Abstract
In yeast (Saccharomyces cerevisiae), the synthesis of tRNAs by RNA polymerase III (RNAP III) down-regulates the transcription of the nearby RNAP II-transcribed genes by a mechanism that is poorly understood. To clarify the basis of this tRNA gene-mediated (TGM) silencing, here, conducting a bioinformatics analysis of available ChIP-chip and ChIP-sequencing genomic data from yeast, we investigated whether the RNAP III transcriptional machinery can recruit protein factors required for RNAP II transcription. An analysis of 46 genome-wide protein-density profiles revealed that 12 factors normally implicated in RNAP II-mediated gene transcription are more enriched at tRNA than at mRNA loci. These 12 factors typically have RNA-binding properties, participate in the termination stage of the RNAP II transcription, and preferentially localize to the tRNA loci by a mechanism that apparently is based on the RNAP III transcription level. The factors included two kinases of RNAP II (Bur1 and Ctk1), a histone demethylase (Jhd2), and a mutated form of a nucleosome-remodeling factor (Spt6) that have never been reported to be recruited to tRNA loci. Moreover, we show that the expression levels of RNAP II-transcribed genes downstream of tRNA loci correlate with the distance from the tRNA gene by a mechanism that depends on their orientation. These results are consistent with the notion that pre-tRNAs recruit RNAP II-associated factors, thereby reducing the availability of these factors for RNAP II transcription and contributing, at least in part, to the TGM-silencing mechanism.
Highlights
In yeast (Saccharomyces cerevisiae), the synthesis of tRNAs by RNA polymerase III (RNAP III) down-regulates the transcription of the nearby RNAP II–transcribed genes by a mechanism that is poorly understood
We report that some protein factors implicated in the termination stage of RNAP II transcription appear to be significantly recruited at RNAP III–transcribed loci by a mechanism that is positively correlated with their RNA-binding properties and with the RNAP III occupancy
To investigate the mechanistic basis of tRNA gene–mediated (TGM) silencing, we evaluated the possibility that RNAP III transcriptional machinery could recruit specific RNAP II–associated factors
Summary
To investigate the mechanistic basis of TGM silencing, we evaluated the possibility that RNAP III transcriptional machinery could recruit specific RNAP II–associated factors. Large datasets related to the ChIP-chip and ChIP-sequencing. Proteins significantly more enriched at tRNA than at mRNA loci are indicated by bold text: *, p value (t test) Ͻ 0.00002; **, p value (t test) Ͻ 0.0002; ***, p value (t test) Ͻ 0.02
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