The Drosophila insulator proteins CTCF and CP190 link enhancer blocking to body patterning

Insulator sequences guide the function of distantly located enhancer elements to the appropriate target genes by blocking inappropriate interactions. In Drosophila, five different insulator binding proteins have been identified, Zw5, BEAF-32, GAGA factor, Su(Hw) and dCTCF. Only dCTCF has a known conserved counterpart in vertebrates. Here we find that the structurally related factors dCTCF and Su(Hw) have distinct binding targets. In contrast, the Su(Hw) interacting factor CP190 largely overlapped with dCTCF binding sites and interacts with dCTCF. Binding of dCTCF to targets requires CP190 in many cases, whereas others are independent of CP190. Analysis of the bithorax complex revealed that six of the borders between the parasegment specific regulatory domains are bound by dCTCF and by CP190 in vivo. dCTCF null mutations affect expression of Abdominal-B, cause pharate lethality and a homeotic phenotype. A short pulse of dCTCF expression during larval development rescues the dCTCF loss of function phenotype. Overall, we demonstrate the importance of dCTCF in fly development and in the regulation of abdominal segmentation.     

Retrovirus silencer blocking by the cHS4 insulator is CTCF independent

Silencing of retrovirus vectors poses a significant obstacle to genetic manipulation of stem cells and their use in gene therapy. We describe a mammalian silencer blocking assay using insulator elements positioned between retrovirus silencer elements and an LCRβ-globin reporter transgene. In transgenic mice, we show that retrovirus silencers are blocked by the cHS4 insulator. Silencer blocking is independent of the CTCF binding site and is most effective when flanking the internal reporter transgene. These data distinguish silencer blocking activity by cHS4 from its enhancer blocking activity. Retrovirus vectors can be created at high titer with one but not two internal dimer cHS4 cores. cHS4 in the LTRs has no effect on expression in transduced F9 cells, suggesting that position effect blocking is not sufficient to escape silencing. The Drosophila insulators gypsy and Scs fail to block silencing in transgenic mice, but gypsy stimulates vector expression 2-fold when located in the LTRs of an infectious retrovirus. The silencer blocking assay complements existing insulator assays in mammalian cells, provides new insight into mechanisms of insulation and is a valuable tool to identify additional silencer blocking insulators that cooperate with cHS4 to improve stem cell retrovirus vector design.     

Off-target effects of psychoactive drugs revealed by genome-wide assays in yeast

To better understand off-target effects of widely prescribed psychoactive drugs, we performed a comprehensive series of chemogenomic screens using the budding yeast Saccharomyces cerevisiae as a model system. Because the known human targets of these drugs do not exist in yeast, we could employ the yeast gene deletion collections and parallel fitness profiling to explore potential off-target effects in a genome-wide manner. Among 214 tested, documented psychoactive drugs, we identified 81 compounds that inhibited wild-type yeast growth and were thus selected for genome-wide fitness profiling. Many of these drugs had a propensity to affect multiple cellular functions. The sensitivity profiles of half of the analyzed drugs were enriched for core cellular processes such as secretion, protein folding, RNA processing, and chromatin structure. Interestingly, fluoxetine (Prozac) interfered with establishment of cell polarity, cyproheptadine (Periactin) targeted essential genes with chromatin-remodeling roles, while paroxetine (Paxil) interfered with essential RNA metabolism genes, suggesting potential secondary drug targets. We also found that the more recently developed atypical antipsychotic clozapine (Clozaril) had no fewer off-target effects in yeast than the typical antipsychotics haloperidol (Haldol) and pimozide (Orap). Our results suggest that model organism pharmacogenetic studies provide a rational foundation for understanding the off-target effects of clinically important psychoactive agents and suggest a rational means both for devising compound derivatives with fewer side effects and for tailoring drug treatment to individual patient genotypes.     

A multifunctional turnip crinkle virus replication enhancer revealed by in vivo functional SELEX

The motif1-hairpin (M1H), located on (-)-strands of Turnip Crinkle Virus (TCV)-associated satellite RNA C (satC), is a replication enhancer and recombination hotspot. Results of in vivo genetic selection (SELEX: systematic evolution of ligands by exponential enrichment), where 28 bases of the M1H were randomized and then subjected to selection in plants, revealed that most winners contained one to three short motifs, many of which in their (-)-sense orientation are found in TCV and satC (-)-strand promoter elements. Ability to replicate in protoplasts correlated with fitness to accumulate in plants with one significant exception. Winner UC, containing only a seven-base replacement sequence, was the second most fit winner, yet replicated no better than a 28-base random replacement sequence. Fitness of satC containing different M1H replacement sequences could be due to enhanced satC replication or enhanced ability to affect TCV movement, since satC interferes with TCV virion accumulation, which is correlated with enhanced movement to younger tissue. Cells inoculated with TCV and UC accumulated fewer virions when compared to other winners that replicated better in protoplasts but were less fit in plants. UC, and other first and second round winners, contained structures that were on average 33% more stable in their (+)-strand orientation, and most formed hairpins with a A-rich sequence at the base. These results suggest that M1H replacement sequences contribute to the fitness of satC by either containing (-)-strand elements that enhance satRNA replication and/or a (+)-strand hairpin flanked with single-stranded sequence that enhances TCV movement.     

