title: Protein composition of interband regions in polytene and cell line chromosomes of Drosophila melanogaster.
abstract: BACKGROUND
  Despite many efforts, little is known about distribution and interactions of chromatin proteins which contribute to the specificity of chromomeric organization of interphase chromosomes. To address this issue, we used publicly available datasets from several recent Drosophila genome-wide mapping and annotation projects, in particular, those from modENCODE project, and compared molecular organization of 13 interband regions which were accurately mapped previously.
  
  
  RESULTS
  Here we demonstrate that in interphase chromosomes of Drosophila cell lines, the interband regions are enriched for a specific set of proteins generally characteristic of the "open" chromatin (RNA polymerase II, CHRIZ (CHRO), BEAF-32, BRE1, dMI-2, GAF, NURF301, WDS and TRX). These regions also display reduced nucleosome density, histone H1 depletion and pronounced enrichment for ORC2, a pre-replication complex component. Within the 13 interband regions analyzed, most were around 3-4 kb long, particularly those where many of said protein features were present. We estimate there are about 3500 regions with similar properties in chromosomes of D. melanogaster cell lines, which fits quite well the number of cytologically observed interbands in salivary gland polytene chromosomes.
  
  
  CONCLUSIONS
  Our observations suggest strikingly similar organization of interband chromatin in polytene chromosomes and in chromosomes from cell lines thereby reflecting the existence of a universal principle of interphase chromosome organization.
authors.affiliation: Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia.
authors.forename: Sergey A
authors.initials: SA
authors.lastname: Demakov
authors.forename: Tatyana Yu
authors.initials: TY
authors.lastname: Vatolina
authors.forename: Vladimir N
authors.initials: VN
authors.lastname: Babenko
authors.forename: Valery F
authors.initials: VF
authors.lastname: Semeshin
authors.forename: Elena S
authors.initials: ES
authors.lastname: Belyaeva
authors.forename: Igor F
authors.initials: IF
authors.lastname: Zhimulev
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D002868:Chromosomal Proteins, Non-Histone / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D006657:Histones / Q000235:genetics; D007399:Interphase; D059007:Polytene Chromosomes / Q000235:genetics*
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D006657:Histones
references.citation: Mol Gen Genet. 1993 Apr;238(3):437-43
references.pmid: 8388080
references.citation: Chromosoma. 1982;86(1):77-93
references.pmid: 6756817
references.citation: Adv Genet. 1996;34:1-497
references.pmid: 9348397
references.citation: Results Probl Cell Differ. 1972;4:1-33
references.pmid: 4198831
references.citation: Genetica. 2004 Nov;122(3):311-24
references.pmid: 15609554
references.citation: CRC Crit Rev Biochem. 1981;11(4):303-40
references.pmid: 6171381
references.citation: Cell. 1988 Aug 12;54(4):461-72
references.pmid: 3135939
references.citation: Genetics. 2004 Jun;167(2):761-81
references.pmid: 15238527
references.citation: Nature. 2009 Jun 18;459(7249):927-30
references.pmid: 19536255
references.citation: EMBO J. 2001 Nov 1;20(21):6104-14
references.pmid: 11689450
references.citation: Adv Genet. 1999;39:1-589
references.pmid: 10319426
references.citation: Genetika. 2003 Sep;39(9):1203-11
references.pmid: 14582389
references.citation: Cell. 2010 Oct 15;143(2):212-24
references.pmid: 20888037
references.citation: EMBO J. 1994 Dec 15;13(24):5977-83
references.pmid: 7813435
references.citation: Chromosome Res. 1994 Sep;2(5):398-404
references.pmid: 7981944
references.citation: Proc Natl Acad Sci U S A. 2006 Aug 8;103(32):11970-4
references.pmid: 16882721
references.citation: Genes Dev. 2000 Apr 1;14(7):792-803
references.pmid: 10766736
references.citation: Genes Dev. 2000 Oct 15;14(20):2623-34
references.pmid: 11040216
references.citation: Genes Dev. 1993 Dec;7(12A):2329-44
references.pmid: 8253380
references.citation: Mol Cell Biol. 2007 Apr;27(8):3143-53
references.pmid: 17283052
references.citation: Chromosoma. 2005 May;114(1):54-66
references.pmid: 15821938
references.citation: Mol Cell Biol. 2001 Apr;21(7):2312-23
references.pmid: 11259581
references.citation: EMBO J. 2009 Dec 2;28(23):3635-45
references.pmid: 19834459
references.citation: Int Rev Cytol. 2004;241:203-75
references.pmid: 15548421
references.citation: Chromosoma. 1985;93(1):26-30
references.pmid: 3933923
references.citation: Proc Natl Acad Sci U S A. 2009 Jan 27;106(4):1157-62
references.pmid: 19144915
references.citation: Genetics. 1989 Oct;123(2):337-48
references.pmid: 2555253
references.citation: J Cell Sci. 2004 Aug 15;117(Pt 18):4253-64
references.pmid: 15292401
references.citation: Mol Cell. 2010 Jun 25;38(6):827-41
references.pmid: 20620954
references.citation: Methods Mol Biol. 2004;247:305-24
references.pmid: 14707355
references.citation: Nature. 2011 Mar 24;471(7339):480-5
references.pmid: 21179089
references.citation: J Mol Biol. 1986 Feb 20;187(4):591-601
references.pmid: 3458926
references.citation: Chromosoma. 2009 Dec;118(6):747-61
references.pmid: 19685068
references.citation: EMBO Rep. 2008 Feb;9(2):187-92
references.pmid: 18084186
references.citation: Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9
references.pmid: 18948289
references.citation: Mol Cell. 1999 Jul;4(1):129-35
references.pmid: 10445035
references.citation: Chromosoma. 1989 Mar;97(5):396-412
references.pmid: 2541983
references.citation: EMBO J. 2002 Oct 1;21(19):5245-54
references.pmid: 12356740
references.citation: Genetics. 1994 Mar;136(3):1063-73
references.pmid: 8005415
references.citation: Genes Dev. 2000 Dec 1;14(23):3003-13
references.pmid: 11114889
references.citation: Cell. 1995 Jun 16;81(6):879-89
references.pmid: 7781065
references.citation: Proc Natl Acad Sci U S A. 1996 Jul 9;93(14):7137-42
references.pmid: 8692958
references.citation: Genetica. 2008 Mar;132(3):267-79
references.pmid: 17657571
references.citation: Genetics. 2000 Jul;155(3):1297-311
references.pmid: 10880489
references.citation: Nature. 2003 Nov 6;426(6962):78-83
references.pmid: 14603321
references.citation: Proc Natl Acad Sci U S A. 1977 May;74(5):2079-83
references.pmid: 405671
references.citation: Genome Res. 2010 Feb;20(2):201-11
references.pmid: 19996087
references.citation: Genetika. 2011 May;47(5):597-609
references.pmid: 21786665