The de novo formation of autophagosomes for the targeting of cytosolic material to the vacuole/lysosome is upregulated upon starvation. How autophagosomes acquire membranes remains still unclear. Here, we report that, in yeast, the endoplasmic reticulum (ER)-localized Qa/t-SNARE Ufe1 has a role in autophagy. During starvation, Ufe1 is increasingly exported from the ER and targeted to intracellular sites that contain the autophagy markers Atg8 and Atg9. In addition, Ufe1 interacts with non-ER SNARE proteins implicated in autophagosome formation. Loss of Ufe1 function impairs autophagy and results in fewer and smaller autophagosomes. Unlike conventional cargo, the ER export of Ufe1 is significantly reduced in sec23-1 cells, which affects the coat protein (COP)II complex, already at the permissive temperature. Under the same conditions, sec23-1 cells are hypersensitive to starvation and deficient in autophagy. Our data suggest that ER membranes containing Ufe1 are delivered to sites of autophagosome formation in specific COPII vesicles.

Sikorska et al. find that remodeling of a GPI anchor after its attachment to proteins inside the ER strongly promotes ER export but occurs independently of protein folding, thereby effectively limiting ER quality control, potentially including ER-associated degradation of all GPI-anchored proteins.

No abstract

The RNA exosome provides eukaryotic cells with an essential 3′–5′ exoribonucleolytic activity, which processes or eliminates many classes of RNAs. Its nine-subunit core (Exo9) is structurally related to prokaryotic phosphorolytic exoribonucleases. Yet, yeast and animal Exo9s have lost the primordial phosphorolytic capacity and rely instead on associated hydrolytic ribonucleases for catalytic activity. Here, we demonstrate that Arabidopsis Exo9 has retained a distributive phosphorolytic activity, which contributes to rRNA maturation processes, the hallmark of exosome function. High-density mapping of 3′ extremities of rRNA maturation intermediates reveals the intricate interplay between three exoribonucleolytic activities coordinated by the plant exosome. Interestingly, the analysis of RRP41 protein diversity across eukaryotes suggests that Exo9’s intrinsic activity operates throughout the green lineage, and possibly in some earlier-branching non-plant eukaryotes. Our results reveal a remarkable evolutionary variation of this essential RNA degradation machine in eukaryotes.

How distal regulatory elements control gene transcription and chromatin topology is not clearly defined, yet these processes are closely linked in lineage specification during development. Through allele-specific genome editing and chromatin interaction analyses of the Sox2 locus in mouse embryonic stem cells, we found a striking disconnection between transcriptional control and chromatin architecture. We traced nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletions have no effect on promoter–enhancer interaction frequencies or topological domain organization. Local chromatin architecture maintenance, including at the topologically associating domain (TAD) boundary downstream from the Sox2 enhancer, is widely distributed over multiple transcription factor-bound regions and maintained in a CTCF-independent manner. Furthermore, partial disruption of promoter–enhancer interactions by ectopic chromatin loop formation has no effect on Sox2 transcription. These findings indicate that many transcription factors are involved in modulating chromatin architecture independently of CTCF.

Capture Hi-C (CHi-C) is a new technique for assessing genome organization based on chromosome conformation capture coupled to oligonucleotide capture of regions of interest, such as gene promoters. Chromatin loop detection is challenging because existing Hi-C/4C-like tools, which make different assumptions about the technical biases presented, are often unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined with limited filtering to detect DNA looping interactions, integrating information from biological replicates. ChiCMaxima shows more stringency and robustness compared to previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-C profiles alongside epigenomic tracks. Electronic supplementary material The online version of this article (10.1186/s13059-019-1706-3) contains supplementary material, which is available to authorized users.

21Capture Hi-C (CHi-C) is a new technique for assessing genome organization, based on 22 chromosome conformation capture coupled to oligonucleotide capture of regions of interest 23 such as gene promoters. Chromatin loop detection is challenging, since existing Hi-C/4C-like 24 analyses, which make different assumptions about the technical biases presented, are often 25 unsuitable. We describe a new approach, ChiCMaxima, which uses local maxima combined 26 with a background model to detect DNA looping interactions, integrating information from 27 biological replicates. ChiCMaxima shows more stringency and robustness compared to 28 previously developed tools. The tool includes a GUI browser for flexible visualization of CHi-29 C profiles alongside epigenomic tracks. 30Background 35 The advent of the chromosome conformation capture (3C) technology [1] allowed higher-order 36 chromosome folding to be inferred by identifying spatial proximity between distal genomic 37 sequences, leading to a comprehensive insight of genome topology. As sequencing throughput 38 has increased, it has become feasible to globally assess all chromatin interactions within a 39 population (4C: "one-to-all"; 5C: "many-to-many"; Hi-C: "all-to-all" methods) simply by 40 sequencing all 3C ligation products or a selected subset of them [2][3][4][5]. In fact, Hi-C interaction 41 maps can give insight into chromosome folding at different scales, depending on the sequencing 42 depth (and hence resolution) of the study [6, 7]. However, the strength of Hi-C in assessing all 43 possible chromatin interactions is also one of its major disadvantages: the numbers of possible 44 3 ligation products that can be detected is much greater than current sequencing output. Recently, 45 several groups have coupled Hi-C (or another 3C derivative) to sequence capture with pools of 46 oligonucleotides complementary to thousands of restriction fragment ends [8][9][10][11][12]. Such "CHi-47 C" (Capture Hi-C) methods allow the simultaneous and higher resolution mapping of chromatin 48 interactions for large subsets of the genome, such as all promoters or DNase hypersensitive 49 sites. For example, promoter-centered interactomes have already been used to assign 50 epigenomic status and follow enhancer looping dynamics throughout development, as well as 51 to characterize disease-linked intergenic sequence polymorphisms [13][14][15][16][17]. Despite being 52 highly informative, CHi-C datasets have specific properties that set them apart from other 3C-53 like techniques, which require specialized analytical tools to take these aspects into account. 54The majority of CHi-C strategies involve large numbers (thousands) of genomically dispersed 55 baits for which interacting regions are detected. The asymmetry between the number of baits 56 and the number of detected interacting regions leads to an asymmetry of CHi-C contact 57 matrices, confounding standard Hi-C normalization approaches. In addition, individual baits 58 have variable capture efficiencies which introduce...

How distal regulatory elements control gene transcription and chromatin topology is not clearly defined, yet these processes are closely linked in lineage specification during development. Through allele-specific genome editing and chromatin interaction analyses of the Sox2 locus in mouse embryonic stem cells, we found a striking disconnection between transcriptional control and chromatin architecture. We trace nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletions have no effect on promoter-enhancer interaction frequencies or topological domain organization. Local chromatin architecture maintenance, including at the topologically associating domain (TAD) boundary downstream of the Sox2 enhancer, is widely distributed over multiple transcription factor-bound regions and maintained in a CTCF-independent manner. Furthermore, disruption of promoter-enhancer interactions by ectopic chromatin loop formation has no effect on Sox2 expression. These findings indicate that many transcription factors are involved in modulating chromatin architecture independently of CTCF.