%0 Journal Article %A Laurence Ettwiller %A John Buswell %A Erbay Yigit %A Ira Schildkraut %T A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome %D 2015 %R 10.1101/034785 %J bioRxiv %P 034785 %X We have developed Cappable-seq that specifically captures primary RNA transcripts by enzymatically modifying the 5’ triphosphorylated end of RNA with a selectable tag. We first applied Cappable-seq to E. coli, achieving up to 50 fold enrichment of primary transcripts and identifying an unprecedented 16539 transcription start sites (TSS) genome-wide at single base resolution. We also applied Cappable-seq to a mouse cecum sample and for the first time identified TSS in a microbiome. Furthermore, Cappable-seq universally depletes ribosomal RNA and reduces the complexity of the transcriptome to a single quantifiable tag per TSS enabling digital profiling of gene expression in any microbiome. %U https://www.biorxiv.org/content/biorxiv/early/2015/12/17/034785.full.pdf