PT  - JOURNAL ARTICLE
AU  - Philip P. Adams
AU  - Gabriele Baniulyte
AU  - Caroline Esnault
AU  - Kavya Chegireddy
AU  - Navjot Singh
AU  - Molly Monge
AU  - Ryan K. Dale
AU  - Gisela Storz
AU  - Joseph T. Wade
TI  - Regulatory roles of 5′ UTR and ORF-internal RNAs detected by 3′ end mapping
AID  - 10.1101/2020.07.18.207399
DP  - 2020 Jan 01
TA  - bioRxiv
PG  - 2020.07.18.207399
4099  - http://biorxiv.org/content/early/2020/11/25/2020.07.18.207399.short
4100  - http://biorxiv.org/content/early/2020/11/25/2020.07.18.207399.full
AB  - Many bacterial genes are regulated by RNA elements in their 5′ untranslated regions (UTRs). However, the full complement of these elements is not known even in the model bacterium Escherichia coli. Using complementary RNA-sequencing approaches, we detected large numbers of 3′ ends in 5′ UTRs and open reading frames (ORFs), suggesting extensive regulation by premature transcription termination. We documented regulation for multiple transcripts, including spermidine induction involving Rho and translation of an upstream ORF for an mRNA encoding a spermidine efflux pump. In addition to discovering novel sites of regulation, we detected short, stable RNA fragments derived from 5′ UTRs and sequences internal to ORFs. Characterization of three of these transcripts, including an RNA internal to an essential cell division gene, revealed that they have independent functions as sRNA sponges. Thus, these data uncover an abundance of cis- and trans-acting RNA regulators in bacterial 5′ UTRs and internal to ORFs.Competing Interest StatementThe authors have declared no competing interest.