Title:Protein and Genetic Composition of Four Chromatin Types in Drosophila melanogaster Cell Lines
VOLUME: 18 ISSUE: 2
Author(s):Lidiya V. Boldyreva, Fyodor P. Goncharov, Olga V. Demakova, Tatyana Yu. Zykova, Victor G. Levitsky, Nikolay N. Kolesnikov, Alexey V. Pindyurin, Valeriy F. Semeshin and Igor F. Zhimulev
Affiliation:Institute of Molecular and Cellular Biology of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090
Keywords:Drosophila, Cell lines, Chromatin types, Polytene chromosomes, Interbands, Genome-wide protein binding data.
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.
