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Volume 9   Issue 1   Year 2014
Fedoseyeva V.B.

Theoretical Estimation of Nucleosome Density for Gene Sequences of Different Orthologs upon Euchromatic and Heterochromatic Locations

Mathematical Biology & Bioinformatics. 2014;9(1):273-285.

doi: 10.17537/2014.9.273.

References

  1. Weiler KS, Wakimoto BT. Heterochromatin and gene expression in Drosophila. Annu. Rev. Genet. 1995;29:577-605. doi: 10.1146/annurev.ge.29.120195.003045
  2. Schotta G, Ebert A, Dorn R, Reuter G. Position-effect variegation and the genetic dissection of chromatin regulation in Drosophila. Semin. Cell Dev. Biol. 2003;14:67-75. doi: 10.1016/S1084-9521(02)00138-6
  3. Hower M, Dimitri P, Berloco M, Wakimoto B. Cis-effects of heterochromatin on heterochromatic and euchromatic gene activity in Drosophila melanogaster. Genetics. 1995;140:1033-1045.
  4. Sun F-L, Cuaycong MH, Elgin SCR. Long-range nucleosome ordering is associated with gene silencing in Drosophila melanogaster pericentric heterochromatin. Mol. Cell. Biol. 2001;21:2867-2879. doi: 10.1128/MCB.21.8.2867-2879.2001
  5. Noma K, Allis CD, Grewal SI. Transitions in distinct histone H3 methylation patterns at the heterochromatin domain boundaries. Science. 2001;293:1150-1155. doi: 10.1126/science.1064150
  6. Verschure P, Van der Kraan I, De Leeuw W, Van der Vlag J, Carpenter AE, Belmont AS, Van Drier R. In vivo HP1 targeting causes large-scale chromatin condensation and enhanced histone lysine methylation. Mol. Cell. Biol. 2005;25:4552-4564. doi: 10.1128/MCB.25.11.4552-4564.2005
  7. Stewart MD, Li J, Wong J. Relationship between histone H3 lysine 9 methylation, transcription repression and heterochromatin protein1 recruitment. Mol. Cell. Biol. 2005;25:2525-2538. doi: 10.1128/MCB.25.7.2525-2538.2005
  8. Jacob SA, Khorasanizadeh S. Structure of HP1 chromodomain bound to lysine 9-methylated histone H3 tail. Science. 2002;295:2080-2083. doi: 10.1126/science.1069473
  9. Nielsen PR, Nietlespach D, Mott HR, Callaghan J, Bannister A, Kouzarides T, Murzin AG, Mursin NV, Laue ED. Structure of the HP1 chromodomain bound to histone h3 methylated at lysine 9. Nature. 2002;416:103-107. doi: 10.1038/nature722
  10. De Wit E, Greil F, van Steensel B. High-resolution mapping reveals links of HP1 with active and inactive chromatin components. PLoS Genetics. 2007;3(3):e38. doi: 10.1371/journal.pgen.0030038
  11. Riddle NC, Monoda A, Kharchenko PV, Alekseyenko AA, Schwartz YB, Tolstorukov MY, Gorchakov AA, Jaffe JD, Kennedy C, Linder-Basso D et al. Plasticity in patterns of histone modifications and chromosomal proteins in Drosophila heterochromatin. Genome Research. 2011;21:147-163. doi: 10.1101/gr.110098.110
  12. Pal-Bhadra M, Leibovitch BA, Gandhi SG, Chikka MR, Bhadra U, Birchler JA, Elgin SC. Heterochromatic silencing and HP1 localization in Drosophila are dependent on the RNAi machinery. Science. 2004;303:669-672. doi: 10.1126/science.1092653
  13. Fagegaltier D, Bouge A-L, Berry B, Poisot E, Sismeiro O, Coppee J-Y, Theodore L, Voinnet O, Antoniewski C. The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila. Proc. Natl. Acad. Sci. USA. 2009;106:21258-21263. doi: 10.1073/pnas.0809208105
  14. Aravin AA, Lagos-Quintana M, Yalcin A, Zavolan M, Marks D, Snyder D, Gaasterland T, Meyer J, Tuschl T. The small RNA profile during Drosophila melanogaster development. Dev . Cell. 2003;5:337-350. doi: 10.1016/S1534-5807(03)00228-4
  15. Reihart BJ, Bratel DP. Small RNAs correspond to centromere heterochromatin repeats. Science. 2002;297:1831-1838. doi: 10.1126/science.1077183
  16. Fedoseyeva VB, Alexandrov AA. Large-scale periodicity of nucleosome positioning signal in pericentric regions of chromosomes (Drosophila melanogaster). J. Biomol. Struct. Dynam. 2013. doi:10.1080/0739110.2013.844081. doi: 10.1080/07391102.2013.786490
  17. Devlin RH, Brendan B, Wakimoto BT. The organization and expression of the light gene, a heterochromatic gene of Drosophila. Genetics. 1990;123:129-140.
