The LC3 conjugation machinery specifies the loading of RNA-binding proteins into extracellular vesicles (smRNA-seq dataset)

We employed small non-coding RNA sequecing to profile the small RNAs in extracellular vesicles (EVs) from WT cells and cells deficient for the LC3 conjugation machinery EVs from wild-type, ATG7-/- and ATG12-/- HEK293T cells and corresponding cell samples were collected after 24h of serum starvation. Total RNA from wild-type, ATG7-/- and ATG12-/- HEK293T EVs and cells was isolated and used for the preparation of uniquely barcoded small RNA sequencing libraries (n=3). Results of single-end 50 base pair sequencing on two separate lanes of a HiSeq4000 for these samples revealed dramatic differences in the small RNA profiles of EVs from ATG7-/- and ATG12-/- cells relative to EVs from wild-type cells. Specifically, EVs from ATG7-/- and ATG12-/- cell were found to have reduced levels of numerous small nucleolar RNAs (snoRNAs), and more limited affects upon discrete microRNA and transfer RNA (tRNA) species. Overall, these results are supportive of a role for the LC3-conjugation machinery in specifying RNA-binding proteins and RNAs into EVs for secretion outside the cell.