Transcriptional Silencing affects transcription at a step between activator binding and Pol II recruitment.
Lingyi Chen, Jonathan Widom
BMBCB, Northwestern University, 2153 Sheridan Road, Evanston, IL, 60208, USA
Transcriptional silencing is a phenomenon in which the transcription of genes by RNA polymerase II or III is repressed, depending on the chromosomal location of a gene. There are two prevailing models for transcriptional silencing: one supposes that steric hindrance prevents access of activators to the silenced DNA; the other supposes that silencing primarily affects some event(s) downstream of preinitiation complex recruitment. To distinguish these two models, we study chromosomal DNA accessibility with three different types of exogenous proteins as probes: a prokaryotic DNA binding protein (LexA), restriction enzymes, and the Dam DNA methyltransferase. In addition, we use a chromatin immunoprecipitation assay to probe the occupancy of an endogenous activator, Ppr1p. Our data suggest that regulated DNA accessibility contributes quantitatively to silencing, but that it does not, on its own, provide an all-or-nothing response. We further study the occupancies of Pol II at heterochromatic genes in silenced and active states. We find that transcriptional silencing only modestly affects Ppr1p occupancy, yet it significantly reduces Pol II occupancy. Thus, in contrast to the two current models, our data suggest that transcriptional silencing mainly acts at a step between activator binding and Pol II recruitment.
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