Identification and characterization of ToRC, a novel ISWI-containing ATP-dependent chromatin assembly complex.

SNF2-like motor proteins, such as ISWI, cooperate with histone chaperones in the assembly and remodeling of chromatin. Here we describe a novel, evolutionarily conserved, ISWI-containing complex termed ToRC (Toutatis-containing chromatin remodeling complex). ToRC comprises ISWI, Toutatis/TIP5 (TTF-I-interacting protein 5), and the transcriptional corepressor CtBP (C-terminal-binding protein). ToRC facilitates ATP-dependent nucleosome assembly in vitro. All three subunits are required for its maximal biochemical activity. The toutatis gene exhibits strong synthetic lethal interactions with CtBP. Thus, ToRC mediates, at least in part, biological activities of CtBP and Toutatis. ToRC subunits colocalize in euchromatic arms of polytene chromosomes. Furthermore, nuclear localization and precise distribution of ToRC in chromosomes are dependent on CtBP. ToRC is involved in CtBP-mediated regulation of transcription by RNA polymerase II in vivo. For instance, both Toutatis and CtBP are required for repression of genes of a proneural gene cluster, achaete-scute complex (AS-C), in Drosophila larvae. Intriguingly, native C-terminally truncated Toutatis isoforms do not associate with CtBP and localize predominantly to the nucleolus. Thus, Toutatis forms two alternative complexes that have differential distribution and can participate in distinct aspects of nuclear DNA metabolism.

Novel homogeneous photocatalyst for oxygen to hydrogen peroxide reduction in aqueous media.

An isoquinolinium-pyrrole donor-acceptor dyad was found to exhibit photocatalytic activity in oxygen-to-peroxide photoreduction with oxalate as a sacrificial electron donor. The concentration of hydrogen peroxide was shown to reach a plateau of 0.57 mM. The screening of related pyridinium-pyrrole dyads showed the importance of the isoquinoline moiety in securing the photocatalytic activity.

PEG-modified aziridines for stereoselective synthesis of water-soluble fulleropyrrolidines.

Diastereoselective synthesis of water-soluble fullerene compounds bearing a pharmacophore pyrrolofullerene-2',5'-dicarboxylate unit is reported. The stereocontrol of the product configuration is achieved through stereospecificity of two consecutive concerted reactions: electrocyclic aziridine ring opening followed by 1,3-dipolar cycloaddition of the resulting azomethyne ylide. The solubility in water (up to 20 µM through direct dissolution) is secured by introducing a polyethylene glycol (PEG) hydrophilic pendant. The structure and molecular-mass distribution of the resulting PEGylated fulleropyrrolidines are exhaustively characterized by 1H, 13C NMR and HRMS. According to absorbance spectroscopy, AFM and DLS studies, the synthesized compound tends to aggregate in aqueous media forming associates of ca. 4-9 nm radius surrounded by a solvation shell resulting in an effective hydrodynamic diameter of ca. 90 nm. In view of notable solubility in water, well-defined chemical structure and resemblance to the compounds with known anti-HIV activity, the synthesized PEGylated diethyl trans-pyrrolofullerene-2',5'-dicarboxylate might be an attractive candidate for biological evaluation.

Diastereospecific and Highly Site-Selective Functionalization of C70 Fullerene by a Reaction with Diethyl N-Arylaziridine-2,3-dicarboxylates.

The diastereospecific and highly site-selective cycloaddition of N-arylazomethine ylides generated in situ from diethyl N-arylaziridine-2,3-dicarboxylates to C70 fullerene is reported. The reaction provides C70 fulleropyrrolidines in up to hundreds on a milligram scale as α- and ß-adducts in a 4:1 ratio with a controlled stereochemical outcome: cis-aziridines give exclusively trans-adducts, and trans-aziridines give only cis-adducts. The 1H and 13C{1H} NMR spectra for different isomeric adducts were recorded and analyzed to identify some characteristic features, which permit an easy identification of isomeric adducts of this type.

Partially Assembled Nucleosome Structures at Atomic Detail.

