RNA⁻Protein Interactions Prevent Long RNA Duplex Formation: Implications for the Design of RNA-Based Therapeutics.

ABSTRACT: Cells frequently simultaneously express RNAs and cognate antisense transcripts without necessarily leading to the formation of RNA duplexes. Here, we present a novel transcriptome-wide experimental approach to ascertain the presence of accessible double-stranded RNA structures based on sequencing of RNA fragments longer than 18 nucleotides that were not degraded by single-strand cutting nucleases. We applied this approach to four different cell lines with respect to three different treatments (native cell lysate, removal of proteins, and removal of ribosomal RNA and proteins). We found that long accessible RNA duplexes were largely absent in native cell lysates, while the number of RNA duplexes was dramatically higher when proteins were removed. The majority of RNA duplexes involved riboso

SUBMITTER: Bindewald E 

PROVIDER: S-EPMC6321275 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature