Tissue-specific regulation of gene expression via unproductive splicing.

Eukaryotic gene expression is regulated post-transcriptionally by a mechanism called unproductive splicing, in which mRNA is triggered to degrade by the nonsense-mediated decay (NMD) pathway as a result of regulated alternative splicing (AS). Only a few dozen unproductive splicing events (USEs) are currently documented, and many more remain to be identified. Here, we analyzed RNA-seq experiments from the Genotype-Tissue Expression (GTEx) Consortium to identify USEs, in which an increase in the NMD isoform splicing rate is accompanied by tissue-specific down-regulation of the host gene. To characterize RNA-binding proteins (RBPs) that regulate USEs, we superimposed these results with RBP footprinting data and experiments on the response of the transcriptome to the perturbation of expression of a large panel of RBPs. Concordant tissue-specific changes between the expression of RBP and USE splicing rate revealed a high-confidence regulatory network including 27 tissue-specific USEs with strong evidence of RBP binding. Among them, we found previously unknown PTBP1-controlled events in the DCLK2 and IQGAP1 genes, for which we confirmed the regulatory effect using small interfering RNA (siRNA) knockdown experiments in the A549 cell line. In sum, we present a transcriptomic pipeline that allows the identification of tissue-specific USEs, potentially many more than were reported here using stringent filters.

Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale.

MOTIVATION: Analysis of allele-specific expression is strongly affected by the technical noise present in RNA-seq experiments. Previously, we showed that technical replicates can be used for precise estimates of this noise, and we provided a tool for correction of technical noise in allele-specific expression analysis. This approach is very accurate but costly due to the need for two or more replicates of each library. Here, we develop a spike-in approach which is highly accurate at only a small fraction of the cost. RESULTS: We show that a distinct RNA added as a spike-in before library preparation reflects technical noise of the whole library and can be used in large batches of samples. We experimentally demonstrate the effectiveness of this approach using combinations of RNA from species distinguishable by alignment, namely, mouse, human, and Caenorhabditis elegans. Our new approach, controlFreq, enables highly accurate and computationally efficient analysis of allele-specific expression in (and between) arbitrarily large studies at an overall cost increase of ∼5%. AVAILABILITY AND IMPLEMENTATION: Analysis pipeline for this approach is available at GitHub as R package controlFreq (github.com/gimelbrantlab/controlFreq).

Phenoxaphosphonium Mixed Ylides in Ring Expansion Reaction.

Treatment of mixed phosphonium-iodonium ylides featuring a six-membered phenoxaphosphonium fragment with aqueous tetrafluoroboronic acid induces a rearrangement, resulting in expansion of the phosphacycle and oxidation of the phosphorus atom. The target difficult-to-access dibenzo[b,f][1,4]oxaphosphepine oxides (3 examples) were isolated in excellent yields (up to 95%) as mixtures of stereoisomers. Hydrolysis of a five-membered mixed ylide, a dibenzophosphole derivative, predominantly preserves the phosphole system with cycle expansion occurring as a side process.

Mice deficient in synaptic protease neurotrypsin show impaired spaced long-term potentiation and blunted learning-induced modulation of dendritic spines.

Neurotrypsin (NT) is a neuronal trypsin-like serine protease whose mutations cause severe mental retardation in humans. NT is activated in vitro by Hebbian-like conjunction of pre- and postsynaptic activities, which promotes the formation of dendritic filopodia via proteolytic cleavage of the proteoglycan agrin. Here, we investigated the functional importance of this mechanism for synaptic plasticity, learning, and extinction of memory. We report that juvenile neurotrypsin-deficient (NT-/-) mice exhibit impaired long-term potentiation induced by a spaced stimulation protocol designed to probe the generation of new filopodia and their conversion into functional synapses. Behaviorally, juvenile NT-/- mice show impaired contextual fear memory and have a sociability deficit. The latter persists in aged NT-/- mice, which, unlike juvenile mice, show normal recall but impaired extinction of contextual fear memories. Structurally, juvenile mutants exhibit reduced spine density in the CA1 region, fewer thin spines, and no modulation in the density of dendritic spines following fear conditioning and extinction in contrast to wild-type littermates. The head width of thin spines is reduced in both juvenile and aged NT-/- mice. In vivo delivery of adeno-associated virus expressing an NT-generated fragment of agrin, agrin-22, but not a shorter agrin-15, elevates the spine density in NT-/- mice. Moreover, agrin-22 co-aggregates with pre- and postsynaptic markers and increases the density and size of presynaptic boutons and presynaptic puncta, corroborating the view that agrin-22 supports the synaptic growth.