The evidence is now overwhelming that partially assembled nucleosome states (PANS) are as important as the canonical nucleosome structure for the understanding of how accessibility to genomic DNA is regulated in cells. We use a combination of molecular dynamics simulation and atomic force microscopy to deliver, in atomic detail, structural models of three key PANS: the hexasome (H2A·H2B)·(H3·H4)2, the tetrasome (H3·H4)2, and the disome (H3·H4). Despite fluctuations of the conformation of the free DNA in these structures, regions of protected DNA in close contact with the histone core remain stable, thus establishing the basis for the understanding of the role of PANS in DNA accessibility regulation. On average, the length of protected DNA in each structure is roughly 18 basepairs per histone protein. Atomistically detailed PANS are used to explain experimental observations; specifically, we discuss interpretation of atomic force microscopy, Förster resonance energy transfer, and small-angle x-ray scattering data obtained under conditions when PANS are expected to exist. Further, we suggest an alternative interpretation of a recent genome-wide study of DNA protection in active chromatin of fruit fly, leading to a conclusion that the three PANS are present in actively transcribing regions in a substantial amount. The presence of PANS may not only be a consequence, but also a prerequisite for fast transcription in vivo.

A role for tuned levels of nucleosome remodeler subunit ACF1 during Drosophila oogenesis.

The Chromatin Accessibility Complex (CHRAC) consists of the ATPase ISWI, the large ACF1 subunit and a pair of small histone-like proteins, CHRAC-14/16. CHRAC is a prototypical nucleosome sliding factor that mobilizes nucleosomes to improve the regularity and integrity of the chromatin fiber. This may facilitate the formation of repressive chromatin. Expression of the signature subunit ACF1 is restricted during embryonic development, but remains high in primordial germ cells. Therefore, we explored roles for ACF1 during Drosophila oogenesis. ACF1 is expressed in somatic and germline cells, with notable enrichment in germline stem cells and oocytes. The asymmetrical localization of ACF1 to these cells depends on the transport of the Acf1 mRNA by the Bicaudal-D/Egalitarian complex. Loss of ACF1 function in the novel Acf1(7) allele leads to defective egg chambers and their elimination through apoptosis. In addition, we find a variety of unusual 16-cell cyst packaging phenotypes in the previously known Acf1(1) allele, with a striking prevalence of egg chambers with two functional oocytes at opposite poles. Surprisingly, we found that the Acf1(1) deletion--despite disruption of the Acf1 reading frame--expresses low levels of a PHD-bromodomain module from the C-terminus of ACF1 that becomes enriched in oocytes. Expression of this module from the Acf1 genomic locus leads to packaging defects in the absence of functional ACF1, suggesting competitive interactions with unknown target molecules. Remarkably, a two-fold overexpression of CHRAC (ACF1 and CHRAC-16) leads to increased apoptosis and packaging defects. Evidently, finely tuned CHRAC levels are required for proper oogenesis.

Linker histone H1 is essential for Drosophila development, the establishment of pericentric heterochromatin, and a normal polytene chromosome structure.

We generated mutant alleles of Drosophila melanogaster in which expression of the linker histone H1 can be down-regulated over a wide range by RNAi. When the H1 protein level is reduced to approximately 20% of the level in wild-type larvae, lethality occurs in the late larval - pupal stages of development. Here we show that H1 has an important function in gene regulation within or near heterochromatin. It is a strong dominant suppressor of position effect variegation (PEV). Similar to other suppressors of PEV, H1 is simultaneously involved in both the repression of euchromatic genes brought to the vicinity of pericentric heterochromatin and the activation of heterochromatic genes that depend on their pericentric localization for maximal transcriptional activity. Studies of H1-depleted salivary gland polytene chromosomes show that H1 participates in several fundamental aspects of chromosome structure and function. First, H1 is required for heterochromatin structural integrity and the deposition or maintenance of major pericentric heterochromatin-associated histone marks, including H3K9Me(2) and H4K20Me(2). Second, H1 also plays an unexpected role in the alignment of endoreplicated sister chromatids. Finally, H1 is essential for organization of pericentric regions of all polytene chromosomes into a single chromocenter. Thus, linker histone H1 is essential in Drosophila and plays a fundamental role in the architecture and activity of chromosomes in vivo.

Synthesis of new porphyrin-fullerene dyads capable of forming charge-separated states on a microsecond lifetime scale.

A series of covalently linked axially symmetric porphyrin-fullerene dyads with a rigid pyrrolo[3,4-c]pyrrolic linker enabling a fixed and orthogonal arrangement of the chromophores has been synthesized and studied by means of transient absorption spectroscopy and cyclic voltammetry. The lifetime of the charge-separated state has been found to depend on the substituents on the porphyrin core, reaching up to 4 µs for a species with meso-(p-MeOC6H4) substituents. The ground and excited electronic states of model compounds have been calculated at the DFT and TD-DFT B3LYP(6-31G(d)) levels of theory and analyzed with regard to the effect of the substituent on the stabilization of the charge-separated state in the porphyrin-fullerene ensemble with a view to explaining the observed dependence.

