Transposable elements (TEs) occupy a large fraction of metazoan genomes and pose 
a constant threat to genomic integrity. This threat is particularly critical in 
germ cells, as changes in the genome that are induced by TEs will be transmitted 
to the next generation. Small noncoding piwi-interacting RNAs (piRNAs) recognize 
and silence a diverse set of TEs in germ cells. In mice, piRNA-guided transposon 
repression correlates with establishment of CpG DNA methylation on their 
sequences, yet the mechanism and the spectrum of genomic targets of piRNA 
silencing are unknown. Here we show that in addition to DNA methylation, the 
piRNA pathway is required to maintain a high level of the repressive H3K9me3 
histone modification on long interspersed nuclear elements (LINEs) in germ 
cells. piRNA-dependent chromatin repression targets exclusively full-length 
elements of actively transposing LINE families, demonstrating the remarkable 
ability of the piRNA pathway to recognize active elements among the large number 
of genomic transposon fragments.