Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster

BMC Genomics

Volumn 12, Issue , 2011, Pages

  Demakov, Sergey A ^a   Yu Vatolina, Tatyana ^a   Babenko, Vladimir N ^b   Semeshin, Valery F ^a   Belyaeva, Elena S ^a   Zhimulev, Igor F ^a  

^a INSTITUTE OF MOLECULAR AND CELLULAR BIOLOGY   (Russian Federation)

^b INSTITUTE OF CYTOLOGY AND GENETICS   (Russian Federation)

Author keywords

[No Author keywords available]

Indexed keywords

BEAF32 PROTEIN; CHRIZ PROTEIN; DMI2 PROTEIN; GAF PROTEIN; HISTONE H1; NUCLEAR PROTEIN; NURF301 PROTEIN; ORC2 PROTEIN; RNA POLYMERASE II; TRX PROTEIN; UNCLASSIFIED DRUG; WDS PROTEIN; HISTONE; NONHISTONE PROTEIN;

ARTICLE; CELL LINE; CHROMATIN; CHROMOSOME ANALYSIS; CHROMOSOME STRUCTURE; DROSOPHILA MELANOGASTER; INTERPHASE; NONHUMAN; NUCLEOSOME; POLYTENE CHROMOSOME; PROTEIN ANALYSIS; PROTEIN DEPLETION; SALIVARY GLAND; ANIMAL; GENETICS;

DROSOPHILA MELANOGASTER;

ANIMALS; CHROMATIN; CHROMOSOMAL PROTEINS, NON-HISTONE; DROSOPHILA MELANOGASTER; HISTONES; INTERPHASE; POLYTENE CHROMOSOME;

EID: 81255178672     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-12-566     Document Type: Article

References (52)

