A study published in Science (2008) reveals that divergent transcription occurs from active promoters in mammalian cells, challenging the traditional view of unidirectional RNA polymerase II (RNAPII) initiation. Transcription start site-associated RNAs (TSSa-RNAs) are transcribed divergently from active protein-coding gene promoters, with anti-sense and sense TSSa-RNA peaks located upstream and downstream of the TSS, respectively. These RNAs are associated with both sense and anti-sense directions, and their presence suggests that divergent transcription is common at active promoters. TSSa-RNAs are found in over half of all mouse genes and are detected in all cell types examined. They are not Dicer products and are most frequently 17 nucleotides long, with a mean length of 20 nucleotides. TSSa-RNAs surround promoters in divergent orientations, with sense TSSa-RNAs mapping downstream of the TSS and anti-sense TSSa-RNAs mapping upstream. These RNAs are associated with overlapping sets of gene promoters and are not dependent on head-to-head gene pairs or genes with multiple TSSs. A majority of ES cell TSSa-RNA associated genes have both sense and anti-sense TSSa-RNAs, indicating that individual TSSs produce both RNA sub-types. These results suggest that divergent transcription is a common feature of mammalian TSSs. TSSa-RNAs are associated with genes expressed at varying levels in ES cells, but are biased towards higher levels of gene expression. They are found at the majority of highly and moderately expressed genes and are associated with CpG island promoters. The number of TSSa-RNA observations per gene correlates positively with gene expression levels, with a notable increase in the sense:anti-sense ratio found at the highest levels of expression. This increase suggests that a fraction of these reads from the most active genes arise from mRNA turnover. TSSa-RNAs do not represent the 5' end of transcripts, suggesting they mark regions of RNAPII pausing rather than initiation. Pausing has been observed at many genes, most notably Drosophila Hsp70, where it maintains RNAPII in a state poised for activation upon heat shock. The results suggest the presence of anti-sense paused RNAPII upstream of many TSSs. The position of paused, anti-sense RNAPII centers around 250 nt upstream of the TSS. This suggests the existence of an undefined mechanism that discriminates between the sense and anti-sense polymerase for productive elongation.A study published in Science (2008) reveals that divergent transcription occurs from active promoters in mammalian cells, challenging the traditional view of unidirectional RNA polymerase II (RNAPII) initiation. Transcription start site-associated RNAs (TSSa-RNAs) are transcribed divergently from active protein-coding gene promoters, with anti-sense and sense TSSa-RNA peaks located upstream and downstream of the TSS, respectively. These RNAs are associated with both sense and anti-sense directions, and their presence suggests that divergent transcription is common at active promoters. TSSa-RNAs are found in over half of all mouse genes and are detected in all cell types examined. They are not Dicer products and are most frequently 17 nucleotides long, with a mean length of 20 nucleotides. TSSa-RNAs surround promoters in divergent orientations, with sense TSSa-RNAs mapping downstream of the TSS and anti-sense TSSa-RNAs mapping upstream. These RNAs are associated with overlapping sets of gene promoters and are not dependent on head-to-head gene pairs or genes with multiple TSSs. A majority of ES cell TSSa-RNA associated genes have both sense and anti-sense TSSa-RNAs, indicating that individual TSSs produce both RNA sub-types. These results suggest that divergent transcription is a common feature of mammalian TSSs. TSSa-RNAs are associated with genes expressed at varying levels in ES cells, but are biased towards higher levels of gene expression. They are found at the majority of highly and moderately expressed genes and are associated with CpG island promoters. The number of TSSa-RNA observations per gene correlates positively with gene expression levels, with a notable increase in the sense:anti-sense ratio found at the highest levels of expression. This increase suggests that a fraction of these reads from the most active genes arise from mRNA turnover. TSSa-RNAs do not represent the 5' end of transcripts, suggesting they mark regions of RNAPII pausing rather than initiation. Pausing has been observed at many genes, most notably Drosophila Hsp70, where it maintains RNAPII in a state poised for activation upon heat shock. The results suggest the presence of anti-sense paused RNAPII upstream of many TSSs. The position of paused, anti-sense RNAPII centers around 250 nt upstream of the TSS. This suggests the existence of an undefined mechanism that discriminates between the sense and anti-sense polymerase for productive elongation.