OrthoQuantum: visualizing evolutionary repertoire of eukaryotic proteins.

Extensive amounts of data from next-generation sequencing and omics studies have led to the accumulation of information that provides insight into the evolutionary landscape of related proteins. Here, we present OrthoQuantum, a web server that allows for time-efficient analysis and visualization of phylogenetic profiles of any set of eukaryotic proteins. It is a simple-to-use tool capable of searching large input sets of proteins. Using data from open source databases of orthologous sequences in a wide range of taxonomic groups, it enables users to assess coupled evolutionary patterns and helps define lineage-specific innovations. The web interface allows to perform queries with gene names and UniProt identifiers in different phylogenetic clades and supplement presence with an additional BLAST search. The conservation patterns of proteins are coded as binary vectors, i.e., strings that encode the presence or absence of orthologous proteins in other genomes. These strings are used to calculate top-scoring correlation pairs needed for finding co-inherited proteins which are simultaneously present or simultaneously absent in specific lineages. Profiles are visualized in combination with phylogenetic trees in a JavaScript-based interface. The OrthoQuantum v1.0 web server is freely available at http://orthoq.bioinf.fbb.msu.ru along with documentation and tutorial.

CsAr, CsXe, and RbXe B2Σ1/2+ Interatomic Potentials Determined from Absorption Spectra and Calculations of Franck-Condon Factors for Free-Free Optical Transitions of Atomic Collision Pairs.

Interatomic potentials for the B2Σ1/2+ states of CsAr, CsXe, and RbXe have been determined through comparisons of experimental B ← X absorption spectra for alkali vapor-rare gas mixtures with calculations of the Franck-Condon factors (FCFs) associated with free-free transitions of thermal atomic pairs. Simulations of optical transitions of alkali-rare gas atomic pairs between the thermal and vibrational continua of the X2Σ1/2+ and B2Σ1/2+ states of the molecule, responsible for the blue satellites of the Cs and Rb D2 resonance lines in a rare gas background, require the incorporation of ground-state J values above ∼400 into the FCF calculations and proper normalization of the free-particle wave functions. Absorption spectra computed on the basis of several X and B state interatomic potentials available in the literature were found to be sensitive to the height of the B2Σ1/2+ state barrier, as well as the X2Σ1/2+ state repulsive wall contour and the location of the van der Waals minimum. Other spectral simulations entailed iterative modifications to a selected B2Σ1/2+ interatomic potential, again coupled with comparison to experimental B ← X spectra. Comparisons of calculated spectra with experiment yield a CsXe B2Σ1/2+ potential, for example, exhibiting a barrier height of 76 cm-1 at 5.2 Å and yet is nearly flat at smaller values of internuclear separation (R). The latter contrasts with previous theoretical calculations of VB(R) in the vicinity of the barrier maximum. For the CsAr molecule, the B2Σ1/2+ barrier height was found to be 221 cm-1, which is within 3% of the value determined from pseudopotential calculations incorporating the spin-orbit effect. Reproducing Cs-rare gas experimental absorption spectra also requires the existence of a broad, shallow potential well lying beyond the B2Σ1/2+ barrier that, for CsAr, has a dissociation energy (De ∼ 24 cm-1) a factor of 3 larger than values predicted by theory. Similar results are obtained for the RbXe and CsXe complexes.

Comparison of the Patency and Regenerative Potential of Biodegradable Vascular Prostheses of Different Polymer Compositions in an Ovine Model.

