In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field

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A central enzyme in the pathway of de novo lipogenesis, fatty acid synthase (FAS) 1 catalyzes all of the steps in the conversion of malonyl-CoA to palmitate. Expression of the FAS gene is controlled primarily at the level of transcription and is responsive to both hormonal and nutritional signals (1, 2). Previous work has shown that sterol regulatory element-binding proteins (SREBPs) play a critical role in the transcriptional regulation of a number of genes in the lipogenic pathway, including FAS, steroyl-CoA desaturase (SCD-1), and acetyl-CoA carboxylase (ACC) (3-8). Three SREBP isoforms have been described: SREBP-1a and Ϫ1c (also called ADD1), which are derived from the same gene through alternative splicing, and SREBP-2, which is encoded by a separate gene (9, 10). Although their transcriptional targets overlap significantly, studies suggest that SREBP-1 preferentially activates genes involved in lipogenesis, whereas SREBP-2 preferentially activates genes in the cholesterol biosynthetic pathway (11-14). SREBPs have been shown to regulate FAS expression through direct interaction with the FAS promoter at multiple sites (7, 15). Overexpression of nuclear SREBP-1 is sufficient to induce expression of the FAS gene in cultured cells as well as transgenic mice (5,8). Recent work has also implicated the nuclear receptors LXR␣ and LXR␤ in the control of lipogenesis. Both LXRs bind to DNA and regulate transcription of target genes in a heterodimeric complex with RXR (16). Although early studies on LXRs focused on their role in cholesterol metabolism, mice carrying a targeted disruption in the LXR␣ gene were noted to be deficient in expression of FAS, SCD-1, ACC, and SREBP-1, consistent with a role in lipogenesis as well (17). Further support for this idea came with the observation that the administration of the synthetic LXR ligand T1317 to mice triggers induction of the lipogenic pathway and raises plasma triglyceride levels (18). The demonstration that the SREBP-1c promoter is a direct target for regulation by LXR/RXR heterodimers provided a straightforward explanation for the ability of LXR ligands to induce hepatic lipogenesis (19,20). Until now, the effects of LXR activation on the expression of lipogenic genes, including FAS, have been presumed to be entirely indirect.We demonstrate here that the FAS promoter is a direct target for regulation by the LXR/RXR heterodimer as well as SREBPs. This novel mechanism for the regulation of FAS expression and lipogenesis by LXRs has implications for the development of LXR agonists as modulators of human lipid metabolism. EXPERIMENTAL PROCEDURESReagents and Plasmids-Expression plasmids for RXR␣ and LXR␣, and nuclear SREBP-1a, -1c, and -2 have been described (21,22). GW3965 (23) and T0901317 (18) were provided by Timothy M. Willson (GlaxoSmithKline). Ligands were dissolved in Me 2 SO prior to use in cell culture. The Ϫ1594, Ϫ700, Ϫ150, and Ϫ135 rat FAS promoter luciferase reporter constructs were described previously (3). Mutations were

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