Evolutionary Divergence of Phosphorylation to Regulate Interactive Protein Networks in Lower and Higher Species.

The phosphorylation of proteins affects their functions in extensively documented circumstances. However, the role of phosphorylation in many interactive networks of proteins remains very elusive due to the experimental limits of exploring the transient interaction in a large complex of assembled proteins induced by stimulation. Previous studies have suggested that phosphorylation is a recent evolutionary process that differently regulates ortholog proteins in numerous lineages of living organisms to create new functions. Despite the fact that numerous phospho-proteins have been compared between species, little is known about the organization of the full phospho-proteome, the role of phosphorylation to orchestrate large interactive networks of proteins, and the intertwined phospho-landscape in these networks. In this report, we aimed to investigate the acquired role of phosphate addition in the phenomenon of protein networking in different orders of living organisms. Our data highlighted the acquired status of phosphorylation in organizing large, connected assemblages in Homo sapiens. The protein networking guided by phosphorylation turned out to be prominent in humans, chaotic in yeast, and weak in flies. Furthermore, the molecular functions of GO annotation enrichment regulated by phosphorylation were found to be drastically different between flies, yeast, and humans, suggesting an evolutionary drift specific to each species.

Transcriptome-wide-scale-predicted dsRNAs potentially involved in RNA homoeostasis are remarkably excluded from genes with no/very low expression in all developmental stages.

RNA interference (RNAi) refers to a conserved posttranscriptional mechanism for the degradation of RNA by short dsRNAs. A genome-wide analysis of mRNAs that are complementary to RNAs of variable length that are transcribed from the full transcriptome and susceptible to being loaded onto Argonaute type 2 was performed through computational searches in the Drosophila model. We report the segments of RNAs that are complementary to mRNAs originating from introns, the exons of mRNAs and lncRNAs as a potential source of siRNAs. A full catalogue of the mRNAs that fulfill these criteria is presented, along with the quantification of multiple annealing. The catalogue was assessed for biological validation using three published lists: two for Ago2-associated RNAs and one for dsRNAs isolated from a crude extract. A broad spectrum of mRNAs were found to theoretically form intermolecular segmental dsRNAs, which should qualify them as Dicer/Ago2 substrates if they exist in vivo. These results suggest a genome-wide scale of mRNA homoeostasis via RNAi metabolism and could extend the known roles of canonical miRNAs and hairpin RNAs. The distribution of the genes for which transcripts are engaged in intermolecular segmental pairing is largely lacking in the gene collections defined as showing no expression in each individual developmental stage from early embryos to adulthood. This trend was also observed for the genes showing very low expression from the 8-12-hour embryonic to larval stage 2. This situation was also suggested by the 3 lists generated with minimal 20-, 25- and 30-base pairing lengths.

Direct Evidence of Lithium Ion Migration in Resistive Switching of Lithium Cobalt Oxide Nanobatteries.

Lithium cobalt oxide nanobatteries offer exciting prospects in the field of nonvolatile memories and neuromorphic circuits. However, the precise underlying resistive switching (RS) mechanism remains a matter of debate in two-terminal cells. Herein, intriguing results, obtained by secondary ion mass spectroscopy (SIMS) 3D imaging, clearly demonstrate that the RS mechanism corresponds to lithium migration toward the outside of the Lix CoO2 layer. These observations are very well correlated with the observed insulator-to-metal transition of the oxide. Besides, smaller device area experimentally yields much faster switching kinetics, which is qualitatively well accounted for by a simple numerical simulation. Write/erase endurance is also highly improved with downscaling - much further than the present cycling life of usual lithium-ion batteries. Hence very attractive possibilities can be envisaged for this class of materials in nanoelectronics.

Molecular Alloys of Neutral Gold/Nickel Dithiolene Complexes in Single-Component Semiconductors.

