|
|
|
|
|
Cited |
|
|
|
|
| |
Shared |
|
|
|
|
| |
Discussed |
|
|
|
|