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

Vladimir N. Babenko, Igor V. Makunin, Irina V. Brusentsova, Elena S. Belyaeva, Daniil A. Maksimov, Stepan N. Belyakin, P. Maróy, Lyubov A. Vasil'eva, Igor F. Zhimulev

Research output: Contribution to journalArticle

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Abstract

Background: Eukaryotic genomes are organized in extended domains with distinct features intimately linking genome structure, replication pattern and chromatin state. Recently we identified a set of long late replicating euchromatic regions that are underreplicated in salivary gland polytene chromosomes of D. melanogaster.Results: Here we demonstrate that these underreplicated regions (URs) have a low density of P-element and piggyBac insertions compared to the genome average or neighboring regions. In contrast, Minos-based transposons show no paucity in URs but have a strong bias to testis-specific genes. We estimated the suppression level in 2,852 stocks carrying a single P-element by analysis of eye color determined by the mini-white marker gene and demonstrate that the proportion of suppressed transgenes in URs is more than three times higher than in the flanking regions or the genomic average. The suppressed transgenes reside in intergenic, genic or promoter regions of the annotated genes. We speculate that the low insertion frequency of P-elements and piggyBacs in URs partially results from suppression of transgenes that potentially could prevent identification of transgenes due to complete suppression of the marker gene. In a similar manner, the proportion of suppressed transgenes is higher in loci replicating late or very late in Kc cells and these loci have a lower density of P-elements and piggyBac insertions. In transgenes with two marker genes suppression of mini-white gene in eye coincides with suppression of yellow gene in bristles.Conclusions: Our results suggest that the late replication domains have a high inactivation potential apparently linked to the silenced or closed chromatin state in these regions, and that such inactivation potential is largely maintained in different tissues.

Original languageEnglish
Article number318
JournalBMC Genomics
Volume11
Issue number1
DOIs
Publication statusPublished - May 21 2010

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Transgenes
Genome
Genes
Chromatin
Chromosomes, Human, 13-15
Eye Color
Polytene Chromosomes
Intergenic DNA
Salivary Glands
Genetic Promoter Regions
Testis

ASJC Scopus subject areas

  • Biotechnology
  • Genetics

Cite this

Babenko, V. N., Makunin, I. V., Brusentsova, I. V., Belyaeva, E. S., Maksimov, D. A., Belyakin, S. N., ... Zhimulev, I. F. (2010). Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome. BMC Genomics, 11(1), [318]. https://doi.org/10.1186/1471-2164-11-318

Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome. / Babenko, Vladimir N.; Makunin, Igor V.; Brusentsova, Irina V.; Belyaeva, Elena S.; Maksimov, Daniil A.; Belyakin, Stepan N.; Maróy, P.; Vasil'eva, Lyubov A.; Zhimulev, Igor F.

In: BMC Genomics, Vol. 11, No. 1, 318, 21.05.2010.

Research output: Contribution to journalArticle

Babenko, VN, Makunin, IV, Brusentsova, IV, Belyaeva, ES, Maksimov, DA, Belyakin, SN, Maróy, P, Vasil'eva, LA & Zhimulev, IF 2010, 'Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome', BMC Genomics, vol. 11, no. 1, 318. https://doi.org/10.1186/1471-2164-11-318
Babenko VN, Makunin IV, Brusentsova IV, Belyaeva ES, Maksimov DA, Belyakin SN et al. Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome. BMC Genomics. 2010 May 21;11(1). 318. https://doi.org/10.1186/1471-2164-11-318
Babenko, Vladimir N. ; Makunin, Igor V. ; Brusentsova, Irina V. ; Belyaeva, Elena S. ; Maksimov, Daniil A. ; Belyakin, Stepan N. ; Maróy, P. ; Vasil'eva, Lyubov A. ; Zhimulev, Igor F. / Paucity and preferential suppression of transgenes in late replication domains of the D. melanogaster genome. In: BMC Genomics. 2010 ; Vol. 11, No. 1.
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AU - Belyakin, Stepan N.

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