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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.

Original publication

DOI

10.1126/science.1224350

Type

Journal article

Journal

Science

Publication Date

02/11/2012

Volume

338

Pages

671 - 675

Keywords

Exosome Multienzyme Ribonuclease Complex, Genes, Fungal, Genome, Fungal, Mutation, Nucleic Acid Conformation, Phosphoprotein Phosphatases, Promoter Regions, Genetic, RNA Polymerase II, RNA Stability, RNA, Fungal, RNA, Messenger, RNA, Untranslated, Saccharomyces cerevisiae, Saccharomyces cerevisiae Proteins, Transcription, Genetic, mRNA Cleavage and Polyadenylation Factors