The lack of suitable autologous grafts and the impossibility of using synthetic prostheses for small artery reconstruction make it necessary to develop alternative efficient vascular grafts. In this study, we fabricated an electrospun biodegradable poly(ε-caprolactone) (PCL) prosthesis and poly(3-hydroxybutyrate-co-3-hydroxyvalerate)/poly(ε-caprolactone) (PHBV/PCL) prosthesis loaded with iloprost (a prostacyclin analog) as an antithrombotic drug and cationic amphiphile with antibacterial activity. The prostheses were characterized in terms of their drug release, mechanical properties, and hemocompatibility. We then compared the long-term patency and remodeling features of PCL and PHBV/PCL prostheses in a sheep carotid artery interposition model. The research findings verified that the drug coating of both types of prostheses improved their hemocompatibility and tensile strength. The 6-month primary patency of the PCL/Ilo/A prostheses was 50%, while all PHBV/PCL/Ilo/A implants were occluded at the same time point. The PCL/Ilo/A prostheses were completely endothelialized, in contrast to the PHBV/PCL/Ilo/A conduits, which had no endothelial cells on the inner layer. The polymeric material of both prostheses degraded and was replaced with neotissue containing smooth-muscle cells; macrophages; proteins of the extracellular matrix such as type I, III, and IV collagens; and vasa vasorum. Thus, the biodegradable PCL/Ilo/A prostheses demonstrate better regenerative potential than PHBV/PCL-based implants and are more suitable for clinical use.

ortho2align: a sensitive approach for searching for orthologues of novel lncRNAs.

BACKGROUND: Many novel long noncoding RNAs have been discovered in recent years due to advances in high-throughput sequencing experiments. Finding orthologues of these novel lncRNAs might facilitate clarification of their functional role in living organisms. However, lncRNAs exhibit low sequence conservation, so specific methods for enhancing the signal-to-noise ratio were developed. Nevertheless, current methods such as transcriptomes comparison approaches or searches for conserved secondary structures are not applicable to novel, previously unannotated lncRNAs by design. RESULTS: We present ortho2align-a versatile sensitive synteny-based lncRNA orthologue search tool with statistical assessment of sequence conservation. This tool allows control of the specificity of the search process and optional annotation of found orthologues. ortho2align shows similar performance in terms of sensitivity and resource usage as the state-of-the-art method for aligning orthologous lncRNAs but also enables scientists to predict unannotated orthologous sequences for lncRNAs in question. Using ortho2align, we predicted orthologues of three distinct classes of novel human lncRNAs in six Vertebrata species to estimate their degree of conservation. CONCLUSIONS: Being designed for the discovery of unannotated orthologues of novel lncRNAs in distant species, ortho2align is a versatile tool applicable to any genomic regions, especially weakly conserved ones. A small amount of input files makes ortho2align easy to use in orthology studies as a single tool or in bundle with other steps that researchers will consider sensible. ortho2align is available as an Anaconda package with its source code hosted at https://github.com/dmitrymyl/ortho2align .

Studying RNA-DNA interactome by Red-C identifies noncoding RNAs associated with various chromatin types and reveals transcription dynamics.

Non-coding RNAs (ncRNAs) participate in various biological processes, including regulating transcription and sustaining genome 3D organization. Here, we present a method termed Red-C that exploits proximity ligation to identify contacts with the genome for all RNA molecules present in the nucleus. Using Red-C, we uncovered the RNA-DNA interactome of human K562 cells and identified hundreds of ncRNAs enriched in active or repressed chromatin, including previously undescribed RNAs. Analysis of the RNA-DNA interactome also allowed us to trace the kinetics of messenger RNA production. Our data support the model of co-transcriptional intron splicing, but not the hypothesis of the circularization of actively transcribed genes.

New Cysteine-Containing PEG-Glycerolipid Increases the Bloodstream Circulation Time of Upconverting Nanoparticles.

Upconverting nanoparticles have unique spectral and photophysical properties that make them suitable for development of theranostics for imaging and treating large and deep-seated tumors. Nanoparticles based on NaYF4 crystals doped with lanthanides Yb3+ and Er3+ were obtained by the high-temperature decomposition of trifluoroacetates in oleic acid and 1-octadecene. Such particles have pronounced hydrophobic properties. Therefore, to obtain stable dispersions in aqueous media for the study of their properties in vivo and in vitro, the polyethylene glycol (PEG)-glycerolipids of various structures were obtained. To increase the circulation time of PEG-lipid coated nanoparticles in the bloodstream, long-chain substituents are needed to be attached to the glycerol backbone using ether bonds. To prevent nanoparticle aggregation, an L-cysteine-derived negatively charged carboxy group should be included in the lipid molecule.