Control of band filling or doping of molecular (semi)conductors can be performed by substitutional insertion of molecules with a similar shape but a different electron count, with one more or one less electron. This strategy has been explored here within the semiconducting, single-component, radical gold dithiolene complex [AuOC4] bearing para-butoxyphenyl substituents. Alloying with the corresponding neutral nickel dithiolene complex [NiOC4] lacking one electron afforded a complete isostructural series [NiOC4]1-x[AuOC4]x, spanning the whole composition range from x = 0 to x = 1 by 0.1 increments, further characterized by X-ray diffraction and EDX analyses. Magnetic susceptibility data confirm the antiferromagnetic interactions between neighboring radical gold dithiolene complexes. The electrical conductivity increases exponentially with the x gold fraction, while the activation energy remains constant in the more conducting, gold-rich samples. This behavior is tentatively assigned to the tunneling barriers of variable width (with x) but of constant height, separating more conducting gold-rich segments. Comparison of redox potentials for the 1e(-) oxidation and reduction of both [NiOC4] and [AuOC4] dithiolene complexes indicates that the [NiOC4] nickel complex does not act as a dopant for the radical [AuOC4] complex.

A network embedding approach to identify active modules in biological interaction networks.

The identification of condition-specific gene sets from transcriptomic experiments is important to reveal regulatory and signaling mechanisms associated with a given cellular response. Statistical methods of differential expression analysis, designed to assess individual gene variations, have trouble highlighting modules of small varying genes whose interaction is essential to characterize phenotypic changes. To identify these highly informative gene modules, several methods have been proposed in recent years, but they have many limitations that make them of little use to biologists. Here, we propose an efficient method for identifying these active modules that operates on a data embedding combining gene expressions and interaction data. Applications carried out on real datasets show that our method can identify new groups of genes of high interest corresponding to functions not revealed by traditional approaches. Software is available at https://github.com/claudepasquier/amine.

CELF2 Sustains a Proliferating/OLIG2+ Glioblastoma Cell Phenotype via the Epigenetic Repression of SOX3.

Glioblastomas (GBs) are incurable brain tumors. The persistence of aggressive stem-like tumor cells after cytotoxic treatments compromises therapeutic efficacy, leading to GBM recurrence. Forcing the GBM cells to irreversibly abandon their aggressive stem-like phenotype may offer an alternative to conventional cytotoxic treatments. Here, we show that the RNA binding protein CELF2 is strongly expressed in mitotic and OLIG2-positive GBM cells, while it is downregulated in differentiated and non-mitotic cells by miR-199a-3p, exemplifying GBM intra-tumor heterogeneity. Using patient-derived cells and human GBM samples, we demonstrate that CELF2 plays a key role in maintaining the proliferative/OLIG2 cell phenotype with clonal and tumorigenic properties. Indeed, we show that CELF2 deficiency in patient-derived GSCs drastically reduced tumor growth in the brains of nude mice. We further show that CELF2 promotes TRIM28 and G9a expression, which drive a H3K9me3 epigenetic profile responsible for the silencing of the SOX3 gene. Thus, CELF2, which is positively correlated with OLIG2 and Ki67 expression in human GBM samples, is inversely correlated with SOX3 and miR-199a-3p. Accordingly, the invalidation of SOX3 in CELF2-deficient patient-derived cells rescued proliferation and OLIG2 expression. Finally, patients expressing SOX3 above the median level of expression tend to have a longer life expectancy. CELF2 is therefore a crucial target for the malignant potential of GBM and warrants attention when developing novel anticancer strategies.

Design and evaluation of a crystalline hybrid of molecular conductors and molecular rotors.

