title: Protein and Genetic Composition of Four Chromatin Types inDrosophila melanogasterCell Lines.
abstract: BACKGROUND
  Recently, we analyzed genome-wide protein binding data for the Drosophila cell lines S2, Kc, BG3 and Cl.8 (modENCODE Consortium) and identified a set of 12 proteins enriched in the regions corresponding to interbands of salivary gland polytene chromosomes. Using these data, we developed a bioinformatic pipeline that partitioned the Drosophila genome into four chromatin types that we hereby refer to as aquamarine, lazurite, malachite and ruby.
  
  
  RESULTS
  Here, we describe the properties of these chromatin types across different cell lines. We show that aquamarine chromatin tends to harbor transcription start sites (TSSs) and 5' untranslated regions (5'UTRs) of the genes, is enriched in diverse "open" chromatin proteins, histone modifications, nucleosome remodeling complexes and transcription factors. It encompasses most of the tRNA genes and shows enrichment for non-coding RNAs and miRNA genes. Lazurite chromatin typically encompasses gene bodies. It is rich in proteins involved in transcription elongation. Frequency of both point mutations and natural deletion breakpoints is elevated within lazurite chromatin. Malachite chromatin shows higher frequency of insertions of natural transposons. Finally, ruby chromatin is enriched for proteins and histone modifications typical for the "closed" chromatin. Ruby chromatin has a relatively low frequency of point mutations and is essentially devoid of miRNA and tRNA genes. Aquamarine and ruby chromatin types are highly stable across cell lines and have contrasting properties. Lazurite and malachite chromatin types also display characteristic protein composition, as well as enrichment for specific genomic features. We found that two types of chromatin, aquamarine and ruby, retain their complementary protein patterns in four Drosophila cell lines.
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Lidiya V
authors.initials: LV
authors.lastname: Boldyreva
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Fyodor P
authors.initials: FP
authors.lastname: Goncharov
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Demakova
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Tatyana Yu
authors.initials: TY
authors.lastname: Zykova
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Victor G
authors.initials: VG
authors.lastname: Levitsky
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Nikolay N
authors.initials: NN
authors.lastname: Kolesnikov
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Alexey V
authors.initials: AV
authors.lastname: Pindyurin
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Valeriy F
authors.initials: VF
authors.lastname: Semeshin
authors.affiliation: 1 Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 2 Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia ; 3 Novosibirsk State University, Novosibirsk 630090, Russia.
authors.forename: Igor F
authors.initials: IF
authors.lastname: Zhimulev
keywords: Cell lines; Chromatin types; Drosophila; Genome-wide protein binding data; Interbands; Polytene chromosomes