A new imaging concept in spin polarimetry based on the spin-filter effect.

The concept of an imaging-type 3D spin detector, based on the combination of spin-exchange interactions in the ferromagnetic (FM) film and spin selectivity of the electron-photon conversion effect in a semiconductor heterostructure, is proposed and demonstrated on a model system. This novel multichannel concept is based on the idea of direct transfer of a 2D spin-polarized electron distribution to image cathodoluminescence (CL). The detector is a hybrid structure consisting of a thin magnetic layer deposited on a semiconductor structure allowing measurement of the spatial and polarization-dependent CL intensity from injected spin-polarized free electrons. The idea is to use spin-dependent electron transmission through in-plane magnetized FM film for in-plane spin detection by measuring the CL intensity from recombined electrons transmitted in the semiconductor. For the incoming electrons with out-of-plane spin polarization, the intensity of circularly polarized CL light can be detected from recombined polarized electrons with holes in the semiconductor. In order to demonstrate the ability of the solid-state spin detector in the image-type mode operation, a spin detector prototype was developed, which consists of a compact proximity focused vacuum tube with a spin-polarized electron source [p-GaAs(Cs,O)], a negative electron affinity (NEA) photocathode and the target [semiconductor heterostructure with quantum wells also with NEA]. The injection of polarized low-energy electrons into the target by varying the kinetic energy in the range 0.5-3.0 eV and up to 1.3 keV was studied in image-type mode. The figure of merit as a function of electron kinetic energy and the target temperature is determined. The spin asymmetry of the CL intensity in a ferromagnetic/semiconductor (FM-SC) junction provides a compact optical method for measuring spin polarization of free-electron beams in image-type mode. The FM-SC detector has the potential for realizing multichannel 3D vectorial reconstruction of spin polarization in momentum microscope and angle-resolved photoelectron spectroscopy systems.

Derivatives of Natural Chlorophylls as Agents for Antimicrobial Photodynamic Therapy.

The rapid growth of drug-resistant bacteria all over the world has given rise to a major research challenge, namely a search for alternative treatments to which bacteria will be unable to develop resistance. Photodynamic therapy is an approach of this kind. It involves the use of photosensitizers in combination with visible light at a certain wavelength to excite the former and generate reactive oxygen species. Various synthetic heterocyclic compounds are used as photosensitizers. Of these, derivatives of natural chlorophylls have a special place due to their properties. This review deals with the use of such compounds in antimicrobial PDT.

Tin Carboxylate Complexes of Natural Bacteriochlorin for Combined Photodynamic and Chemotherapy of Cancer è.

Photodynamic therapy (PDT) is currently one of the most promising methods of cancer treatment. However, this method has some limitations, including a small depth of penetration into biological tissues, the low selectivity of accumulation, and hypoxia of the tumor tissues. These disadvantages can be overcome by combining PDT with other methods of treatment, such as radiation therapy, neutron capture therapy, chemotherapy, etc. In this work, potential drugs were obtained for the first time, the molecules of which contain both photodynamic and chemotherapeutic pharmacophores. A derivative of natural bacteriochlorophyll a with a tin IV complex, which has chemotherapeutic activity, acts as an agent for PDT. This work presents an original method for obtaining agents of combined action, the structure of which is confirmed by various physicochemical methods of analysis. The method of molecular modeling was used to investigate the binding of the proposed drugs to DNA. In vitro biological tests were carried out on several lines of tumor cells: Hela, A549, S37, MCF7, and PC-3. It was shown that the proposed conjugates of binary action for some cell lines had a dark cytotoxicity that was significantly higher (8-10 times) than the corresponding metal complexes of amino acids, which was explained by the targeted chemotherapeutic action of the tin (IV) complex due to chlorin. The greatest increase in efficiency relative to the initial dipropoxy-BPI was found for the conjugate with lysine as a chelator of the tin cation relative to cell lines, with the following results: S-37 increased 3-fold, MCF-7 3-fold, and Hela 2.4-fold. The intracellular distribution of the obtained agents was also studied by confocal microscopy and showed a diffuse granular distribution with predominant accumulation in the near nuclear region.

