Regulatory DNA from a diverse group of Drosophila genes causes silencing of the linked reporter gene mini-white in the P-element vector CaSpeR. This silencing can occur in flies heterozygous for the P-element construct but is often enhanced in flies homozygous for the construct. In Drosophila, somatic chromosomes are paired and this pairing is important for the enhancement of silencing in most cases. Thus, this type of silencing has been called pairing-sensitive silencing. Many of the DNA fragments that cause pairing-sensitive silencing are regulatory elements required for the activity of the Polycomb group of transcriptional repressors (Polycomb group response elements, PREs). However, some PREs do not appear to cause pairing-sensitive silencing, and some fragments of DNA that cause pairing-sensitive silencing do not appear to act as PREs. I suggest that many PREs are composite elements of sites important for silencing and sites important for "pairing" or bringing together distant DNA elements. Both activities may be required for PRE function. In a related phenomenon, fragments of DNA included within P-element vectors can cause those transposons to insert in the genome near the parent gene of the included DNA (transposon homing). I suggest that DNA fragments that cause transposon homing or pairing-sensitive silencing are bound by protein complexes that can interact to bring together distant DNA fragments.