Combining recent concepts from the fields of molecular conductivity and molecular machinery we set out to design a crystalline molecular conductor that also possesses a molecular rotor. We report on the structures, electronic and physical properties, and dynamics of two solids with a common 1,4-bis(carboxyethynyl)bicyclo[2.2.2]octane (BABCO) functional rotor. One, [nBu(4)N(+)](2)[BABCO][BABCO(-)](2), is a colorless insulator where the dicarboxylic acid cocrystallizes with two of its monoanionic conjugated bases. The other is self-assembled by electrocrystallization in the form of black, shiny needles, with highly conducting molecular slabs of (EDT-TTF-CONH(2))(2)(+) (EDT-TTF = ethylenedithiotetrathiafulvalene) and anionic [BABCO(-)] rotors. Using variable-temperature (5-300 K) proton spin-lattice relaxation, (1)H T(1)(-1), we were able to assign two types of Brownian rotators in [nBu(4)N(+)](2)[BABCO][BABCO(-)](2). We showed that neutral BABCO groups have a rotational frequency of 120 GHz at 300 K with a rotational barrier of 2.03 kcal mol(-1). Rotors on the BABCO(-) sites experience stochastic 32 GHz jumps at the same temperature over a rotational barrier of 2.72 kcal mol(-1). In contrast, the BABCO(-) rotors within the highly conducting crystals of (EDT-TTF-CONH(2))(2)(+)[BABCO(-)] are essentially "braked" at room temperature. Notably, these crystals possess a conductivity of 5 S cm(-1) at 1 bar, which increases rapidly with pressure up to 50 S cm(-1) at 11.5 kbar. Two regimes with different activation energies E(a) for the resistivity (180 K above 50 and 400 K below) are observed at ambient pressure; a metallic state is stabilized at ca. 8 kbar, and an insulating ground state remains below 50 K at all pressures. We discuss two likely channels by which the motion of the rotors might become slowed down in the highly conducting solid. One is defined as a low-velocity viscous regime inherent to a noncovalent, physical coupling induced by the cooperativity between five C(sp3)-H···O hydrogen bonds engaging any rotor and five BABCO units in its environment. The rotational barrier calculated with the effect of this set of hydrogen bonds amounts to 7.3 kcal mol(-1). Another is quantum dissipation, a phenomenon addressing the difference of dynamics of the rotors in the two solids with different electrical properties, by which the large number of degrees of freedom of the low dimensional electron gas may serve as a bath for the dissipation of the energy of the rotor motion, the two systems being coupled by the Coulomb interaction between the charges of the rotors (local moments and induced dipoles) and the charges of the carriers.

Temporal and sequential order of nonoverlapping gene networks unraveled in mated female Drosophila.

In this study, we reanalyzed available datasets of gene expression changes in female Drosophila head induced by mating. Mated females present metabolic phenotypic changes and display behavioral characteristics that are not observed in virgin females, such as repulsion to male sexual aggressiveness, fidelity to food spots selected for oviposition, and restriction to the colonization of new niches. We characterize gene networks that play a role in female brain plasticity after mating using AMINE, a novel algorithm to find dysregulated modules of interacting genes. The uncovered networks of altered genes revealed a strong specificity for each successive period of life span after mating in the female head, with little conservation between them. This finding highlights a temporal order of recruitment of waves of interconnected genes which are apparently transiently modified: the first wave disappears before the emergence of the second wave in a reversible manner and ends with few consolidated gene expression changes at day 20. This analysis might document an extended field of a programmatic control of female phenotypic traits by male seminal fluid.

Persistent Properties of a Subpopulation of Cancer Cells Overexpressing the Hedgehog Receptor Patched.

Despite the development of new therapeutic strategies, cancer remains one of the leading causes of mortality worldwide. One of the current major challenges is the resistance of cancers to chemotherapy treatments inducing metastases and relapse of the tumor. The Hedgehog receptor Patched (Ptch1) is overexpressed in many types of cancers. We showed that Ptch1 contributes to the efflux of doxorubicin and plays an important role in the resistance to chemotherapy in adrenocortical carcinoma (ACC), a rare cancer which presents strong resistance to the standard of care chemotherapy treatment. In the present study, we isolated and characterized a subpopulation of the ACC cell line H295R in which Ptch1 is overexpressed and more present at the cell surface. This cell subpopulation is more resistant to doxorubicin, grows as spheroids, and has a greater capability of clonogenicity, migration, and invasion than the parental cells. Xenograft experiments performed in mice and in ovo showed that this cell subpopulation is more tumorigenic and metastatic than the parental cells. These results suggest that this cell subpopulation has cancer stem-like or persistent cell properties which were strengthened by RNA-seq. If present in tumors from ACC patients, these cells could be responsible for therapy resistance, relapse, and metastases.

Large spontaneous polarization and clear hysteresis loop of a room-temperature hybrid ferroelectric based on mixed-halide [BiI3Cl2] polar chains and methylviologen dication.