Calciprotein Particles Link Disturbed Mineral Homeostasis with Cardiovascular Disease by Causing Endothelial Dysfunction and Vascular Inflammation.

An association between high serum calcium/phosphate and cardiovascular events or death is well-established. However, a mechanistic explanation of this correlation is lacking. Here, we examined the role of calciprotein particles (CPPs), nanoscale bodies forming in the human blood upon its supersaturation with calcium and phosphate, in cardiovascular disease. The serum of patients with coronary artery disease or cerebrovascular disease displayed an increased propensity to form CPPs in combination with elevated ionised calcium as well as reduced albumin levels, altogether indicative of reduced Ca2+-binding capacity. Intravenous administration of CPPs to normolipidemic and normotensive Wistar rats provoked intimal hyperplasia and adventitial/perivascular inflammation in both balloon-injured and intact aortas in the absence of other cardiovascular risk factors. Upon the addition to primary human arterial endothelial cells, CPPs induced lysosome-dependent cell death, promoted the release of pro-inflammatory cytokines, stimulated leukocyte adhesion, and triggered endothelial-to-mesenchymal transition. We concluded that CPPs, which are formed in the blood as a result of altered mineral homeostasis, cause endothelial dysfunction and vascular inflammation, thereby contributing to the development of cardiovascular disease.

The First Selenoanhydride in the Series of Chlorophyll a Derivatives, Its Stability and Photoinduced Cytotoxicity.

In this work, we obtained the first selenium-containing chlorin with a chalcogen atom in exlocycle E. It was shown that the spectral properties were preserved in the target compound and the stability increased at two different pH values, in comparison with the starting purpurin-18. The derivatives have sufficiently high fluorescence and singlet oxygen quantum yields. The photoinduced cytotoxicity of sulfur- and selenium-anhydrides of chlorin p6 studied for the first time in vitro on the S37 cell line was found to be two times higher that of purpurin-18 and purpurinimide studied previously. Moreover, the dark cytotoxicity increased four-fold in comparison with the latter compounds. Apparently, the increase in the dark cytotoxicity is due to the interaction of the pigments studied with sulfur- and selenium-containing endogenous intracellular compounds. Intracellular distributions of thioanhydride and selenoanhydride chlorin p6 in S37 cells were shown in cytoplasm by diffusion distribution. The intracellular concentration of the sulfur derivative turned out to be higher and, as a consequence, its photoinduced cytotoxicity was higher as well.

Meet the Cerium(IV) Phosphate Sisters: CeIV (OH)PO4 and CeIV 2 O(PO4 )2.

Two new cerium(IV) phosphates were obtained: cerium(IV) hydroxidophosphate, Ce(OH)PO4 , and cerium(IV) oxidophosphate, Ce2 O(PO4 )2 , which were shown to complement the classes of isostructural compounds M(OH)PO4 and R2 O(PO4 )2 , where M=Th, U and R=Th, U, Np, Zr. Ce2 O(PO4 )2 oxidophosphate is formed by elimination of H2 O from the crystal structure of Ce(OH)PO4 during its thermal decomposition. The structures of Ce(OH)PO4 and Ce2 O(PO4 )2 are related to each other with the same Cmce space group and similar unit cell parameters (a=6.9691(3) Å, b=9.0655(4) Å, c=12.2214(4) Å, V=772.13(8) Å3 , Z=8; a=7.0220(4) Å, b=8.9894(5) Å, c=12.544(1) Å, V=791.8(1) Å3 , Z=4, respectively).

Coloc-stats: a unified web interface to perform colocalization analysis of genomic features.

