Благодарности

Работа была частично поддержана Гос. контрактом N 07.514.11.4003.

Литература

1. Deal RB, Henikoff JG, Henikoff S. Genome-wide kinetics of nucleosome turnover determined by metabolic labeling of histones // Science. 2010. V. 328. P.1161-1164.

2. Cohanim AB, Haran TE. The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes // Nucleic Acids Res. 2009. V. 37(19). P. 6466-6476.

3. Gupta S, Dennis J, Thurman RE, Kingston R, Stamatoyannopoulos JA, Noble WS. Predicting human nucleosome occupancy from primary sequence // PLoS Comput Biol. 2008. I4:eI000134.

4. Kaplan N, Moore IK, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, LeProust EM, Hughes TR, Lieb JD, Widom J, Segal E. The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome // Nature. 2009. V. 458. P. 362-366.

5. Kaplan N, Moore I, Fondufe-Mittendorf Y, Gossett AJ, Tillo D, Field Y, Hughes TR, Lieb JD, Widom J, Segal E. Nucleosome sequence preferences influence in vivo nucleosome organization // Nat Struct Mol Biol. 2010. V. 17(8). P. 918-920.

6. Karlin S, Altschul SF. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes // Proc Natl Acad Sci U S A. 1990. V. 87(6). P. 2264-2268.

7. Kiyama R, Trifonov EN. What positions nucleosomes?--A model // FEBS Lett. 2002. V. 523(1-3). P. 7-11

8. Locke G, Tolkunov D, Moqtaderi Z, Struhl K, Morozov AV. High-throughput sequencing reveals a simple model of nucleosome energetic // Proc Natl Acad Sci U S A. 2010. V. 107(49). P. 20998-21003.

9. Macas J, Meszaros T, Nouzova M. PlantSat: a specialized database for plant satellite repeats // Bioinformatics. 2002. V. 18. P. 28-35.

10. Ringrose L. How do RNA sequence, DNA sequence, and chromatin properties regulate splicing? // F1000 Biol Rep. 2010. 2:74.

11. Segal E, Widom J. What controls nucleosome positions? // Trends Genet. 2009. V. 25. P. 335-343.

12. Schones DE, Cui K, Cuddapah S, Roh TY, Barski A, Wang Z, Wei G, Zhao K. Dynamic regulation of nucleosome positioning in the human genome // Cell. 2008. V. 132(5). P. 887-898.

13. Spies N, Nielsen CB, Padgett RA, Burge CB. Biased chromatin signatures around polyadenylation sites and exons // Mol Cell 2009, 36(2):245-254.

14. Sussman JL, Trifonov EN. Possibility of nonkinked packing of DNA in chromatin // Proc Natl Acad Sci U S A. 1978. V. 75(1). P. 103-107.

15. Tanaka Y, Nakai K. An assessment of prediction algorithms for nucleosome positioning // Genome Inform. 2009. V. 23(1). P. 169-178.

16. Trifonov EN. Sequence-dependent deformational anisotropy of chromatin DNA. Nucleic Acids Res. 1980. V. 8(17). P. 165-171.

17. Trifonov EN. Cracking the chromatin code: Precise rule of nucleosome positioning // Phys Life Rev. 2011. V. 8(1). P. 39-50.

18. Valouev A, Ichikawa J, Tonthat T, Stuart J, Ranade S, Peckham H, Zeng K, Malek JA, Costa G, McKernan K, Sidow A, Fire A, Johnson SM. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning // Genome Res. 2008. V. 18(7). P. 1051-1063.

19. Valouev A, Johnson SM, Boyd SD, Smith CL, Fire AZ, Sidow A. Determinants of nucleosome organization in primary human cells // Nature. 2011. V. 474(7352). P. 516-522

20. Xi L, Fondufe-Mittendor Y, Xia L, Flatow J, Widom J, Wang J-P. Predicting nucleosome positioning using a duration Hidden Markov Model // BMC Bioinformatics. 2010. doi:10.1186/1471-2105-11-346.