Abstract
Eukaryotic genomes are extensively transcribed, forming both messenger RNAs (mRNAs) and noncoding RNAs (ncRNAs). ncRNAs made by RNA polymerase II often initiate from bidirectional promoters (nucleosome-depleted chromatin) that synthesize mRNA and ncRNA in opposite directions. We demonstrate that, by adopting a gene-loop conformation, actively transcribed mRNA encoding genes restrict divergent transcription of ncRNAs. Because gene-loop formation depends on a protein factor (Ssu72) that coassociates with both the promoter and the terminator, the inactivation of Ssu72 leads to increased synthesis of promoter-associated divergent ncRNAs, referred to as Ssu72-restricted transcripts (SRTs). Similarly, inactivation of individual gene loops by gene mutation enhances SRT synthesis. We demonstrate that gene-loop conformation enforces transcriptional directionality on otherwise bidirectional promoters.
Publication types
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Research Support, N.I.H., Extramural
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Research Support, Non-U.S. Gov't
MeSH terms
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Exosome Multienzyme Ribonuclease Complex / metabolism
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Genes, Fungal*
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Genome, Fungal
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Mutation
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Nucleic Acid Conformation
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Phosphoprotein Phosphatases / metabolism
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Promoter Regions, Genetic
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RNA Polymerase II / metabolism
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RNA Stability
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RNA, Fungal / genetics
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RNA, Fungal / metabolism
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RNA, Messenger / genetics*
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RNA, Messenger / metabolism
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RNA, Untranslated / genetics*
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RNA, Untranslated / metabolism
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Saccharomyces cerevisiae / genetics*
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Saccharomyces cerevisiae / metabolism
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Saccharomyces cerevisiae Proteins / metabolism
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Transcription, Genetic*
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mRNA Cleavage and Polyadenylation Factors / metabolism
Substances
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RNA, Fungal
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RNA, Messenger
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RNA, Untranslated
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SSU72 protein, S cerevisiae
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Saccharomyces cerevisiae Proteins
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mRNA Cleavage and Polyadenylation Factors
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RNA Polymerase II
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Exosome Multienzyme Ribonuclease Complex
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RRP6 protein, S cerevisiae
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Phosphoprotein Phosphatases