Differences in the properties of antibodies and natural antiglobulin-homoreactants revealed by the method of human IgG chemical modification]

The naturally occurring antiglobulin factors - homoreactants, contained by human IgG preparations, are inactivated as a result of incubation in a solution of sodium rhodanide (3 - 5 M) and sodium desoxycholate (0.005M). Staphylococcal antitoxin contained by the same human IgG preparations is resistant to the action of the reagents. The data obtained indicate the differences in the structure of homoreactants and antibodies.     

Differences in the biophysical properties of membrane and cytoplasm of apoptotic cells revealed using dielectrophoresis

We have used dielectrophoresis to determine the dielectric properties of human chronic myelogeneous leukaemic (K562) cells during apoptosis (programmed cell death). Our results indicate that K562 cells increase markedly in cytoplasmic conductivity from 0.28 S/m to 0.50 S/m within the first 4 h following treatment with staurosporine, which then lasts beyond 12 h, whilst cell shrinkage increases the capacitance of the membrane from 9.7 mF/m2 to 20 mF/m2. After 24 and 48 h of incubation with staurosporine, multiple sub-populations were detected, highlighted by the dielectric changes that the cell undergoes before death. By comparing these results with those obtained by common apoptosis monitoring techniques Annexin V and TMRE (tetramethylrhodamine ethylester), it is possible to infer the role of ion efflux in the progress of apoptosis. The use of dielectrophoresis for monitoring apoptosis offers a number of benefits as it is both rapid and non-invasive. It can also be used in parallel with other assays in high-throughput screening applications.     

Differences in cue-dependent spatial navigation may be revealed by in-depth swimming analysis

Several factors can influence allocentric navigation in the Morris water maze (MWM), including the number of available distal visual cues. Using in-depth analytical measures investigating platform-based and swimming behaviour, we examine and compare animals exposed to either one or three distal visual cues during MWM acquisition. We demonstrate that, although animals exposed to one cue can acquire the task as well as those in a multiple cue condition, several subtle differences between the groups’ swimming behaviours are noted. Both groups actively use cues to guide them to the platform, but changing the number of cues alters the animals’ patterns of behaviour, wherein exposure to a single cue leads to a simpler strategy in which the cue appears to act as a beacon for navigation.     

The two faces of the purple membrane. II. Differences in surface charge properties revealed by ferritin binding.

The two faces of the purple membrane of Halobacterium halobium possess different surface charge densities. The binding of ferritin to the two faces as a function of pH and ionic strength was investigated by electron microscopy. The combination of these experiments with metal decoration reveals that one the extracellular face is relatively homogeneous with respect to the pK values of its titrable groups pK values approx. 3 to 3.6) whereas the opposite face shows two distinct ranges of pK values, centred at about pK 2 and 4.2. Below pH 3 and between pH 4 and 5 this face carries the higher surface charge density.     

Differences in black pigmentation in lepidopteran cuticles as revealed by light and electron microscopy

Summary Black cuticles of larvae and pupae from various Lepidoptera were studied by light and electron microscopy. There are striking differences in the representation of black pigmentation, especially at the ultrastructural level. Two types may be described: 1. With the light microscope black melanin-like grana, electron-dense electron microscopically, are found in the distal parts of the exocuticle. This type is demonstrated in larvae of Celerio euphorbiae, Papilio machaon, and Phalera bucephala. 2. With the light microscope a dark homogeneous layer in the distal exocuticle can be recognized, however, electron microscopically no structures correlated with this dark pigment layer. This type of pigmentation was present in pupae of Pieris brassicae and Aglais urticae; in Pieris larvae the dark pigmented layer appeared to be limited to the epicuticle. In Celerio processes of the epidermal cells are involved in transporting precursors to the exocuticle. The conclusion was reached that black pigmentation in cuticles is based on different mechanisms as proposed by structural features. The two likely mechanisms are melanization and sclerotization.This work was supported by the Deutsche Forschungsgemeinschaft (SFB 87, project A1, granted to Prof. Bückmann)     

Epigenetic blocking of an enhancer region controls irradiation-induced proapoptotic gene expression in Drosophila embryos

Drosophila embryos are highly sensitive to gamma-ray-induced apoptosis at early but not later, more differentiated stages during development. Two proapoptotic genes, reaper and hid, are upregulated rapidly following irradiation. However, in post-stage-12 embryos, in which most cells have begun differentiation, neither proapoptotic gene can be induced by high doses of irradiation. Our study indicates that the sensitive-to-resistant transition is due to epigenetic blocking of the irradiation-responsive enhancer region (IRER), which is located upstream of reaper but is also required for the induction of hid in response to irradiation. This IRER, but not the transcribed regions of reaper/hid, becomes enriched for trimethylated H3K27/H3K9 and forms a heterochromatin-like structure during the sensitive-to-resistant transition. The functions of histone-modifying enzymes Hdac1(rpd3) and Su(var)3-9 and PcG proteins Su(z)12 and Polycomb are required for this process. Thus, direct epigenetic regulation of two proapoptotic genes controls cellular sensitivity to cytotoxic stimuli.