Condensin Promotes Position Effects within Tandem DNA Repeats via the RITS Complex

Abstract

Summary: Tandem repetitive DNA is highly abundant in eukaryotic genomes and contributes to transcription control and genome stability. However, how the individual sequences within tandem repeats behave remains largely unknown. Here we develop a collection of fission yeast strains with a reporter gene inserted at different units in a tandem repeat array. We show that, contrary to what is usually assumed, transcriptional silencing and replication timing among the individual repeats differ significantly. RNAi-mediated H3K9 methylation is essential for the silencing position effect. A short hairpin RNA of ura4+ induces silencing in trans within the tandem array in a position-dependent manner. Importantly, the position effect depends on the condensin subunit, cut3+. Cut3 promotes the position effect via interaction with the RNA-induced transcriptional silencing (RITS) complex. This study reveals variations in silencing within tandem DNA repeats and provides mechanistic insights into how DNA repeats at the individual level are regulated. : How the individual sequences within tandem repeats behave remains poorly understood. He et al. show that the heterochromatin silencing between individual units within a peri-centromeric tandem array can vary significantly. They further show that condensin and RNAi components are important for the distinct silencing states in individual repeats.