Functional genomics assays produce sets of genomic regions as one of their main outputs. To biologically interpret such region-sets, researchers often use colocalization analysis, where the statistical significance of colocalization (overlap, spatial proximity) between two or more region-sets is tested. Existing colocalization analysis tools vary in the statistical methodology and analysis approaches, thus potentially providing different conclusions for the same research question. As the findings of colocalization analysis are often the basis for follow-up experiments, it is helpful to use several tools in parallel and to compare the results. We developed the Coloc-stats web service to facilitate such analyses. Coloc-stats provides a unified interface to perform colocalization analysis across various analytical methods and method-specific options (e.g. colocalization measures, resolution, null models). Coloc-stats helps the user to find a method that supports their experimental requirements and allows for a straightforward comparison across methods. Coloc-stats is implemented as a web server with a graphical user interface that assists users with configuring their colocalization analyses. Coloc-stats is freely available at https://hyperbrowser.uio.no/coloc-stats/.

The Low-Threshold Calcium Channel Cav3.2 Mediates Burst Firing of Mature Dentate Granule Cells.

Mature granule cells are poorly excitable neurons that were recently shown to fire action potentials, preferentially in bursts. It is believed that the particularly pronounced short-term facilitation of mossy fiber synapses makes granule cell bursting a very effective means of properly transferring information to CA3. However, the mechanism underlying the unique bursting behavior of mature granule cells is currently unknown. Here, we show that Cav3.2 T-type channels at the axon initial segment are responsible for burst firing of mature granule cells in rats and mice. Accordingly, Cav3.2 knockout mice fire tonic spikes and exhibit impaired bursting, synaptic plasticity and dentate-to-CA3 communication. The data show that Cav3.2 channels are strong modulators of bursting and can be considered a critical molecular switch that enables effective information transfer from mature granule cells to the CA3 pyramids.

Application of sorting and next generation sequencing to study 5΄-UTR influence on translation efficiency in Escherichia coli.

Yield of protein per translated mRNA may vary by four orders of magnitude. Many studies analyzed the influence of mRNA features on the translation yield. However, a detailed understanding of how mRNA sequence determines its propensity to be translated is still missing. Here, we constructed a set of reporter plasmid libraries encoding CER fluorescent protein preceded by randomized 5΄ untranslated regions (5΄-UTR) and Red fluorescent protein (RFP) used as an internal control. Each library was transformed into Escherchia coli cells, separated by efficiency of CER mRNA translation by a cell sorter and subjected to next generation sequencing. We tested efficiency of translation of the CER gene preceded by each of 48 natural 5΄-UTR sequences and introduced random and designed mutations into natural and artificially selected 5΄-UTRs. Several distinct properties could be ascribed to a group of 5΄-UTRs most efficient in translation. In addition to known ones, several previously unrecognized features that contribute to the translation enhancement were found, such as low proportion of cytidine residues, multiple SD sequences and AG repeats. The latter could be identified as translation enhancer, albeit less efficient than SD sequence in several natural 5΄-UTRs.

StereoGene: rapid estimation of genome-wide correlation of continuous or interval feature data.

MOTIVATION: Genomics features with similar genome-wide distributions are generally hypothesized to be functionally related, for example, colocalization of histones and transcription start sites indicate chromatin regulation of transcription factor activity. Therefore, statistical algorithms to perform spatial, genome-wide correlation among genomic features are required. RESULTS: Here, we propose a method, StereoGene, that rapidly estimates genome-wide correlation among pairs of genomic features. These features may represent high-throughput data mapped to reference genome or sets of genomic annotations in that reference genome. StereoGene enables correlation of continuous data directly, avoiding the data binarization and subsequent data loss. Correlations are computed among neighboring genomic positions using kernel correlation. Representing the correlation as a function of the genome position, StereoGene outputs the local correlation track as part of the analysis. StereoGene also accounts for confounders such as input DNA by partial correlation. We apply our method to numerous comparisons of ChIP-Seq datasets from the Human Epigenome Atlas and FANTOM CAGE to demonstrate its wide applicability. We observe the changes in the correlation between epigenomic features across developmental trajectories of several tissue types consistent with known biology and find a novel spatial correlation of CAGE clusters with donor splice sites and with poly(A) sites. These analyses provide examples for the broad applicability of StereoGene for regulatory genomics. AVAILABILITY AND IMPLEMENTATION: The StereoGene C ++ source code, program documentation, Galaxy integration scripts and examples are available from the project homepage http://stereogene.bioinf.fbb.msu.ru/. CONTACT: favorov@sensi.org. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.