After manual verification of the data obtained and a comparison with predicted operons, we identified 2266 TSS (transcription start sites) and 2128 transcript ends (Additional file 15: Table S10).
Our study identified 1,210 transcription start sites (TSSs) and 655 transcript ends as well as 39 riboswitches and cis-regulatory regions, 39 cis-antisense non-coding RNAs and 47 small RNAs potentially acting in trans.
The transcript ends for these novel islet transcripts were significantly enriched for transcription factor binding by PDX1, NKX6.1, MAFA and NEUROD1 (not shown) compared to random positions.
The transcript ends with the court reporter's parenthetical note: "(People crying, leaving the gallery)".
The genome-wide identification of transcription start sites, enabled by high-throughput sequencing of a cDNA library enriched for native 5′ transcript ends, is ideally suited for the analysis of promoters.
Therefore, it seems that functional interactions of transcript ends has evolved prior to the development of mRNA capping and polyadenylation.
Transcript ends were defined using the annotations from the RNA-sequencing dataset, to exclude 5' and 3' untranslated regions from the intergenic sequence.
Intergenic regions of S. cerevisiae were defined as sequences between transcript ends of all SGD-annotated genes, including uncharacterized, dubious, and coding regions.
RNA was isolated from both cell lines, transcript ends were mapped by 5'- and 3'-RACE, and full-length cDNAs were prepared and sequenced.
It should be noted that while U133Plus2 arrays have an average of one probeset per transcript, our clone selection process was designed to provide an over-representation of probesets on U133Plus2 arrays that would allow addressing possible alternative polyadenylation sites and possible alternative 3' transcript ends.