Synthesis and spectroscopic and electrochemical properties of an axially symmetric fullerene-porphyrin dyad with a rigid pyrrolo[3,4-c]pyrrole spacer.

A new approach to porphyrinofullerene donor-acceptor dyads, based on consecutive 1,3-dipolar cycloaddition of azomethine ylides, generated from bis-aziridinedicarboxylate, to C60 and to porphyrin with a maleimidophenyl substituent, was developed. A synthesis of the axially symmetric porphyrin-fullerene-C60 ensemble 5 with a novel rigid pyrrolo[3,4-c]pyrrolic linker was realized. Theoretical, electrochemical, and spectroscopic studies of compound 5 showed that it is capable of forming a charge-separated state.

Protein complex of Drosophila ATRX/XNP and HP1a is required for the formation of pericentric beta-heterochromatin in vivo.

ATRX belongs to the family of SWI2/SNF2-like ATP-dependent nucleosome remodeling molecular motor proteins. Mutations of the human ATRX gene result in a severe genetic disorder termed X-linked alpha-thalassemia mental retardation (ATR-X) syndrome. Here we perform biochemical and genetic analyses of the Drosophila melanogaster ortholog of ATRX. The loss of function allele of the Drosophila ATRX/XNP gene is semilethal. Drosophila ATRX is expressed throughout development in two isoforms, p185 and p125. ATRX185 and ATRX125 form distinct multisubunit complexes in fly embryo. The ATRX185 complex comprises p185 and heterochromatin protein HP1a. Consistently, ATRX185 but not ATRX125 is highly concentrated in pericentric beta-heterochromatin of the X chromosome in larval cells. HP1a strongly stimulates biochemical activities of ATRX185 in vitro. Conversely, ATRX185 is required for HP1a deposition in pericentric beta-heterochromatin of the X chromosome. The loss of function allele of the ATRX/XNP gene and mutant allele that does not express p185 are strong suppressors of position effect variegation. These results provide evidence for essential biological functions of Drosophila ATRX in vivo and establish ATRX as a major determinant of pericentric beta-heterochromatin identity.

Bisaziridine tetracarboxylates as building blocks in the stereoselective synthesis of C60-fullerene diads and dumbbell-like bis-C60-fullerene triads.

The synthesis of alkoxycarbonyl-substituted bisaziridines with the two aziridine units connected by conjugated p-phenylene, partly conjugated 1,1'-biphenyl-4,4'-diyl, and nonconjugated 4,4'-methylenediphenyl linkers was developed. The reaction of azomethine ylides derived from the bisaziridines with fullerene C(60) was optimized and used for the stereoselective preparation of both the monoadducts (C(60)-linker-aziridine dicarboxylate), and the dumbbell bisadducts (C(60)-linker-C(60)). The reasons for the observed selectivity of the azomethine ylide formation and cycloaddition were theoretically studied at the DFT B3LYP/6-31G(d) level or at the ONIOM B3LYP/6-31G(d):B3LYP/STO-3G level for fullerene-containing molecules.

An efficient approach to azirino and pyrrolo-fused dibenzazepines. Conformations of substituted dibenzo[c,f]pyrrolo[1,2-a]azepines.

An effective approach to azepino-fused heterocycles is described. trans-1-Aryl-7,11b-dihydro-1H-azirino[1,2-a]dibenzo[c,f]azepines were synthesised via a domino sequence: isomerization of gem-dichloroaziridine-intramolecular Friedel-Crafts acylation of the tethered benzene ring catalysed by SnCl(4) and subsequent hydride induced intramolecular cyclization. Cycloaddition of dibenzazepinium ylides, generated by heating these aziridines, to activated C[double bond]C, C[triple bond]C dipolarophiles and fullerene C(60), leads to derivatives of dibenzo[c,f]pyrrolo[1,2-a]azepine. The reaction proceeds with complete stereoselectivity via cycloaddition of only W-ylide, which due to the high barrier does not undergo E,Z-isomerization under the reaction conditions. It was found that 2,3,9,13b-tetrahydro-1H-dibenzo[c,f]pyrrolo[1,2-a]azepine systems can exist in conformations of two types depending on the substituents at the pyrrolidine carbons in ß-position with respect to nitrogen. Details of cycloaddition reactions and the conformational behavior of cycloadducts were studied by DFT calculations at the B3LYP/6-31G(d) level.

Transcriptional activity of the telomeric retrotransposon HeT-A in Drosophila melanogaster is stimulated as a consequence of subterminal deficiencies at homologous and nonhomologous telomeres.