1. Zhimulev IF. Morphology and structure of polytene chromosomes. Adv Genet 1996, 34:1-497.
2. Beermann W. Chromomeres and genes. Results and problems in cell differentiation 1972, 4:1-33. Berlin, Heidelberg, New York: Springer, Beermann W.
3. Zhimulev IF, Belyeva ES, Semeshin VF. Informational content of polytene chromosome bands and puffs. CRC Crit Rev Biochem 1981, 11:303-340.
4. Zhimulev IF, Belyaeva ES, Semeshin VF, Koryakov DE, Demakov SA, et al. Polytene Chromosomes: 70 Years of Genetic Research. Int Rev Cytol 2004, 241:203-275.
5. Jamrich M, Greenleaf AL, Bautz EK. Localization of RNA polymerase in polytene chromosomes of Drosophila melanogaster. Proc Natl Acad Sci USA 1977, 74:079-83.
6. Sass H, Bautz EKF. Interbands of polytene chromosomes: binding sites and start points for RNA polymerase. Chromosoma 1982, 86:77-93. 10.1007/BF00330731, 6756817.
7. Weeks JR, Hardin SE, Shen J, Lee JM, Greenleaf AL. Locus-specific variation in phosphorylation state of RNA polymerase II in vivo: correlation with gene activity and transcript processing. Genes Dev 1993, 7:2329-2344. 10.1101/gad.7.12a.2329, 8253380.
8. Kaplan CD, Morris JR, Wu C, Winston F. Spt5 and spt6 are associated with active transcription and have characteristics of general elongation factors in D. melanogaster. Genes Dev 2000, 14:2623-2634. 10.1101/gad.831900, 316994, 11040216.
9. Gerber M, Ma J, Dean K, Eissenberg JC, Shilatifard A. Drosophila ELL is associated with actively elongating RNA polymerase II on transcriptionally active sites in vivo. EMBO J 2001, 20(21):6104-6114. 10.1093/emboj/20.21.6104, 125687, 11689450.
10. Lis JT, Mason P, Peng J, Price DH, Werner J. P-TEFb kinase recruitment and function at heat shock loci. Genes Dev 2000, 14:792-803. 316500, 10766736.
11. Park JM, Gim BS, Kim JM, Yoon JH, Kim HS, et al. Drosophila Mediator complex is broadly utilized by diverse gene-specific transcription factors at different types of core promoters. Mol Cell Biol 2001, 21(7):2312-2323. 10.1128/MCB.21.7.2312-2323.2001, 86865, 11259581.
12. Stokes DG, Tartof KD, Perry RP. CHD1 is concentrated in interbands and puffed regions of Drosophila polytene chromosomes. Proc Natl Acad Sci USA 1996, 93:7137-7142. 10.1073/pnas.93.14.7137, 38949, 8692958.
13. Jin Y, Wang Y, Walker DL, Dong H, Conley C, Johansen J, Johansen KM. JIL-1: a novel chromosomal tandem kinase implicated in transcriptional regulation in Drosophila. Mol Cell 1999, 4:129-135. 10.1016/S1097-2765(00)80195-1, 10445035.
14. Armstrong JA, Papoulas O, Daubresse G, Sperling AS, Lis JT, et al. The Drosophila BRM complex facilitates global transcription by RNA polymerase II. EMBO J 2002, 21:5245-5254. 10.1093/emboj/cdf517, 129039, 12356740.
15. Markov AV, Zakharov AA, Galkin AP, Strunnikov AV, Smirnov AF. Cohesin complexes in polytene chromosomes of Drosophila melanogaster are located in interbands. Genetika 2003, 39(9):1203-1211. (in Russian).
16. Tariq M, Nussbaumer U, Chen Y, Beisel C, Paro R. Trithorax requires Hsp90 for maintenance of active chromatin at sites of gene expression. Proc Natl Acad Sci USA 2009, 106:1157-1162. 10.1073/pnas.0809669106, 2633526, 19144915.
17. Raja SJ, Charapitsa I, Conrad T, Vaquerizas JM, Gebhardt P, et al. The nonspecific lethal complex is a transcriptional regulator in Drosophila. Mol Cell 2010, 38(6):827-41. 10.1016/j.molcel.2010.05.021, 20620954.
18. Tenney K, Gerber M, Ilvarsonn A, Schneider J, Gause M, et al. Drosophila Rtf1 functions in histone methylation, gene expression, and Notch signaling. Proc Natl Acad Sci USA 2006, 103(32):11970-11974. 10.1073/pnas.0603620103, 1567682, 16882721.
19. Carré C, Ciurciu A, Komonyi O, Jacquier C, Fagegaltier D, Pidoux J, Tricoire H, Tora L, Boros IM, Antoniewski C. The Drosophila NURF remodelling and the ATAC histone acetylase complexes functionally interact and are required for global chromosome organization. EMBO reports 2007, 9:187-192. 2246414, 18084186.
20. Lavender JS, Birley AJ, Palmer MJ, Kuroda MI, Turner BM. Histone H4 acetylated at lysine 16 and other components of the Drosophila dosage compensation pathway colocalize on the male X through mitosis. Chromosome Res 1994, 2:398-404. 10.1007/BF01552799, 7981944.
21. Nowak SJ, Corces VG. Phosphorylation of histone H3 correlates with transcriptionally active loci. Genes Dev 2000, 14:3003-3013. 10.1101/gad.848800, 317109, 11114889.
22. Sedkov Y, Cho E, Petruk S, Cherbas L, Smith ST, et al. Methylation at lysine 4 of histone H3 in ecdysone-dependent development of Drosophila. Nature 2003, 426(6962):78-83. 10.1038/nature02080, 2743927, 14603321.
23. Zhao K, Hart CM, Laemmli UK. Visualization of chromosomal domains with boundary element-associated factor BEAF-32. Cell 1995, 81:879-89. 10.1016/0092-8674(95)90008-X, 7781065.
24. Raff JW, Kellum R, Alberts B. The Drosophila GAGA transcription factor is associated with specific regions of heterochromatin throughout the cell cycle. EMBO J 1994, 13:5977-5983. 395573, 7813435.
25. Balasov M, Huijbregts RPH, Chesnokov I. Role of the Orc6 Protein in Origin Recognition Complex-Dependent DNA Binding and Replication in Drosophila melanogaster. Mol Cell Biol 2007, 27(8):3143-3153. 10.1128/MCB.02382-06, 1899928, 17283052.
26. Eggert H, Gortchakov A, Saumweber H. Identification of the Drosophila interband-specific protein Z4 as a DNA-binding zinc-finger protein determining chromosomal structure. Cell Sci 2004, 117:4253-4264.
