In the Drosophila germline, retrotransposons are silenced by the 
PIWI-interacting RNA (piRNA) pathway. piRNA pathway mutations lead to 
overexpression and mobilization of retrotransposons in the germline. In 
different organisms, small RNAs were shown to be implicated in the 
posttranscriptional degradation of mRNA and/or transcriptional repression of the 
homologous locus. In Drosophila, the mechanism of piRNA-mediated silencing is 
still far from being understood. Transcriptional silencing implies a 
piRNA-mediated formation of repressive chromatin which diminishes the 
transcriptional capacity of the target locus. Nuclear Run-On (NRO) assay allows 
a direct estimation of the density of transcribing polymerases at specific 
genomic regions. Here we describe the NRO protocol on Drosophila ovarian tissues 
which can be useful for investigation of the transcriptional silencing in the 
female germline.