PT  - JOURNAL ARTICLE
AU  - Laurence Ettwiller
AU  - John Buswell
AU  - Erbay Yigit
AU  - Ira Schildkraut
TI  - A novel enrichment strategy reveals unprecedented number of novel transcription start sites at single base resolution in a model prokaryote and the gut microbiome
AID  - 10.1101/034785
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 034785
4099  - http://biorxiv.org/content/early/2015/12/17/034785.short
4100  - http://biorxiv.org/content/early/2015/12/17/034785.full
AB  - 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.