  18. Yasuhara JC, DeCrease CH, Wakimoto BT. Evolution of heterochromatic genes of Drosophila. Proc. Natl. Acad. Sci. USA. 2005;102:10958-10963. doi: 10.1073/pnas.0503424102
  19. Tolstorukov MY, Colasanti AV, McCandlish DM, Olson WK, Zhurkin VB. A novel roll and slide mechanism of DNA folding in chromatin: implication for nucleosome positioning. J. Mol. Biol. 2007;371:725-738. doi: 10.1016/j.jmb.2007.05.048
  20. Wang D, Ulyanov NB, Zhurkin VB. Sequence-dependent kink-and-slide deformations of nucleosome DNA facilitated by histone arginines bound in the minor groove. J. Biomol. Struct. Dynam. 2010;27:843-859. doi: 10.1080/07391102.2010.10508586
  21. Lahm A, Suck D. DNase I –induced DNA conformation 2A structure of the DNase I-octamer comple. J. Mol. Biol. 1991;222:645-667. doi: 10.1016/0022-2836(91)90502-W
  22. Suck D. DNA recognition by DNase I. J. Mol. Recognit. 1994;7:65-70. doi: 10.1002/jmr.300070203
  23. Weston SA, Lahm A, Suck D. X-ray structure of the DNase I-d(GGTATACC)2 complex at 2.3 A resolution. J. Mol. Biol. 1992;226:1237-1256. doi: 10.1016/0022-2836(92)91064-V
  24. Luger K, Mader AW, Richmond RK, Sargent DF, Richmond TJ. Crystal structure of nucleosome core particle 2.8 Å resolution. Nature. 1997;389:251-260. doi: 10.1038/38444
  25. Oguel C, Foloppe N, Hartmann B. Understanding the sequence dependence of DNA groove dimentions: implications for DNA interactions. PLoS One. 2010;5:e15931. doi:10.1371/journal.0015931. doi: 10.1371/journal.pone.0015931
  26. Drew HR, Travers AA. DNA structural variations in the E.coli tyrT promoter. Cell. 1984;37:491-502. doi: 10.1016/0092-8674(84)90379-9
  27. Drew HR, Travers AA. DNA bending and its relation to nucleosome positioning. J. Mol. Biol. 1985;186:773-790. doi: 10.1016/0022-2836(85)90396-1
  28. Lomonossoff GP, Butler PJG, Klug A. Sequence dependent variation in the conformation of DNA. J. Mol. Biol. 1984;149:745-760. doi: 10.1016/0022-2836(81)90356-9
  29. Bruckner I, Sanchez R, Suck D, Pondor S. Sequence –dependent bending propensity of DNA as revealed by DNase I: parameters for trinucleotides. EMBO J. 1995;114:1812-1818.
  30. Satchwell SC, Drew HR, Travers AA. Sequence periodicities in chicken nucleosome. J. Mol. Biol. 1986;191:659-675. doi: 10.1016/0022-2836(86)90452-3
  31. Fedoseyeva VB, Alexandrov AA. Analysis and development of the computer methods of nucleosome localization on DNA fragments with different AT-content. J. Biomol. Struct. Dynam. 2007;24:481-488. doi: 10.1080/07391102.2007.10507136
  32. Bruckner I, Sanchez R, Suck D, Pongor S. Trinucleotide models for DNA bending propensity: comparison of models based on DNase I digestion and nucleosome packaging data. J. Biomol. Struct. Dynam. 1995;13:309-317. doi: 10.1080/07391102.1995.10508842
  33. Martinez-Garcia JF, Estruch E, Perez-Ortin JE. Chromatin structure of the 5' flanking region of the yeast LEU2 gene. Mol. Gen. Genet. 1989;217:464-470. doi: 10.1007/BF02464918
  34. Shimizu M, Roth SY, Szent-Gyorgui C, Simpson RT. Nucleosomes are positioned with base pair precision adjacent to the alpha 2 operator in Saccharomyces cerevisiae. EMBO J. 1991;10:3033-3041.
