1. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
2. Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
3. Department of Cell Biology, Sciences III, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland
4. European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
5. These authors contributed equally to this work.

Correspondence to: Lars M. Steinmetz¹ Correspondence and requests for materials should be addressed to L.M.S. (Email: larsms@embl.de).

Abstract

Genome-wide pervasive transcription has been reported in many eukaryotic organisms^{1, 2, 3, 4, 5, 6, 7}, revealing a highly interleaved transcriptome organization that involves hundreds of previously unknown non-coding RNAs⁸. These recently identified transcripts either exist stably in cells (stable unannotated transcripts, SUTs) or are rapidly degraded by the RNA surveillance pathway (cryptic unstable transcripts, CUTs). One characteristic of pervasive transcription is the extensive overlap of SUTs and CUTs with previously annotated features, which prompts questions regarding how these transcripts are generated, and whether they exert function⁹. Single-gene studies have shown that transcription of SUTs and CUTs can be functional, through mechanisms involving the generated RNAs^{10, 11} or their generation itself^{12, 13, 14}. So far, a complete transcriptome architecture including SUTs and CUTs has not been described in any organism. Knowledge about the position and genome-wide arrangement of these transcripts will be instrumental in understanding their function^{8, 15}. Here we provide a comprehensive analysis of these transcripts in the context of multiple conditions, a mutant of the exosome machinery and different strain backgrounds of Saccharomyces cerevisiae. We show that both SUTs and CUTs display distinct patterns of distribution at specific locations. Most of the newly identified transcripts initiate from nucleosome-free regions (NFRs) associated with the promoters of other transcripts (mostly protein-coding genes), or from NFRs at the 3' ends of protein-coding genes. Likewise, about half of all coding transcripts initiate from NFRs associated with promoters of other transcripts. These data change our view of how a genome is transcribed, indicating that bidirectionality is an inherent feature of promoters. Such an arrangement of divergent and overlapping transcripts may provide a mechanism for local spreading of regulatory signals—that is, coupling the transcriptional regulation of neighbouring genes by means of transcriptional interference or histone modification.

1. European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
2. Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
3. Department of Cell Biology, Sciences III, University of Geneva, 30 Quai E. Ansermet, 1211 Geneva 4, Switzerland
4. European Molecular Biology Laboratory, European Bioinformatics Institute, Cambridge CB10 1SD, UK
5. These authors contributed equally to this work.

Correspondence to: Lars M. Steinmetz¹ Correspondence and requests for materials should be addressed to L.M.S. (Email: larsms@embl.de).

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