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 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.