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Frontiers of Electrical and Electronic Engineering

ISSN 2095-2732

ISSN 2095-2740(Online)

CN 10-1028/TM

Front. Electr. Electron. Eng.    2008, Vol. 3 Issue (4) : 388-393    https://doi.org/10.1007/s11460-008-0085-4
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
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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
 Cite this article:   
DAI Zhiming,DAI Xianhua,FENG Jihua, et al. Insights into DNA signals for nucleosome positioning[J]. Front. Electr. Electron. Eng., 2008, 3(4): 388-393.
 URL:  
https://academic.hep.com.cn/fee/EN/10.1007/s11460-008-0085-4
https://academic.hep.com.cn/fee/EN/Y2008/V3/I4/388
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
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