Open Access Research article

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

Sergey A Demakov1, Tatyana Yu Vatolina1, Vladimir N Babenko2, Valery F Semeshin1, Elena S Belyaeva1 and Igor F Zhimulev1*

Author Affiliations

1 Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia

2 Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Novosibirsk, 630090, Russia

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BMC Genomics 2011, 12:566  doi:10.1186/1471-2164-12-566

Published: 18 November 2011

Additional files

Additional file 1:

Figure S1. Localization of proteins and DNA elements around 13 interband regions of cell lines chromosomes. Top: molecular and genetic maps (20 kb) of these regions are centered at positions (solid vertical lines) of reference transposons (triangles) that were used for cytological identification and cloning the DNA around reference transposons in interbands. Exact molecular coordinates of transposon insertions are given in Additional File 2 Table S1. Horizontal arrows denote positions and orientation of known genes (FlyBase Genes r. 5.12). Vertical red arrows correspond to P-transposon integration sites referenced in FlyBase (when insertion sites were too close, their number is indicated above the arrow). For the region 3C6/C7, P-element integration regions lacking precise molecular localization are denoted by horizontal lines; faswb deletion is shown as square brackets. Bottom: data on the densities of nucleosomes, distributions of 9 chromatin states and binding sites for chromatin proteins in S2 cell line as presented on the modENCODE website [48], as well as distributions of histone H1 depleted regions (H1-dips) according to [40], the five-colored chromatin types [35] and binding sites for ORC proteins according to [52] in Kc167 cell line. Regions most likely corresponding to interbands are delimited by vertical dashed lines.

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Additional file 2:

Tables S1-S8. Supplemental Tables 1-8. Table S1 Molecular coordinates of integration sites of P-transgenes used to map interbands. Table S2 Accession numbers of chromatin proteins. Table S3 List of proteins analyzed and number of regions with positive scores. Table S4 Frequencies of protein localization in 13 interband regions and in random DNA samplings of D. melanogaster genome and band sequences. Table S5 Distribution of P transposon insertions within interband regions. Table S6 Number of pair-wise overlaps between DNA fragments bound by the chromatin proteins analyzed. Table S7 Pair-wise correlation scores for proteins analyzed. Table S8 P-value scores for pair-wise correlations between DNA fragments associated with the chromatin proteins analyzed.

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Additional file 3:

Figure S2. Frequency of chromatin states in 13 regions of D. melanogaster genome that correspond to interbands in polytene chromosomes. A - 5 "colored" chromatin states according to [35]; B - 9 chromatin types according to [36]. Sizes of DNA segments centered at the insertion sites of reference P-transposons (X axis); Percentage of DNA fragments associated with a particular type of chromatin calculated for each segment (Y axis).

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