MYC activity at enhancers drives prognostic transcriptional programs through an epigenetic switch.

The transcription factor MYC is overexpressed in most cancers, where it drives multiple hallmarks of cancer progression. MYC is known to promote oncogenic transcription by binding to active promoters. In addition, MYC has also been shown to invade distal enhancers when expressed at oncogenic levels, but this enhancer binding has been proposed to have low gene-regulatory potential. Here, we demonstrate that MYC directly regulates enhancer activity to promote cancer type-specific gene programs predictive of poor patient prognosis. MYC induces transcription of enhancer RNA through recruitment of RNA polymerase II (RNAPII), rather than regulating RNAPII pause-release, as is the case at promoters. This process is mediated by MYC-induced H3K9 demethylation and acetylation by GCN5, leading to enhancer-specific BRD4 recruitment through its bromodomains, which facilitates RNAPII recruitment. We propose that MYC drives prognostic cancer type-specific gene programs through induction of an enhancer-specific epigenetic switch, which can be targeted by BET and GCN5 inhibitors.

Overview and Challenges of Large-Scale Cultivation of Photosynthetic Microalgae and Cyanobacteria.

Microalgae and cyanobacteria are diverse groups of organisms with great potential to benefit societies across the world. These organisms are currently used in food, feed, pharmaceutical and cosmetic industries. In addition, a variety of novel compounds are being isolated. Commercial production of photosynthetic microalgae and cyanobacteria requires cultivation on a large scale with high throughput. However, scaling up production from lab-based systems to large-scale systems is a complex and potentially costly endeavor. In this review, we summarise all aspects of large-scale cultivation, including aims of cultivation, species selection, types of cultivation (ponds, photobioreactors, and biofilms), water and nutrient sources, temperature, light and mixing, monitoring, contamination, harvesting strategies, and potential environmental risks. Importantly, we also present practical recommendations and discuss challenges of profitable large-scale systems associated with economical design, effective operation and maintenance, automation, and shortage of experienced phycologists.

Promoter sequence and architecture determine expression variability and confer robustness to genetic variants.

Genetic and environmental exposures cause variability in gene expression. Although most genes are affected in a population, their effect sizes vary greatly, indicating the existence of regulatory mechanisms that could amplify or attenuate expression variability. Here, we investigate the relationship between the sequence and transcription start site architectures of promoters and their expression variability across human individuals. We find that expression variability can be largely explained by a promoter's DNA sequence and its binding sites for specific transcription factors. We show that promoter expression variability reflects the biological process of a gene, demonstrating a selective trade-off between stability for metabolic genes and plasticity for responsive genes and those involved in signaling. Promoters with a rigid transcription start site architecture are more prone to have variable expression and to be associated with genetic variants with large effect sizes, while a flexible usage of transcription start sites within a promoter attenuates expression variability and limits genotypic effects. Our work provides insights into the variable nature of responsive genes and reveals a novel mechanism for supplying transcriptional and mutational robustness to essential genes through multiple transcription start site regions within a promoter.

Histone H4 lysine 20 mono-methylation directly facilitates chromatin openness and promotes transcription of housekeeping genes.

Histone lysine methylations have primarily been linked to selective recruitment of reader or effector proteins that subsequently modify chromatin regions and mediate genome functions. Here, we describe a divergent role for histone H4 lysine 20 mono-methylation (H4K20me1) and demonstrate that it directly facilitates chromatin openness and accessibility by disrupting chromatin folding. Thus, accumulation of H4K20me1 demarcates highly accessible chromatin at genes, and this is maintained throughout the cell cycle. In vitro, H4K20me1-containing nucleosomal arrays with nucleosome repeat lengths (NRL) of 187 and 197 are less compact than unmethylated (H4K20me0) or trimethylated (H4K20me3) arrays. Concordantly, and in contrast to trimethylated and unmethylated tails, solid-state NMR data shows that H4K20 mono-methylation changes the H4 conformational state and leads to more dynamic histone H4-tails. Notably, the increased chromatin accessibility mediated by H4K20me1 facilitates gene expression, particularly of housekeeping genes. Altogether, we show how the methylation state of a single histone H4 residue operates as a focal point in chromatin structure control. While H4K20me1 directly promotes chromatin openness at highly transcribed genes, it also serves as a stepping-stone for H4K20me3-dependent chromatin compaction.

Development of Growth Media from Agricultural By-Products for Cultivation of PUFA-Producing Sicyoidochytrium minutum.

