Insights into DNA signals for nucleosome positioning
DAI Zhiming, DAI Xianhua, FENG Jihua, XIANG Qian, DENG Yangyang, WANG Jiang
Author information+
Department of Electronic Engineering, Sun Yat-sen University
Show less
History+
Published
05 Dec 2008
Issue Date
05 Dec 2008
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
DAI Zhiming, DAI Xianhua, FENG Jihua, XIANG Qian, DENG Yangyang, WANG Jiang.
Insights into DNA signals for nucleosome positioning. Front. Electr. Electron. Eng., 2008, 3(4): 388‒393 https://doi.org/10.1007/s11460-008-0085-4
{{custom_sec.title}}
{{custom_sec.title}}
{{custom_sec.content}}
This is a preview of subscription content, contact us for subscripton.
References
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
AI Summary ×
Note: Please note that the content below is AI-generated. Frontiers Journals website shall not be held liable for any consequences associated with the use of this content.