A novel regulator of autophagosome biogenesis and lipid droplet dynamicsMorel, Etienne; Codogno, Patrice
doi: 10.15252/embr.201846858pmid: 30131347
Autophagosome biogenesis is the key event associated with the stress‐responsive autophagic pathway, allowing the capture of specific cargoes and their delivery to the lysosomal degradative compartment. Although the endoplasmatic reticulum (ER) appears to be central for the assembly of autophagosomal membranes, it is also involved in several events regulating trafficking and local signaling, e.g., the establishment of contact sites with other organelles, the vesicular transport to the Golgi apparatus, and the biogenesis and turnover of lipid droplets. In this issue of EMBO reports, Moretti et al identify the ER transmembrane protein TMEM41B as a novel regulator of autophagosome biogenesis and unravel its involvement in lipid droplet dynamics, also highlighting the role of ER components at the interface of lipid metabolism and regulation of autophagy.
X10 expansion microscopy enables 25‐nm resolution on conventional microscopesTruckenbrodt, Sven; Maidorn, Manuel; Crzan, Dagmar; Wildhagen, Hanna; Kabatas, Selda; Rizzoli, Silvio O
doi: 10.15252/embr.201845836pmid: 29987134
Expansion microscopy is a recently introduced imaging technique that achieves super‐resolution through physically expanding the specimen by ~4×, after embedding into a swellable gel. The resolution attained is, correspondingly, approximately fourfold better than the diffraction limit, or ~70 nm. This is a major improvement over conventional microscopy, but still lags behind modern STED or STORM setups, whose resolution can reach 20–30 nm. We addressed this issue here by introducing an improved gel recipe that enables an expansion factor of ~10× in each dimension, which corresponds to an expansion of the sample volume by more than 1,000‐fold. Our protocol, which we termed X10 microscopy, achieves a resolution of 25–30 nm on conventional epifluorescence microscopes. X10 provides multi‐color images similar or even superior to those produced with more challenging methods, such as STED, STORM, and iterative expansion microscopy (iExM). X10 is therefore the cheapest and easiest option for high‐quality super‐resolution imaging currently available. X10 should be usable in any laboratory, irrespective of the machinery owned or of the technical knowledge.
Chemical and genetic control of IFNγ‐induced MHCII expressionWijdeven, Ruud H; Luijn, Marvin M; Wierenga‐Wolf, Annet F; Akkermans, Jimmy J; Elsen, Peter J; Hintzen, Rogier Q; Neefjes, Jacques
doi: 10.15252/embr.201745553pmid: 30021835
The cytokine interferon‐γ (IFNγ) can induce expression of MHC class II (MHCII) on many different cell types, leading to antigen presentation to CD4+ T cells and immune activation. This has also been linked to anti‐tumour immunity and graft‐versus‐host disease. The extent of MHCII upregulation by IFNγ is cell type‐dependent and under extensive control of epigenetic regulators and signalling pathways. Here, we identify novel genetic and chemical factors that control this form of MHCII expression. Loss of the oxidative stress sensor Keap1, autophagy adaptor p62/SQSTM1, ubiquitin E3‐ligase Cullin‐3 and chromatin remodeller BPTF impair IFNγ‐mediated MHCII expression. A similar phenotype is observed for arsenite, an oxidative stressor. Effects of the latter can be reversed by the inhibition of HDAC1/2, linking oxidative stress conditions to epigenetic control of MHCII expression. Furthermore, dimethyl fumarate, an antioxidant used for the treatment of several autoimmune diseases, impairs the IFNγ response by manipulating transcriptional control of MHCII. We describe novel pathways and drugs related to oxidative conditions in cells impacting on IFNγ‐mediated MHCII expression, which provide a molecular basis for the understanding of MHCII‐associated diseases.
An unusual suspect in cocaine addictionLoureiro, Michael; Lüscher, Christian
doi: 10.15252/embr.201846743pmid: 30082330
Most Mage family members code for antigens on melanoma tumor cells. Maged1 is the black sheep, promiscuously found in normal adult cells, including neurons of the basal ganglia and prefrontal cortex. In this issue of EMBO reports, De Backer et al propose an unexpected role for Maged1. Acute effects of cocaine, such as enhanced locomotion and reinforcement, are gone in mice in which the gene is deleted. In a painstaking combinatorial approach comparing several conditional gene knockout (KO) mouse lines, the authors parse the relevant neural circuits.
Budding yeast Rif1 binds to replication origins and protects DNA at blocked replication forksHiraga, Shin‐ichiro; Monerawela, Chandre; Katou, Yuki; Shaw, Sophie; Clark, Kate RM; Shirahige, Katsuhiko; Donaldson, Anne D
doi: 10.15252/embr.201846222pmid: 30104203
Despite its evolutionarily conserved function in controlling DNA replication, the chromosomal binding sites of the budding yeast Rif1 protein are not well understood. Here, we analyse genome‐wide binding of budding yeast Rif1 by chromatin immunoprecipitation, during G1 phase and in S phase with replication progressing normally or blocked by hydroxyurea. Rif1 associates strongly with telomeres through interaction with Rap1. By comparing genomic binding of wild‐type Rif1 and truncated Rif1 lacking the Rap1‐interaction domain, we identify hundreds of Rap1‐dependent and Rap1‐independent chromosome interaction sites. Rif1 binds to centromeres, highly transcribed genes and replication origins in a Rap1‐independent manner, associating with both early and late‐initiating origins. Interestingly, Rif1 also binds around activated origins when replication progression is blocked by hydroxyurea, suggesting association with blocked forks. Using nascent DNA labelling and DNA combing techniques, we find that in cells treated with hydroxyurea, yeast Rif1 stabilises recently synthesised DNA. Our results indicate that, in addition to controlling DNA replication initiation, budding yeast Rif1 plays an ongoing role after initiation and controls events at blocked replication forks.