The demand for novel sources of marine oils, which contain polyunsaturated fatty acids (PUFAs), has increased due to the realization of the importance of PUFAs, e.g., docosahexaenoic acid (DHA), in the human diet. However, the natural supply is limited. By-product peptones (BYPP) intended as a growth medium for the PUFA-producing strain Sicyoidochytrium minutum of family Thraustochytriaceae were produced after several experiments on the pancreatic digestion of bovine lungs and spleens. S. minutum was able to grow in a medium containing BYPP made from the pancreatic digestion of lung and spleen with glycerol, resulting in 1.14 ± 0.03 g cell dry weight (CDW)/L and 1.44 ± 0.24 g CDW/L, respectively, after 5 days of incubation at 25 °C, compared to 1.92 ± 0.25 g CDW/L in Basal Medium (BM) containing tryptone, peptone, and glycerol. The lipid content, obtained after growth in lung BYPP media with glycerol as a carbon source, was significantly higher (28.17% ± 1.33 of dry weight) than in the control basal medium (BM) (21.72% ± 2.45); however, DHA as a percentage of total fatty acids was lower in BYPP than in the control BM (25.24% ± 1.56 and 33.02% ± 2.37, respectively). It is concluded that low-value by-products from abattoirs can be used as ingredients for the cultivation of oligogenic Thraustochytriaceae.

High expression of the vacuole membrane protein 1 (VMP1) is a potential marker of poor prognosis in HER2 positive breast cancer.

BACKGROUND: Fusion genes result from genomic structural changes, which can lead to alterations in gene expression that supports tumor development. The aim of the study was to use fusion genes as a tool to identify new breast cancer (BC) genes with a role in BC progression. METHODS: Fusion genes from breast tumors and BC cell lines were collected from publications. RNA-Seq data from tumors and cell lines were retrieved from databanks and analyzed for fusions with SOAPfuse or the analysis was purchased. Fusion genes identified in both tumors (n = 1724) and cell lines (n = 45) were confirmed by qRT-PCR and sequencing. Their individual genes were ranked by selection criteria that included correlation of their mRNA level with copy number. The expression of the top ranked gene was measured by qRT-PCR in normal tissue and in breast tumors from an exploratory cohort (n = 141) and a validation cohort (n = 277). Expression levels were correlated with clinical and pathological factors as well as the patients' survival. The results were followed up in BC cohorts from TCGA (n = 818) and METABRIC (n = 2509). RESULTS: Vacuole membrane protein 1 (VMP1) was the most promising candidate based on specific selection criteria. Its expression was higher in breast tumor tissue than normal tissue (p = 1x10-4), and its expression was significantly higher in HER2 positive than HER2 negative breast tumors in all four cohorts analyzed. High expression of VMP1 associated with breast cancer specific survival (BCSS) in cohort 1 (hazard ratio (HR) = 2.31, CI 1.27-4.18) and METABRIC (HR = 1.26, CI 1.02-1.57), and also after adjusting for HER2 expression in cohort 1 (HR = 2.03, CI 1.10-3.72). BCSS was not significant in cohort 2 or TCGA cohort, which may be due to differences in treatment regimens. CONCLUSIONS: The results suggest that high VMP1 expression is a potential marker of poor prognosis in HER2 positive BC. Further studies are needed to elucidate how VMP1 could affect pathways supportive of tumorigenesis.

Isolation, Characterization and Biotechnological Potentials of Thraustochytrids from Icelandic Waters.

The following study reports on the first thraustochytrid isolates identified from Iceland. They were collected from three different locations off the northern coast of the country (Location A, Skagaströnd; Location B, Hveravík; and Location C, Eyjafjörður). Using 18S rDNA sequence analysis, isolates from Locations A and B were identified within the Thraustochytrium kinnei species while other isolates within the Sicyoidochytrium minutum species when compared to other known strains. Cells isolated from Locations A ( 2 . 10 ± 0 . 70 g/L) and B ( 1 . 54 ± 0 . 17 g/L) produced more biomass than the ones isolated from Location C ( 0 . 43 ± 0 . 02 g/L). This study offers the first-time examination of the utility of byproducts from fisheries as a nitrogen source in media formulation for thraustochytrids. Experiments showed that isolates produced more biomass (per unit of substrate) when cultured on nitrogen of marine ( 2 . 55 ± 0 . 74 g/L) as compared to of commercial origin (  1 . 06 ± 0 . 57 g/L). Glycerol ( 2 . 43 ± 0 . 56 g/L) was a better carbon source than glucose ( 1 . 84 ± 0 . 57 g/L) in growth studies. Fatty acid (FA) profiles showed that the isolates from Location C (S. minutum) had low ratios of monounsaturated ( 4 . 21 ± 2 . 96 % ) and omega-6 ( 0 . 68 ± 0 . 59 % ) FAs. However, the isolates also had high ratios of docosahexaenoic acid (DHA; 35 . 65 ± 1 . 73 % ) and total omega-3 FAs ( 40 . 39 ± 2 . 39 % ), indicating that they could serve as a source of marine oils for human consumption and in aquaculture feeds. The T. kinnei isolates from Location A could be used in biodiesel production due to their high ratios of monounsaturated ( 18 . 38 ± 6 . 27 % ) long chain ( 57 . 43 ± 8 . 27 % ) FAs.