The search for hybrid organic-inorganic materials, which have the great advantage that they can be synthesized at moderate temperature (T < 200 °C), remains a great challenge in the field of ferroelectrics. Here, a room-temperature ferroelectric material with interesting characteristics, (MV)[BiI(3)Cl(2)] (MV(2+) = methylviologen), is reported. Its structure is based on polar inorganic chains resulting from a remarkable Cl/I segregation induced by methylviologen entities, which coincide with the fourfold polar axis of the tetragonal structure. Of great importance is that this room-temperature hybrid ferroelectric displays a clear electrical hysteresis loop with a large spontaneous polarization (>15 µC·cm(-2)).

Computational search of hybrid human/SARS-CoV-2 dsRNA reveals unique viral sequences that diverge from those of other coronavirus strains.

The role of the RNAi/Dicer/Ago system in degrading RNA viruses has been elusive in mammals in the past, which has prompted authors to think that interferon (IFN) synthesis is essential in this clade, relegating the RNAi defense strategy against viral infection as an accessory function. However, recent publications highlight the existence of abundant viral small interference and micro RNAs (VsiRNAs and VmiRNAs) in both cell-line and whole organism based experiments, indicating a contribution of these molecules in host responses and/or viral replication. We explore the theoretical possibility that RNAi triggered by SARS-CoV-2 might degrade some host transcripts in the opposite direction, although this hypothesis seems counterintuitive. The SARS-CoV-2 genome was therefore computationally searched for exact intrapairing within the viral RNA and exact hybrid pairing with the human transcriptome over a minimum of 20 bases in length. Minimal segments of 20-base lengths of SARS-CoV-2 RNA were found based on the theoretical matching with existing complementary strands in the human host transcriptome. Few human genes potentially annealing with SARS-CoV-2 RNA, including mitochondrial deubiquitinase USP30, the subunit of ubiquitin protein ligase complex FBXO21 and two long noncoding RNAs, were retrieved. The hypothesis that viral-originated RNAi might mediate degradation of host transcriptome messages was corroborated by published high throughput sequencing of RNA from infected tissues and cultured cells, clinical observation and phylogenetic comparative analysis, indicating a strong specificity of these SARS-CoV-2 hybrid pairing sequences for human genomes.

SETMAR Shorter Isoform: A New Prognostic Factor in Glioblastoma.

Recent evidence suggests that the chimeric protein SETMAR is a factor of interest in cancer, especially in glioblastoma. However, little is known about the expression of this protein in glioblastoma tissues, and no study has been done to assess if SETMAR could be a prognostic and/or diagnostic marker of glioblastoma. We analyzed protein extracts of 47 glioblastoma samples coming from a local and a national cohort of patients. From the local cohort, we obtained localized biopsies from the central necrosis area, the tumor, and the perilesional brain. From the French Glioblastoma Biobank (FGB), we obtained three types of samples: from the same tumors before and after treatment, from long survivors, and from very short survivors. We studied the correlations between SETMAR amounts, clinical profiles of patients and other associated proteins (PTN, snRNP70 and OLIG2). In glioblastoma tissues, the shorter isoform of SETMAR (S-SETMAR) was predominant over the full-length isoform (FL-SETMAR), and the expression of both SETMAR variants was higher in the tumor compared to the perilesional tissues. Data from the FGB showed that SETMAR amounts were not different between the initial tumors and tumor relapses after treatment. These data also showed a trend toward higher amounts of S-SETMAR in long survivors. In localized biopsies, we found a positive correlation between good prognosis and large amounts of S-SETMAR in the perilesional area. This is the main result presented here: survival in Glioblastoma is correlated with amounts of S-SETMAR in perilesional brain, which should be considered as a new relevant prognosis marker.

Photochromism, electrical properties, and structural investigations of a series of hydrated methylviologen halobismuthate hybrids: influence of the anionic oligomer size and iodide doping on the photoinduced properties and on the dehydration process.