Drosophila melanogaster telomeres have two DNA domains: a terminal array of retrotransposons and a subterminal repetitive telomere-associated sequence (TAS), a source of telomere position effect (TPE). We reported previously that deletion of the 2L TAS array leads to dominant suppression of TPE by stimulating in trans expression of a telomeric transgene. Here, we compared the transcript activities of a w transgene inserted between the retrotransposon and TAS arrays at the 2L telomere in genotypes with different lengths of the 2L TAS. In contrast to individuals bearing a wild-type 2L homologue, flies with a TAS deficiency showed a significant increase in the level of telomeric w transcript during development, especially in pupae. Moreover, we identified a read-through w transcript initiated from a retrotransposon promoter in the terminal array. Read-through transcript levels also significantly increased with the presence of a 2L TAS deficiency in trans, indicating a stimulating force of the TAS deficiency on retrotransposon promoter activity. The read-through transcript contributes to total w transcript, although most w transcript originates at the w promoter. While silencing of transgenes in nonhomologous telomeres is suppressed by 2L TAS deficiencies, suggesting a global effect, the overall level of HeT-A transcripts is not increased under similar conditions.

Stereoselective cycloaddition of dibenzoxazepinium ylides to acetylenes and fullerene C60. Conformational behavior of 3-aryldibenzo[b,f]pyrrolo[1,2-d][1,4]oxazepine systems.

Cycloaddition of dibenzoxazepinium ylides to acetylene carboxylates leads to cis-3-aryl-3,13b-dihydrodibenzo[b,f]pyrrolo[1,2-d][1,4]oxazepinecarboxylates, which smoothly dehydrogenate to the corresponding pyrrole derivatives. The o-bromophenyl-substituted pyrrole, in contrast to the pyrroline analogue, demonstrates atropoisomerism. Stereoselective cycloaddition of dibenzoxazepinium ylides to fullerene C(60) gives rise to fulleropyrrolidines with cis-configuration. Restricted Ph group rotation is found in the phenyl derivative. Only one of two possible atropoisomers is formed in the reaction of o-bromophenyl-substituted ylide with fullerene C(60). Details of cycloaddition and conformational behavior of cycloadducts were studied by DFT computations.

Switching Competition between Electron and Energy Transfers in Porphyrin-Fullerene Dyads.

Porphyrin-fullerene dyads were intensively studied as molecular donor-acceptor systems providing efficient photoinduced charge separation (CS). A practical advantage of the dyads is the possibility to tune its CS process by the porphyrin periphery modification, which allows one to optimize the dyad for particular applications. However, this tuning process is typically composed of a series of trial stages involving the development of complex synthetic schemes. To address the issue, we synthesized a series of dyads with properties switching between electron and energy transfer in both polar (benzonitrile) and nonpolar (toluene) media and developed a computation procedure with sufficient reliability by which we can predict the CS properties of the dyad in different media and design new dyads. The dyads photochemistry was established by conducting ultrafast transient absorption studies in toluene, anisole, and benzonitrile. The most crucial step in computational modeling was to establish a procedure for correction of the electronic-state energies obtained by DFT so that the effects of the electron correlation and the long-range interactions are properly incorporated. We also carried out standard electrochemical measurements and show that our computation approach predicts better thermodynamics of the dyads in different solvents.

Abnormal activity of transcription factors gli in high-grade gliomas.

Malignant transformation is associated with loss of cell differentiation, anaplasia. Transcription factors gli, required for embryonic development, may be involved in this process. We studied the activity of transcription factors gli in high-grade gliomas and their role in maintenance of stem cell state and glioma cell survival. 20 glioma cell lines and a sample of a normal adult brain tissue were used in the present study. We found the expression of gli target genes, including GLI1 and FOXM1, in all tested glioma cell lines, but not in the normal tissue. Interestingly, the expression of gli target genes in some glioma cell lines was observed together with a high level of their transcriptional repressor, Gli3R. Knockdown of GLI3 in one of these lines resulted in decrease of gli target gene expression. These data suggest that Gli3R does not prevent the gli target genes transcription, and gli3 acts in glioma cells more as an activator, than a repressor of transcription. We observed that gli regulated the expression of such genes, as SOX2 or OCT4 that maintain stem cell state, and TET1, involving in DNA demethylation. Treatment with GANT61 or siRNA against GLI1, GLI2, or GLI3 could result in complete glioma cell death, while cyclopamine had a weaker and line-specific effect on glioma cell survival. Thus, the gli transcription factors are abnormally active in high-grade gliomas, regulate expression of genes, maintaining the stem cell state, and contribute to glioma cell survival.

