Journal: Genes & Development

Article Title: Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

doi: 10.1101/gad.328971.119

Figure Lengend Snippet: Extensive genome shuffling during Drosophila evolution. ( A , top ) Hypothetical whole-genome alignments. If no rearrangements have occurred between two species, whole-genome alignments result in matches that perfectly align at the diagonal ( left ). If there was a link between linear proximity and synteny breakpoints, matches would be expected to converge near the diagonal ( middle ). If shuffling happens without linear proximity, matches would occur randomly throughout the whole-chromosome arms ( right ). ( Bottom ) Dotplots showing actual whole-genome alignments between D. melanogaster and D. busckii or D. virilis , respectively. Alignments were performed using Mummer4 . Forward matches (+ strand) are shown in red; reverse matches (− strand) are displayed in blue. Corresponding chromosome arms are indicated with boxes that are displayed connected if chromosome arms are fused in one species. Karyotypes are additionally depicted in Supplemental Figure S2A . ( B ) Association between TAD boundaries and synteny block breakpoints. From the exterior to the interior of the Circos plot. (Turquoise) The 18.80–19.90 Mb region of the chromosome 3L in D. virilis , (light blue) the 15.37–16.47 Mb of the chromosome 3L in D. melanogaster , (heatmaps) Hi-C contact heatmaps with TADs displayed as black triangles, (black radial lines) TAD boundaries, (magenta radial lines) TAD boundaries overlapping with synteny block start or end sites, (gray blocks) genes, (red blocks) BUSCOs, (orange blocks) synteny blocks, (orange arc) conserved synteny block between D. virilis and D. melanogaster in the displayed regions, (red arcs) conserved BUSCOs in the displayed regions.

Article Snippet: D. busckii flies were additionally fed with instant Drosophila medium (Formula 4–24, Carolina Biological Supply Company, catalog number 173202) mixed with instant potato powder on top of the standard Drosophila medium.

Techniques: Blocking Assay, Hi-C

Journal: Genes & Development

Article Title: Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling

doi: 10.1101/gad.328971.119

Figure Lengend Snippet: Enriched Hi-C contacts between binding sites of the dosage compensation complex are maintained throughout Drosophila evolution despite genome shuffling. ( A ) Aggregate Hi-C matrices around pairwise HAS–HAS contacts in D. melanogaster , D. busckii , and D. virilis compared to random and random active (sites in the A compartment within SBs) pairwise contacts. Displayed are the mean observed over expected contacts ratios of corrected Hi-C matrices with an ∼1.7-kb bin size of ∼250 HAS that are on the X chromosome ( n = 246, 213, and 247 in D. melanogaster , D. busckii , and D. virilis , respectively) or a respective number of random regions on the X chromosome. Scheme illustrating the generation of aggregate Hi-C matrices (aggregate plots). ( B ) Distance of HAS used in A to closest TAD boundary compared to the respective number of random sites. ( C ) Aggregate Hi-C matrices centered on TAD boundaries with the lowest insulation score on the X chromosome in D. melanogaster , D. busckii , and D. virilis ( n = 246, 213 and 247 in D. melanogaster , D. busckii , and D. virilis , respectively), and HAS mirrored at their closest TAD boundary (“mirrored” HAS). TAD boundaries show enriched contacts but “mirrored” HAS show no enriched contacts. ( D ) Gene expression (normalized counts) of genes overlapping with HAS compared to “mirrored” HAS is not significantly different (n.s.) by Wilcoxon rank-sum test. Comparison of gene expression was performed using library-size normalized RNA-seq counts from 14- to 20-h aged embryos from modENCODE data sets obtained from and also available on the Chorogenome web server ( http://chorogenome.ie-freiburg.mpg.de/ ). ( E ) Aggregate Hi-C matrices around HAS–HAS or TSS–TSS contacts of genes with equally high expression as genes overlapping with HAS or highly expressed genes in D. melanogaster ( n = 209). Underlying gene expression values are shown in Supplemental Figure S7D . ( F ) Fraction of total orthologous genes (gray) and orthologous genes in common between D. melanogaster and D. busckii (orange) at HAS ( n = 195), at random positions defined in the X chromosome A (active) compartment ( n = 175), at HAS extended by 30 kb in 5′ and 3′ direction ( n = 1380), and at 60-kb random regions defined in the X chromosome A (active) compartment ( n = 838). Reported values are calculated in D. melanogaster . Two-sided two-proportions z -test P -values are shown on the right of the bar plot. Orthologs between D. melanogaster and D. virilis were retrieved from FlyBase.

Article Snippet: D. busckii flies were additionally fed with instant Drosophila medium (Formula 4–24, Carolina Biological Supply Company, catalog number 173202) mixed with instant potato powder on top of the standard Drosophila medium.

Techniques: Hi-C, Binding Assay, Insulation, Gene Expression, Comparison, RNA Sequencing, Expressing

Journal: Autophagy

Article Title: Isorhynchophylline, a natural alkaloid, promotes the degradation of alpha-synuclein in neuronal cells via inducing autophagy.

doi: 10.4161/auto.8.1.18313

Figure Lengend Snippet: Figure 4. IsoRhy induced autophagy in L3 Drosophila larvae fat body. (A) Ninety six hours after egg laying, the L3 larvae were collected and fed on culture medium containing 0.2 mg/ml of IsoRhy for 6 h and fat bodies were isolated for LysoTracker staining. Images were captured using a fluorescence microscope. As positive control, L3 larvae were either fed with 5 mM of rapamycin for 24 h or starved for 3 h to induce autophagy. (B) Quantification of lysotracker-positive spots in each group. Data were presented as the mean ± SEM of one representative experiment from three independent experiments. (***p , 0.001, one-way ANOVA for multiple comparison and Tukey’s test as post hoc test).

Article Snippet: The instant Drosophila food (173212) was purchased from Carolina Biological Supply Company.

Techniques: Isolation, Staining, Fluorescence, Microscopy, Positive Control, Comparison