Pervasive and hidden transcription is widespread in eukaryotes, but its global 
level, the mechanisms from which it originates and its functional significance 
are unclear. Cryptic unstable transcripts (CUTs) were recently described as a 
principal class of RNA polymerase II transcripts in Saccharomyces cerevisiae. 
These transcripts are targeted for degradation immediately after synthesis by 
the action of the Nrd1-exosome-TRAMP complexes. Although CUT degradation 
mechanisms have been analysed in detail, the genome-wide distribution at the 
nucleotide resolution and the prevalence of CUTs are unknown. Here we report the 
first high-resolution genomic map of CUTs in yeast, revealing a class of 
potentially functional CUTs and the intrinsic bidirectional nature of eukaryotic 
promoters. An RNA fraction highly enriched in CUTs was analysed by a 3' 
Long-SAGE (serial analysis of gene expression) approach adapted to deep 
sequencing. The resulting detailed genomic map of CUTs revealed that they derive 
from extremely widespread and very well defined transcription units and do not 
result from unspecific transcriptional noise. Moreover, the transcription of 
CUTs predominantly arises within nucleosome-free regions, most of which 
correspond to promoter regions of bona fide genes. Some of the CUTs start 
upstream from messenger RNAs and overlap their 5' end. Our study of glycolysis 
genes, as well as recent results from the literature, indicate that such 
concurrent transcription is potentially associated with regulatory mechanisms. 
Our data reveal numerous new CUTs with such a potential regulatory role. 
However, most of the identified CUTs corresponded to transcripts divergent from 
the promoter regions of genes, indicating that they represent by-products of 
divergent transcription occurring at many and possibly most promoters. 
Eukaryotic promoter regions are thus intrinsically bidirectional, a fundamental 
property that escaped previous analyses because in most cases divergent 
transcription generates short-lived unstable transcripts present at very low 
steady-state levels.