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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-elemen ts and  piggyBac s 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.

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