During macroautophagy, phagophores establish multiple membrane contact sites (MCSs) with
other organelles that are pivotal for proper phagophore assembly and growth. InS.
cerevisiae, phagophore contacts have been observed with the vacuole, the ER,
and lipid droplets. In situ imaging studies have greatly advanced our understanding of the
structure and function of these sites. Here, we discuss how in situ structural methods
like cryo-CLEM can give unprecedented insights into MCSs, and how they help to elucidate
the structural arrangements of MCSs within cells. We further summarize the current
knowledge of the contact sites in autophagy, focusing on autophagosome biogenesis in the
model organismS. cerevisiae.