Syntheses, X-ray structural analyses, thermal behaviors, photochromism, and electrical properties of a series of methylviologen (MV(2+)) halobismuthate hybrids, namely, (MV)(3)[Bi(4)Cl(18)](H(2)O)(y) (1a, y approximately = 1.7), (MV)(4)[Bi(6)Cl(26)](H(2)O)(y) (2a, y approximately = 1.7), (MV)(4)[Bi(6)Cl(25.6)I(0.4)](H(2)O)(y) (3a, y approximately = 1.5), and (MV)(4)[Bi(6)Cl(24.6)I(1.4)](H(2)O)(y) (4a, y approximately = 1.3), are reported. Because of the thermal effect of a UV lamp or as a result of being heated up to 100 degrees C, all of the above compounds undergo a complete (1a, 2a, and 3a) or a partial (4a) dehydration together, in 2a and 3a, with an impressive structural reorganization involving a 90 degrees rotation of methylviologen dimers and, in 3a, a new Cl/I distribution, finally leading to (MV)(3)[Bi(4)Cl(18)] (1b), (MV)(4)[Bi(6)Cl(26)] (2b), (MV)(4)[Bi(6)Cl(25.6)I(0.4)] (3b), and (MV)(4)[Bi(6)Cl(24.6)I(1.4)](H(2)O)(x) (4a, x approximately = 0.65), respectively. In its turn, 4a (x approximately = 0.65) undergoes an abrupt structural change at 160 degrees C when water molecules are completely removed, leading to (MV)(4)[Bi(6)Cl(24.6)I(1.4)] (4b). Obviously, the two first dehydrated phases can be considered as the n = 2 (1b) and n = 3 (2b) members of the (MV)((2n+2)/2)[Bi(2n)Cl(8n+2)] family, and the ultimate member (n = infinity) with an infinite 1D double-chain inorganic framework, namely, (MV)[Bi(2)Cl(8)], has already been reported. According to the results of structural refinements, some positions of the Cl atoms in the [Bi(6)Cl(26)](8-) anionic cluster of 3a and 4a have been occupied by I atoms, finally leading to iodide-doped materials of the 2a type (percentage of doping: 3a, 1.5%; 4a, 5.4%). Upon UV irradiation, yellow crystals of 2a and 3a (which become 2b and 3b because of the thermal effect of the UV lamp) or yellow crystals of 2b, 3b, and 4a undergo a color change to black crystals (in the case of 2b), as observed in (MV)[Bi(2)Cl(8)], or light-brown crystals (in the cases of 3b and 4a). These photochromic properties are probably due to the photoinduced electron transfer from the anionic part to the methylviologen dications. In contrast, no color change is observed when yellow crystals of 1a or 1b and the iodide-doped (MV)[Bi(2)Cl(8-epsilon)I(epsilon)] material are irradiated. Because the relative positions of methylviologen to the host anionic frameworks are comparable in all structures (the N...Cl distances are about 3.4 A), these results indicate that such kinds of photochemical reactions depend on the dimension of the anionic networks, as well as the iodide doping. The single-crystal electrical conductivity measurements of 2b before and after irradiation were carried out between 150 and 393 K. The results prove that both of them are semiconductors with weak room temperature conductivity and that the band gap of the irradiated crystal (2b, 0.35 eV) is much smaller than that of the original hybrid 2a (1.0 eV).

Computational prediction of miRNA/mRNA duplexomes at the whole human genome scale reveals functional subnetworks of interacting genes with embedded miRNA annealing motifs.

Perfect annealing between microRNAs (miRNAs) and messenger RNAs (mRNAs) was computationally searched at a broad scale in the human genome to determine whether theoretical pairing is restrictively represented in functional subnetworks or is randomly distributed. Massive RNA interference (RNAi) pairing motifs in genes constitute a remarkable subnetwork that displays highly genetically and biochemically interconnected genes. These analyses show unexpected repertoires of genes defined by their congruence in comatching with miRNAs at numerous sites and by their interconnection based on protein/protein interactions or proteins regulating the activity of others. This offers insights into the putatively coregulated homeostasis of large networks of genes by RNAi, whereas other networks seem to be independent of this regulatory mode. Genes accordingly defined by theoretical RNAi pairing cluster mainly in subnetworks related to cellular, metabolic and developmental processes and their regulation. Indeed, genes harboring numerous potential sites of hybridization with miRNAs are highly enriched with GO terms depicting the abovementioned processes and are grouped in a subnetwork of genes that are significantly more highly connected than they would be according to a random distribution. The significant number of interacting genes that present numerous potential comatches with miRNAs suggests that they may be under the control of the integrative and concerted action of multiple miRNAs.

GenMiner: mining non-redundant association rules from integrated gene expression data and annotations.

