Abstract

Hybrid transgenes are often recognized as foreign genetic material by cell surveillance mechanisms and are repressed in expression inversely to their copy numbers. Here, we compare the expression of multiple Adh-promoter-white reporter (Adh-w) inserts in paired and unpaired configurations in Drosophila somatic cells. The unpaired copies exhibit a clear repression at the transcriptional level relative to paired gene dosage effect, which is dependent upon long noncoding RNA, Polycomb and piwi. Deficiency mapping using Adh-w constructs showed that a minimal sequence of 532 bp of the Adh promoter is required for unpaired DNA silencing. Long noncoding RNA detected from this region of the Adh promoter is abundant in the unpaired condition. It serves as a docking site for at least two proteins POLYCOMB and Piwi that are essential for active transcriptional silencing. The lesser abundance of noncoding RNAs in the paired configuration only allows PC binding. An active RNA-Protein complex binds to unpaired copies. The loss-of-function piwi mutation relieves transcriptional silencing even in association with POLYCOMB. It suggests that functional RNA-Piwi complex might create a silencing driven chromatin configuration by accumulating histone modifying enzymes at the Adh-w promoter target. This distinct transcriptional silencing that is stronger for unpaired DNA represents a novel mechanism to repress new transposon and foreign DNA insertions for protection of genome integrity.