Genetic organization of interphase chromosome bands and interbands in Drosophila melanogaster

Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interb...

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Bibliographic Details
Published in:PloS one 2014-07, Vol.9 (7), p.e101631-e101631
Main Authors: Zhimulev, Igor F, Zykova, Tatyana Yu, Goncharov, Fyodor P, Khoroshko, Varvara A, Demakova, Olga V, Semeshin, Valeriy F, Pokholkova, Galina V, Boldyreva, Lidiya V, Demidova, Darya S, Babenko, Vladimir N, Demakov, Sergey A, Belyaeva, Elena S
Format: Article
Language:English
Subjects:
Analysis
Animal genetics
Animals
Banding
Binding sites
Biology and Life Sciences
Cell lines
Cellular biology
Chromatin
Chromatin - genetics
Chromatin - metabolism
Chromosome Banding
Chromosomes
Chromosomes, Insect
Cluster analysis
Cytology
Data processing
Deoxyribonucleic acid
Developmental stages
DNA
DNA Transposable Elements
DNA-Binding Proteins
Drosophila
Drosophila melanogaster
Drosophila melanogaster - genetics
Gene expression
Gene mapping
Gene sequencing
Genes
Genetic aspects
Genetic research
Genome-Wide Association Study
Genomes
Genomics
Genomics - methods
Histones - metabolism
Hypotheses
Insects
Interphase
Laboratories
Localization
Mapping
Origin recognition complex
Physical Chromosome Mapping
Polytene
Polytene Chromosomes
Proteins
Replication
Ribonucleic acid
RNA
RNA polymerase
Tissues
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Summary:Drosophila melanogaster polytene chromosomes display specific banding pattern; the underlying genetic organization of this pattern has remained elusive for many years. In the present paper, we analyze 32 cytology-mapped polytene chromosome interbands. We estimated molecular locations of these interbands, described their molecular and genetic organization and demonstrate that polytene chromosome interbands contain the 5' ends of housekeeping genes. As a rule, interbands display preferential "head-to-head" orientation of genes. They are enriched for "broad" class promoters characteristic of housekeeping genes and associate with open chromatin proteins and Origin Recognition Complex (ORC) components. In two regions, 10A and 100B, coding sequences of genes whose 5'-ends reside in interbands map to constantly loosely compacted, early-replicating, so-called "grey" bands. Comparison of expression patterns of genes mapping to late-replicating dense bands vs genes whose promoter regions map to interbands shows that the former are generally tissue-specific, whereas the latter are represented by ubiquitously active genes. Analysis of RNA-seq data (modENCODE-FlyBase) indicates that transcripts from interband-mapping genes are present in most tissues and cell lines studied, across most developmental stages and upon various treatment conditions. We developed a special algorithm to computationally process protein localization data generated by the modENCODE project and show that Drosophila genome has about 5700 sites that demonstrate all the features shared by the interbands cytologically mapped to date.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0101631