  35. Roberson A, Wolffe AP, Hauserans LJ, Olins DE. The 5S RNA gene minichromosome of Euplotes. Nucl. Acids Res. 1989;17:4699-4712. doi: 10.1093/nar/17.12.4699
  36. Levy-Wilson B, Fortier C, Blackhart BD, McCarthy. DNase I and micrococcal nuclease-hypersensitive sites in the human apolipoprotein B gene are tissue specific. Mol.Cell Biol. 1988;8:71-80.
  37. Thoma F, Bergman LW, Simpson RT. Nuclease digestion of circular TRP1ARS1 chromatin reveals positioned nucleosomes separated by nuclease-sensitive regions. J. Mol.Biol. 1984;177:715-733. doi: 10.1016/0022-2836(84)90046-9
  38. Thoma F. Protein-DNA interactions and nuclease-sensitive regions determine nucleosome positions on yeast plasmid chromatin. J. Mol. Biol. 1986;190:177-190. doi: 10.1016/0022-2836(86)90291-3
  39. Drew HR, Calladine CR. Sequence-specific positioning of core histones on an 860 base-pair DNA. Experiment and theory. J. Mol. Biol. 1987;195:143-173. doi: 10.1016/0022-2836(87)90333-0
  40. Almer A, Horz W. Nuclease hypersensitive regions with adjacent positioned nucleosomes mark the gene boundaries of the PHO5/PHO3 locus in yeast. EMBO J. 1986;5:681-2687.
  41. Almer A, Rudolph H, Hinnen A, Horz W. Removal of positioned nucleosomes from the yeast PHO5 promoter upon PHO5 induction releases additional upstream activating DNA elements. EMBO J. 1986;5:2689-2696.
  42. Capranico G, Jaxel C, Roberge M, Kohn KW, Pommier T. Nucleosome positioning as a critical determinant for the DNA cleavage sites of mammalian DNA topoisomerase II in reconstituted simian virus 40 chromatin. Nucl. Acids Res. 1990;18:4553-4559. doi: 10.1093/nar/18.15.4553
  43. Stein A. Unique positioning of reconstituted nucleosomes occurs in one region of simian virus 40 DNA. J. Biol. Chem. 1987;262:3872-3879.
  44. Tanaka S, Livingstone-Zatchej M, Thoma F. Chromatin structure of the yeast URA3 gene at high resolution provides insight into structure and positioning of nucleosomes in the chromosomal context. J. Mol. Biol. 1996;257:929-934. doi: 10.1006/jmbi.1996.0212
  45. Mengeritsky G, Trifonov EN. Nucleotide sequence-directed mapping of the nucleosomes. Nucl. Acids Res. 1983;11:3833-3851. doi: 10.1093/nar/11.11.3833
  46. Levitsky VG, Ponomarenko MP, Ponomarenko JV, Frolov AC, Kolchanov NA. Nucleosomal DNA property database. Bioinformatics. 1999;15:582-592. doi: 10.1093/bioinformatics/15.7.582
  47. Levitsky VG, Podkolodnaya OA, Kolchanov NA, Podkolodny NI. Nucleosome formation potential of eukaryotic DNA: calculation and promoters analysis. Bioinformatics. 2001;17:998-1010. doi: 10.1093/bioinformatics/17.11.998
  48. Segal E, Fondufe-Mittendorf V, Chen L, Thasstrom A, Field Y, More IK, Wang JP, Widom J. A genomic code for nucleosome positioning. Nature. 2006;442:772-778. doi: 10.1038/nature04979
  49. Ioshikhes IP, Albert I, Zanton SJ, Pugh BF. Nucleosome positions predicted through comparative genomics. Nat. Genet. 2006;38:1210-1215. doi: 10.1038/ng1878
  50. Lee W, Tillo D, Bray N, Morse RH, Davis RW, Hughes TR, Nislow C. A high-resolution atlas of nucleosome occupancy in yeast. Nature Genetics. 2007;39:1235-1244. doi: 10.1038/ng2117
  51. Yuan G-C, Lui Y-J, Dion MF, Clack MD, Wu LF, Altschuler SJ, Rando OJ. Genome-scale identification of nucleosome positions in S. cerevisiae. Science. 2005;309:626-630. doi: 10.1126/science.1112178
