Open Access Research article

Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome

Vladimir N Babenko1, Igor V Makunin1, Irina V Brusentsova1, Elena S Belyaeva1, Daniil A Maksimov1, Stepan N Belyakin1, Peter Maroy2, Lyubov A Vasil'eva3 and Igor F Zhimulev1*

Author Affiliations

1 Department of Molecular and Cellular Biology, Institute of Chemical Biology and Fundamental Medicine SB RAS, Novosibirsk, 630090, Russia

2 Department of Genetics, University of Szeged, Kozepfasor 52, H-6726, Szeged, Hungary

3 Institute of Cytology and Genetics SB RAS, Novosibirsk, 630090, Russia

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BMC Genomics 2010, 11:318  doi:10.1186/1471-2164-11-318

Published: 21 May 2010

Additional files

Additional file 1:

Supplemental Figure S1: Distribution of different transposons in the Drosophila genome. Figure S1. Distribution of different transposons in the Drosophila genome. (A) First column depicts proportion of assembled euchromatic regions of chromosomes X, 2 and 3 occupied by following fraction: 100 bp on both sides from the annotated Transcription Start Sites (TSS) of protein-coding FlyBase Genes 5.12 (+/- 100 bp from TSS), regions between annotated TSS and transcription termination sites except regions occupied by first fraction (Genic-100 bp), and the rest of the genome (Intergenic-100 bp). Other columns show occurrence of different transposons (unique sites) in each genomic fraction. Number of integration sites in each fraction is indicated on the column, and name of transposon vectors are shown below the graph. (B) Distribution of the insertions selected for the analysis of suppression is similar to the distribution of whole sets of unique integration sites of P{EP} and P{EPgy2} transposons.

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Additional file 2:

Supplemental Tables 1-5 and 7-9. Supplemental Tables 1-5 and 7-9.

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Additional file 3:

Supplemental Figure S2: Effect of the insulators on transgene expression. Two different transposons are integrated into the same position 2,101,726 on chr2R (Release 5, dm3). (A) P{EPgy2}EY02768 contains mini-white marker gene. (B) P{SUPor-P}KG00902 has mini-white gene surrounded by Su(Hw) insulators. The insulators prevent mini-white from suppression.

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Additional file 4:

Localization of transgenes analysed for suppression. Genomic positions of P{EP} and P{EPgy2} transgenes in the D. melanogaster genome, BDGP assembly Release 5 (dm3).

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Additional file 5:

Supplemental Figure S3: Distribution of suppressed and active transgenes relative to FlyBase protein-coding genes 5.12. The suppression of transposons was analyzed in three fractions: 100 bp on both sides from the annotated Transcription Start Sites (TSS) of protein-coding FlyBase Genes 5.12 (+/- 100 bp from TSS), regions between annotated TSS and transcription termination sites except regions occupied by first fraction (Genic-100 bp), and the rest of the genome (Intergenic-100 bp). Numbers of the active and suppressed transposons in each fraction are indicated on columns. The proportion of the suppressed transposons in the underreplicated regions (URs) is higher in all fractions compared with the control flank regions or whole genome data but the biggest increase occurs in the regions close to TSS and in the intergenic fraction.

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Additional file 6:

Supplemental Table S6: GO categories of genes enriched with suppressed and active transgenes.

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Additional file 7:

Localization of 51 underreplicated regions. Genomic positions of 51 URs analysed in the paper in the D. melanogaster genome, BDGP assembly Release 5 (dm3).

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