Limiting the Extent of the RDN1 Heterochromatin Domain by a Silencing Barrier and Sir2 Protein Levels in Saccharomyces cerevisiae
Abstract
Limiting the Extent of the RDN1 Heterochromatin Domain by a Silencing Barrier and Sir2 Protein Levels in Saccharomyces cerevisiae ▿ Moumita Biswas 1 , Nazif Maqani 2 , Ragini Rai 1 , Srikala P. Kumaran 1 , Kavitha R. Iyer 1 , Erdem Sendinc 2 , Jeffrey S. Smith 2 and Shikha Laloraya 1 , * 1 Department of Biochemistry, Indian Institute of Science, Bangalore KA 560012, India 2 Department of Biochemistry and Molecular Genetics, University of Virginia Health System, School of Medicine, Charlottesville, Virginia 22908 ABSTRACT In Saccharomyces cerevisiae , transcriptional silencing occurs at the cryptic mating-type loci ( HML and HMR ), telomeres, and ribosomal DNA (rDNA; RDN1 ). Silencing in the rDNA is unusual in that polymerase II (Pol II) promoters within RDN1 are repressed by Sir2 but not Sir3 or Sir4. rDNA silencing unidirectionally spreads leftward, but the mechanism of limiting its spreading is unclear. We searched for silencing barriers flanking the left end of RDN1 by using an established assay for detecting barriers to HMR silencing. Unexpectedly, the unique sequence immediately adjacent to RDN1 , which overlaps a prominent cohesin binding site ( CARL2 ), did not have appreciable barrier activity. Instead, a fragment located 2.4 kb to the left, containing a tRNA Gln gene and the Ty1 long terminal repeat, had robust barrier activity. The barrier activity was dependent on Pol III transcription of tRNA Gln , the cohesin protein Smc1, and the SAS1 and Gcn5 histone acetyltransferases. The location of the barrier correlates with the detectable limit of rDNA silencing when SIR2 is overexpressed, where it blocks the spreading of rDNA heterochromatin. We propose a model in which normal Sir2 activity results in termination of silencing near the physical rDNA boundary, while tRNA Gln blocks silencing from spreading too far when nucleolar Sir2 pools become elevated.