27. Gortchakov AA, Eggert H, Gan M, Mattow J, Zhimulev IF, Saumweber H. Chriz, a chromodomain protein specific for the interbands of Drosophila melanogaster polytene chromosomes. Chromosoma 2005, 114:54-66. 10.1007/s00412-005-0339-3, 15821938.
28. Semeshin VF, Belyaeva ES, Zhimulev IF, Lis JT, Richards G, Bourouis M. Electron microscopical analysis of Drosophila polytene chromosomes. IV. Mapping of morphological structures appearing as a result of transformation of DNA sequences into chromosomes. Chromosoma 1986, 93:461-468.
29. Semeshin VF, Demakov SA, Perez Alonso M, Belyaeva ES, Bonner JJ, Zhimulev IF. Electron microscopical analysis of Drosophila polytene chromosomes. V. Characteristics of structures formed by transposed DNA segments of mobile elements. Chromosoma 1989, 97:396-412. 10.1007/BF00292767, 2541983.
30. Demakov SA, Semeshin VF, Zhimulev IF. Cloning and molecular genetic analysis of Drosophila melanogaster interband DNA. Mol Gen Genet 1993, 238:437-443. 10.1007/BF00292003, 8388080.
31. Demakov S, Gortchakov A, Schwartz Y, Semeshin V, Campuzano S, Modolell J, Zhimulev I. Molecular and genetic organization of Drosophila melanogaster polytene chromosomes: evidence for two types of interband regions. Genetica 2004, 122:311-324. 10.1007/s10709-004-2839-0, 15609554.
32. Semeshin VF, Demakov SA, Shloma VV, Vatolina TY, Gorchakov AA, Zhimulev IF. Interbands behave as decompacted autonomous units in Drosophila melanogaster polytene chromosomes. Genetica 2008, 132:267-79. 10.1007/s10709-007-9170-5, 17657571.
33. Vatolina T, Demakov SA, Semeshin VF, Makunin IV, Babenko VN, et al. Identification and molecular genetic characterization of the polytene chromosome interbands in Drosophila melanogaster. Russian Journal of Genetics 2011, 47(5):15-26.
34. Celniker SE, Dillon LA, Gerstein MB, Gunsalus KC, Henikoff S, et al. Unlocking the secrets of the genome. Nature 2009, 459:927-930. 10.1038/459927a, 2843545, 19536255.
35. Filion GJ, van Bemmel JG, Braunschweig U, Talhout W, Kind J, et al. Systematic protein location mapping reveals five principal chromatin types in Drosophila cells. Cell 2010, 143:212-224. 10.1016/j.cell.2010.09.009, 3119929, 20888037.
36. Kharchenko PV, Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, et al. Comprehensive analysis of the chromatin landscape in Drosophila melanogaster. Nature 2011, 471(7339):480-4855. 10.1038/nature09725, 3109908, 21179089.
37. Rykowski MC, Parmelee SJ, Agard DA, Sedat JW. Precise determination of molecular limits of polytene chromosome band: regulatory sequences for the Notch gene are in the interband. Cell 1988, 54:461-472. 10.1016/0092-8674(88)90067-0, 3135939.
38. Kozlova T, Semeshin VF, Tretyakova IV, Kokoza EB, Pirrotta V, Grafodatskaya VE, Belyaeva ES, Zhimulev IF. Molecular and cytogenetical characterization of the 10A1-2 band and adjoining region in the Drosophila melanogaster polytene X chromosome. Genetics 1994, 136:1063-1073. 1205863, 8005415.
39. Andreyenkova NG, Kokoza EB, Semeshin VF, Belyaeva ES, Demakov SA, Pindyurin AV, Andreyeva EN, Volkova EI, Zhimulev IF. Localization and characteristics of DNA underreplication zone in the 75C region of intercalary heterochromatin in Drosophila melanogaster polytene chromosomes. Chromosoma 2009, 118:747-761. 10.1007/s00412-009-0232-6, 19685068.
40. Braunschweig U, Hogan GJ, Pagie L, van Steensel B. Histone H1 binding is inhibited by histone variant H3.3. The EMBO J 2009, 28:3635-3645.
41. Allan J, Mitchell T, Harborne N, Boehm L, Crane-Robinson C. Roles of H1 domains in determining higher order chromatin structure and H1 location. J Mol Biol 1986, 187:591-601. 10.1016/0022-2836(86)90337-2, 3458926.
42. Zhimulev IF, Belyaeva ES. Variation in the banding pattern of the polytene chromosomes of Drosophila melanogaster larvae. Genetika 1977, 13:1398-1408. (in Russian).
43. Zhimulev IF. Genetic organization of polytene chromosomes. Adv Genet 1999, 39:1-599.
44. Vasquez J, Schedl P. Deletion of an insulator element by the mutation facet-strawberry in Drosophila melanogaster. Genetics 2000, 155:1297-1311. 1461175, 10880489.
45. Bellen HJ, Levis RW, Liao G, He Y, Carlson JW, Tsang G, Evans-Holm M, Hiesinger PR, Schulze KL, Rubin GM, et al. The BDGP gene disruption project: single transposon insertions associated with 40% of Drosophila genes. Genetics 2004, 167:761-781. 10.1534/genetics.104.026427, 1470905, 15238527.
46. Semeshin VF, Belyaeva ES, Shloma VV, Zhimulev IF. Electron microscopy of polytene chromosomes. Methods Mol Biol 2004, 247:305-324.
47. Simon JA, Sutton CA, Lis JT. Localization and expression of transformed DNA sequences within heat shock puffs of Drosophila melanogaster. Chromosoma 1985, 93:26-30. 10.1007/BF01259442, 3933923.
48. modENCODE consortium. , http://www.modENCODE.org
49. NCBI Gene Expression Omnibus. , http://www.ncbi.nlm.nih.gov/gds/
50. Ramos RGP, Grimwade BG, Wharton KA, Scottgale TN, Artavanis-Tsakonas S. Physical and functional definition of the Drosophila Notch locus by P element transformation. Genetics 1989, 123:337-348. 1203805, 2555253.
51. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, et al. FlyBase:enhancing Drosophila Gene Ontology annotations. Nucleic Acids Res 2009, 37:D555-559. 10.1093/nar/gkn788, 2686450, 18948289.
52. MacAlpine HK, Gordân R, Powell SK, Hartemink AJ, MacAlpine DM. Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading. Genome Res 2010, 20:201-211. 10.1101/gr.097873.109, 2813476, 19996087.