Antimicrobial Activity of Marine Bacterial Symbionts Retrieved from Shallow Water Hydrothermal Vents.

Marine sponges and other sessile macro-organisms were collected at a shallow water hydrothermal site in Eyjafjörður, Iceland. Bacteria were isolated from the organisms using selective media for actinomycetes, and the isolates were screened for antimicrobial activity. A total of 111 isolates revealed antimicrobial activity displaying different antimicrobial patterns which indicates production of various compounds. Known test strains were grown in the presence of ethyl acetate extracts from one selected isolate, and a clear growth inhibition of Staphylococcus aureus was observed down to 0.1 % extract concentration in the medium. Identification of isolates shows different species of Actinobacteria with Streptomyces sp. playing the largest role, but also members of Bacilli, Alphaproteobacteria and Gammaproteobacteria. Sponges have an excellent record regarding production of bioactive compounds, often involving microbial symbionts. At the hydrothermal vents, however, the majority of active isolates originated from other invertebrates such as sea anemones or algae. The results indicate that antimicrobial assays involving isolates in full growth can detect activity not visible by other methods. The macro-organisms inhabiting the Eyjafjörður hydrothermal vent area host diverse microbial species in the phylum Actinobacteria with antimicrobial activity, and the compounds responsible for the activity will be subject to further research.

Contamination of cooked peeled shrimp (Pandalus borealis) by Listeria monocytogenes during processing at two processing plants.

Listeria spp. and Listeria monocytogenes contamination was evaluated in cooked peeled shrimp (final or semifinal product, 82 samples) and the shrimp-processing environment (two plants, 613 samples) in eight surveys conducted from 1998 through 2001. Listeria was detected in 12.5% (78) of the 695 samples (11.2% of the samples were positive for L. monocytogenes), but none of the samples of final product contained Listeria. One hundred seventy-two L. monocytogenes isolates were characterized by pulsed-field gel electrophoresis. Cleavage with macrorestriction enzymes AscI and ApaI yielded 14 different pulsotypes in the plants; two types were dominant, one in each plant. Sixty-three of the 106 isolates in plant A and 43 of the 66 isolates in plant B were of the dominant types. Certain strains, mainly of serotypes 1/2c and 4b and pulsotypes 1A and 2H, were persistent for long periods in both plants. Adaptation of good hygienic practices in the processing plants, including strict rules concerning traffic of staff and equipment, and existing hygienic requirements appeared to be effective in preventing contamination between areas within plants and in the final product. The persistence of Listeria strains in these two processing plants indicates the importance of detecting the places in the processing environment (e.g., transporters, equipment, floors, and drains) where L. monocytogenes can survive so that cleaning and disinfection efforts can be directed to such niches.

Tracing Listeria monocytogenes isolates from cold-smoked salmon and its processing environment in Iceland using pulsed-field gel electrophoresis.

Listeria spp. and Listeria monocytogenes contamination of cold-smoked salmon (n=125) and its processing environment (n=522) were evaluated during surveys conducted in 1997-1998 and 2001 as well as in samples of final products analysed in 2001. The overall frequencies of Listeria spp. and L. monocytogenes in samples from all sources were 15.1% and 11.3%, respectively, but the incidence of L. monocytogenes in cold-smoked salmon final products was only 4%. A total of 201 L. monocytogenes isolates were characterised by Pulsed-Field Gel Electrophoresis (PFGE) in order to trace L. monocytogenes contamination in the processing plants. The combination of AscI and ApaI macrorestriction patterns yielded 24 different pulsotypes in 6 plants. One pulsotype observed by AscI restriction digestion comprised 148 of the 167 typed isolates from two processing plants. Two other pulsotypes predominated in samples from raw material, processing environments and final products. The results indicate that raw material, floors, and drains are potential sources of the L. monocytogenes found on cold-smoked salmon products. This highlights the need to readdress the design and cleaning of processing plants and equipment, and staff behavior. Hindering the introduction into and spread of the organism through the processing environment is necessary to avoid jeopardizing safety of the final product.