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. Author manuscript; available in PMC: 2020 Jul 13.
Published in final edited form as: Nat Cell Biol. 2020 Jan 13;22(2):187–199. doi: 10.1038/s41556-019-0450-y

Figure 6. LC3-dependent EV loading and secretion (LDELS) regulates the small non-coding RNA composition of EVs.

Figure 6.

a, Proportion of RNA sequencing (RNA-seq) reads in total cellular RNA from WT, ATG7−/− and ATG12−/− HEK293T cells from the different classes of small non-coding RNA (n=3 biologically independent samples). b, Proportion of RNA-seq reads in total EV RNA from WT, ATG7−/− and ATG12−/− HEK293T cells from the different classes of small non-coding RNA (n=3 biologically independent samples). c, Volcano plot of small non-coding RNAs detected in EVs from WT and ATG7−/− cells quantified by RNA-seq. Results plotted according to -log10 p-values as determined by DESeq2 and log2 fold enrichment (n=3 biologically independent samples; WT/ATG7−/−). Grey dots: RNAs identified with p-value >0.05 and/or log2 fold change between −0.5 and 0.5 (−0.5<log2FC<0.5), and thus, not relatively enriched in EVs from WT or ATG7−/− cells. Log2 fold change reflects WT EV RNA/WT Cell RNA to ATG7−/− EV RNA/ATG7−/− Cell RNA ratio. Black dots: Small non-coding RNAs significantly enriched in EVs from WT or ATG7−/− cells. Red dots: snoRNAs significantly enriched in EVs from WT or ATG7−/− cells. d, Volcano plot of small non-coding RNAs detected in EVs from WT and ATG12−/− cells quantified by RNA-seq. Results were plotted according to -log10 p-values as determined by DESeq2 and log2 fold enrichment (n=3 biologically independent samples; WT/ATG12−/−). Grey dots: RNAs with a p-value >0.05 and/or log2 fold change between −0.5 and 0.5 (−0.5<log2FC<0.5), and thus, not relatively enriched in EVs from WT or ATG12−/− cells. Log2 fold change reflects WT EV RNA/WT Cell RNA to ATG12−/− EV RNA/ATG12−/− Cell RNA ratio. Black dots: Small non-coding RNAs significantly enriched in EVs from WT or ATG12−/− cells. Red dots: snoRNAs significantly enriched in EVs from WT or ATG12−/− cells. e, Venn diagram showing overlap of small non-coding RNAs enriched in EVs from WT cells relative to ATG7−/− or ATG12−/− cells. f, Proportion of different classes of small RNAs enriched in EVs from WT vs. ATG-deficient cells. g, Heatmap of the 67 snoRNAs enriched in EVs from WT cells across all genetic conditions and sample types. Scale indicates intensity, defined as Δ(read counts -mean read count)/SD. Data available in Source Data Fig. 6.