Legacy Research: RNA-mediated regulation in microbes

Our lab employed RNA-seq to perform gene expression studies in bacteria and archaea and to understand their complex transcriptomes. Although prokaryotic transcriptomes were initially considered simple, microbial transcriptome studies revolutionized our understanding of the complexity, plasticity and regulation of microbial RNA (Sorek & Cossart, Nature Reviews Genetics 2010).

Between the years 2009-2018, our lab used high throughput sequencing technologies to discover new small non-coding RNAs (sRNAs) and understand their biological functions. Through our studies and studies of others it became clear that microbial genomes are populated by functional sRNAs, generally 50-500bp long. These sRNAs have been shown to regulate various biological processes including quorum sensing, pathogenesis, stress response, and more. Our data showed extensive transcription of non-coding RNAs from intergenic regions (Yoder-Himes et al, PNAS 2009) and hundreds of cis-antisense RNAs (asRNAs) encoded in bacteria and archaea (Wurtzel et al, 2010; Wurtzel et al, 2012a; Wurtzel et al, 2012b). As part of our studies we defined the "Excludon", a unique antisense-based regulatory structure in bacteria, which is a chimera between antisense RNA and mRNA (Nature Reviews Microbiology, 2013).

Advanced RNA-seq methods, such as RIP-seq and bisulfite-seq were used in the lab to study RNA modifications in humans (Nature, 2012), bacteria and archaea (PLoS Genetics 2013). We also discovered curious cases of circular RNAs expressed in archaeal genomes (Danan et al, 2012), and were interested in the roles of riboswitches in regulating molecular processes in bacteria (Science 2014).

We also developed new technologies for accurate measurements of RNA in microbes. We developed term-seq, a method that allows single-base resolution mapping of RNA 3' ends in bacteria and archaea. We showed that term-seq can identify new riboswitches and attenuators that regulate antibiotic-resistance genes in the human microbiome (Dar et al, Science 2016). We also used term-seq to understand signals of transcription termination in archaea (Dar et al, Nature Microbiology 2016).