Photocurrent in Multilayered Assemblies of Porphyrin-Fullerene Covalent Dyads: Evidence for Channels for Charge Transport.

Specially designed porphyrin-fullerene dyads have been synthesized to verify literature predictions based on quantum chemistry calculations that certain porphyrin-fullerene dyads are able to self-arrange into specific structures providing channels for charge transport in a bulk mass of organic compound. According to AFM and SEM data, the newly synthesized compounds were indeed prone to some kind of self-arrangement, although to a lesser degree than was expected. A dispersion corrected DFT study of the molecular non-covalent interactions performed at the DFT-D3 (B3LYP, 6-31G*) level of theory showed that the least energy corresponded to head-to-head dimers, with close contacts of porphyrin-porphyrin and fullerene-fullerene fragments, thus providing a unit building block of the channel for charge transport. Experimental proof for the existence of channels for charge transport was obtained by observing a photocurrent in a simple photovoltaic cell.

A deficiency screen for dominant suppressors of telomeric silencing in Drosophila.

Heterochromatin is a specialized chromatin structure in chromosomal regions associated with repeated DNA sequences and low concentrations of genes. Formation of heterochromatin is determined in large part by enzymes that modify histones and structural proteins that bind to these modified histones in a cooperative fashion. In Drosophila, mutations in genes that encode heterochromatic proteins are often dominant and increase expression of genes placed into heterochromatic positions. To find components of telomeric heterochromatin in Drosophila, we screened a collection of autosomal deficiencies for dominant suppressors of silencing of a transgene at the telomere of chromosome 2L. While many deficiency chromosomes are associated with dominant suppressors, in the cases tested on chromosome 2 the suppressor mapped to the 2L telomere, rather than the deficiency. We infer that background effects may hamper the search for genes that play a role in telomeric heterochromatin formation and that either very few genes participate in this pathway or mutations in these genes are not dominant suppressors of telomeric position effect. The data also suggest that the 2L telomere region plays a major role in telomeric silencing.

Cis- and trans-acting influences on telomeric position effect in Drosophila melanogaster detected with a subterminal transgene.

One model of telomeric position effect (TPE) in Drosophila melanogaster proposes that reporter genes in the vicinity of telomeres are repressed by subterminal telomere-associated sequences (TAS) and that variegation of these genes is the result of competition between the repressive effects of TAS and the stimulating effects of promoters in the terminal HeT-A transposon array. The data presented here support this model, but also suggest that TPE is more complex. Activity of a telomeric white reporter gene increases in response to deletion of some or all of the TAS on the homolog. Only transgenes next to fairly long HeT-A arrays respond to this trans-interaction. HeT-A arrays of 6-18 kb respond by increasing the number of dark spots on the eye, while longer arrays increase the background eye color or increase the number of spots sufficiently to cause them to merge. Thus, expression of a subtelomeric reporter gene is influenced by the telomere structure in cis and trans. We propose that the forces involved in telomere length regulation in Drosophila are the underlying forces that manifest themselves as TPE. In the wild-type telomere TAS may play an important role in controlling telomere elongation by repressing HeT-A promoter activity. Modulation of this repression by the homolog may thus regulate telomere elongation.

Efficient recovery of centric heterochromatin P-element insertions in Drosophila melanogaster.

Approximately one-third of the human and Drosophila melanogaster genomes are heterochromatic, yet we know very little about the structure and function of this enigmatic component of eukaryotic genomes. To facilitate molecular and cytological analysis of heterochromatin we introduced a yellow(+) (y(+))-marked P element into centric heterochromatin by screening for variegated phenotypes, that is, mosaic gene inactivation. We recovered >110 P insertions with variegated yellow expression from approximately 3500 total mobilization events. FISH analysis of 71 of these insertions showed that 69 (97%) were in the centric heterochromatin, rather than telomeres or euchromatin. High-resolution banding analysis showed a wide but nonuniform distribution of insertions within centric heterochromatin; variegated insertions were predominantly recovered near regions of satellite DNA. We successfully used inverse PCR to clone and sequence the flanking DNA for approximately 63% of the insertions. BLAST analysis of the flanks demonstrated that either most of the variegated insertions could not be placed on the genomic scaffold, and thus may be inserted within novel DNA sequence, or that the flanking DNA hit multiple sites on the scaffold, due to insertions within different transposons. Taken together these data suggest that screening for yellow variegation is a very efficient method for recovering centric insertions and that a large-scale screen for variegated yellow P insertions will provide important tools for detailed analysis of centric heterochromatin structure and function.