Bidirectional promoters generate pervasive transcription in yeast Export

@article{citeulike:3942703, abstract = {Genome-wide pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves hundreds of previously unknown non-coding RNAs. 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 function. Single-gene studies have shown that transcription of SUTs and CUTs can be functional, through mechanisms involving the generated RNAs or their generation itself. 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. 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 32 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\&\#20;that is, coupling the transcriptional regulation of neighbouring genes by means of transcriptional interference or histone modification.}, author = {Xu, Zhenyu and Wei, Wu and Gagneur, Julien and Perocchi, Fabiana and Clauder-Munster, Sandra and Camblong, Jurgi and Guffanti, Elisa and Stutz, Francoise and Huber, Wolfgang and Steinmetz, Lars M.}, citeulike-article-id = {3942703}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nature07728}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nature07728}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/19169243}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=19169243}, doi = {10.1038/nature07728}, issn = {0028-0836}, journal = {Nature}, keywords = {bidirectional, transcripts, yeast}, month = {February}, number = {7232}, pages = {1033--1037}, posted-at = {2009-03-03 17:05:00}, priority = {0}, publisher = {Macmillan Publishers Limited. All rights reserved}, title = {Bidirectional promoters generate pervasive transcription in yeast}, url = {http://dx.doi.org/10.1038/nature07728}, volume = {457}, year = {2009} }

TY - JOUR ID - citeulike:3942703 L3 - citeulike-article-id:3942703 N2 - Genome-wide pervasive transcription has been reported in many eukaryotic organisms, revealing a highly interleaved transcriptome organization that involves hundreds of previously unknown non-coding RNAs. 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 function. Single-gene studies have shown that transcription of SUTs and CUTs can be functional, through mechanisms involving the generated RNAs or their generation itself. 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. 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 32 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 signalsthat is, coupling the transcriptional regulation of neighbouring genes by means of transcriptional interference or histone modification. IS - 7232 JF - Nature SN - 0028-0836 EP - 1037 TI - Bidirectional promoters generate pervasive transcription in yeast PB - Macmillan Publishers Limited. All rights reserved VL - 457 SP - 1033 KW - bidirectional KW - transcripts KW - yeast AU - Xu, Zhenyu AU - Wei, Wu AU - Gagneur, Julien AU - Perocchi, Fabiana AU - Clauder-Munster, Sandra AU - Camblong, Jurgi AU - Guffanti, Elisa AU - Stutz, Francoise AU - Huber, Wolfgang AU - Steinmetz, Lars PY - 2009/02/19/ UR - http://dx.doi.org/10.1038/nature07728 ER -