  52. Shruhl K. Naturally occurring poly(dA-dT) sequences are upstream promoter elements for constitutive transcription in yeast. Proc Natl. Acad. Sci. USA. 1985;82:8419-8423. doi: 10.1073/pnas.82.24.8419
  53. Yuan GC, Lui JS. Genomic sequence is highly predictive of local nucleosome depletion. PLoS Comput. Biol. 2008;4:e13. doi:10.1371/journal.pcbi.0040013. doi: 10.1371/journal.pcbi.0040013
  54. Barski A, Cuddapah S, Cui K, Roh TY, Schones DE, Wang Z, Wei G, Chepelev I, Zhao K. High resolution profiling of histone methylations in the human genome. Cell. 2007;129:823-837. doi: 10.1016/j.cell.2007.05.009
  55. Albert I, Mavrich TN, Tomsho LP, Qi J, Zanton SJ, Schuster SC, Pugh BF. Translational and notational settings of H2A.Z nucleosomes across the Saccharomyces cerevisiae genome. Nature. 2007;446:572-576. doi: 10.1038/nature05632
  56. Mavrich TN, Jiang V, Ioshikhes IP, Li X, Venters BJ, Zanton SJ, Tomsho LP, Qi J, Glasen R, Schuster SC et al. Nucleosome organization in the Drosophila genome. Nature. 2008;453:358-362. doi: 10.1038/nature06929
  57. Schones DE, Cui K, Cuddapah S, Roh TY,Barski A,Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosomes positioning in the human genome. Cell. 2008;132:887-898. doi: 10.1016/j.cell.2008.02.022
  58. Field Y, Kaplan N, Fondufe-Mittendorf Y, Moore IK, Sharon E, Lubling Y, Widom J, Segal E. Distinct modes of regulation by chromatin encoded through nucleosome positioning signals. PLoS Comput. Biol. 2008;4:e1000216. doi:10.1371/journal.pcbi.1000216. doi: 10.1371/journal.pcbi.1000216
  59. Schwabish MA, Struhl K. Evidence for eviction and rapid deposition of histones upon transcription elongation by RNA polymerase II. Mol. Cell Biol. 2004;24:10111-10117. doi: 10.1128/MCB.24.23.10111-10117.2004
  60. Schnitzler R. Control of nucleosome position by DNA sequence and remodeling machine. Cell Biochem.Biophys. 2008;51:6780-6788. doi: 10.1007/s12013-008-9015-6
  61. UCSC Genome Bioinformatics Site. http://www.genome.ucsc.edu (accessed 18 January 2012).
  62. Peckham HE, Thurman RE, Fu Y, Stamatoyannopoulos JA, Noble WS, Struhl K, Weng Z. Nucleosome positioning signals in genomic DNA. Genome Res. 2007;17:1170-1177. doi: 10.1101/gr.6101007
  63. National Center for Biotechnology Information. http://www.ncbi.nlm.nih.gov (accessed 18 January 2012).
  64. Penn State Genome Cartography Project. http://atlas.bx.psu.edu/project/drosophila.html (accessed 21 May 2013).
  65. Khesin RV, Leibovitch B. Influence of deficiency of the histone gene-containing 38B-40 region on X-chromosome template activity and the white gene position effect variegation in Drosophila melanogaster. Mol. Gen. Genet. 1978;162:323-328. doi: 10.1007/BF00268858
  66. A Database of Drosophila Genes & Genomes. http://flybase.org (accessed 8 February 2012).
  67. Wakimoto BI, Hearn MG. The effect of chromosome rearrangements on the expression of heterochromatic genes in chromosome 2L of Drosophila melanogaster. Genetics. 1990;125:141-154.
Table of Contents Original Article
Math. Biol. Bioinf.
2014;9(1):273-285
doi: 10.17537/2014.9.273
published in Russian

Abstract (rus.)
Abstract (eng.)
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