FIB-SEM of cells expressing Atg39 with model of nucleophagy (supplemental to Fig. 9 ). (A) Total volume of FIB-SEM images of cells expressing Atg39-GFP. (B) Bar chart of the quantification of NE blebs and associated lipid droplets (LDs) observed in a total of 52 cells captured within the FIB-SEM volume shown in A. (C) i: Orthogonal view of a block of FIB-SEM images (from A) of a single cell with isotropic resolution of 7 × 7 × 7 nm voxels. ii: Surface rendering of NE (blue), LDs (yellow), mitochondria (magenta), and vacuole (gray); a scanning EM image of a single z plane is also shown. iii: Top-down view of ii. iv: Side view of surface rendering of just NE and LDs. Arrowheads point to NE blebs. v: Annotated SEM image of a single z-slice with ONM blue and LD in yellow. vi: Top-down view of NE and LDs, with arrowheads pointing to NE blebs. vii and viii: Zoomed view and alternate angles of region containing NE blebs and LDs. Scale bars are 200 nm. (D) A proposed outside–in model of nucleophagy. Atg39 localizes to the ONM and connects (directly or indirectly) to the INM through lumenal motifs. Evagination of the INM and selective capture of INM cargo (Heh1) requires Atg39. INM-derived vesicles form after an INM scission event. Subsequent ONM scission would also be required to liberate the NE bleb before its capture by the autophagosome through interactions with the N-terminus of Atg39.