UNLABELLED: GenMiner is an implementation of association rule discovery dedicated to the analysis of genomic data. It allows the analysis of datasets integrating multiple sources of biological data represented as both discrete values, such as gene annotations, and continuous values, such as gene expression measures. GenMiner implements the new NorDi (normal discretization) algorithm for normalizing and discretizing continuous values and takes advantage of the Close algorithm to efficiently generate minimal non-redundant association rules. Experiments show that execution time and memory usage of GenMiner are significantly smaller than those of the standard Apriori-based approach, as well as the number of extracted association rules. AVAILABILITY: The GenMiner software and supplementary materials are available at http://bioinfo.unice.fr/publications/genminer_article/ and http://keia.i3s.unice.fr/?Implementations:GenMiner SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Modulating the framework negative charge density in the system [BDT-TTP*+]/[Re6S5Cl9(1-)]/[Re6(S/Se)6Cl8(2-)]/[Re6S7Cl7(3-)]: templating by isosteric cluster anions of identical symmetry and shape, variations of incommensurate band filling, and electronic structure in 2D metals.

A series of 2D metals, beta-(BDT-TTP)6[Re6Se6Cl8] x (CHCl2-CHCl2)2, 2; beta-(ST-TTP)6[Re6S6Cl8] x (CH2Cl-CHCl2)2, 3; beta-(BDT-TTP)7[Re6S6Cl8]0.5[Re6S7Cl7]0.5 x (CH2Cl2), 4; beta-(BDT-TTP)7[Re6Se6Cl8]0.5[Re6S7Cl7]0.5 x (CH2Cl2), 5; beta-(BDT-TTP)8[Re6S7Cl7] x (CH2Cl2)4, 6 (BDT-TTP and ST-TTP are 2,5-bis(1,3-dithiol-2-ylidene)-1,3,4,6-tetrathiapentalene and 2-(1,3-diselenol-2-ylidene)-5(1,3-dithiol-2-ylidene)-1,3,4,6-tetrathiapentalene, respectively) is reported to have one single beta-slab layered topology despite successive increases of the cluster anion negative charge. The charge density within the templating composite inorganic-neutral molecule slab is shown to remain above a threshold of ca. one negative charge per square nanometer, that is, for cluster anions with two negative charges and higher. Conversely, discrete stacks are shown to be stabilized instead in the semiconducting salts (BDT-TTP)2[Re6S5Cl9], 1 where the cluster anion bears one negative charge only. The electronic structure of salts 2-6 is shown to be very stable and kept almost intact across the series. The templating strategy is shown to fulfill its anticipated potential for deliberate installment of incommensurate band fillings in molecular metals. The deliberate admixture of the 6:1 and 8:1 structures yields novel phases with a 7:1 stoichiometry with the anticipated crystal and electronic structures. The action at the organic-inorganic interface triggered by changing the anion charge yet keeping its shape and volume identical, which ultimately governs the shape of the unit cell, is of paramount importance in defining the Fermi surface of these metallic salts. The present BDT-TTP salts thus provide a series of materials with strongly related but subtly different Fermi surfaces worthy of many physical studies. Shubnikov-de Haas measurements are expected to be particularly interesting since they are especially sensitive to the details of the Fermi surface.

Prediction of miRNA-disease Associations using an Evolutionary Tuned Latent Semantic Analysis.

MicroRNAs, small non-coding elements implied in gene regulation, are very interesting biomarkers for various diseases such as cancers. They represent potential prodigious biotechnologies for early diagnosis and gene therapies. However, experimental verification of microRNA-disease associations are time-consuming and costly, so that computational modeling is a proper solution. Previously, we designed MiRAI, a predictive method based on distributional semantics, to identify new associations between microRNA molecules and human diseases. Our preliminary results showed very good prediction scores compared to other available methods. However, MiRAI performances depend on numerous parameters that cannot be tuned manually. In this study, a parallel evolutionary algorithm is proposed for finding an optimal configuration of our predictive method. The automatically parametrized version of MiRAI achieved excellent performance. It highlighted new miRNA-disease associations, especially the potential implication of mir-188 and mir-795 in various diseases. In addition, our method allowed to detect several putative false associations contained in the reference database.

The Mapping of Predicted Triplex DNA:RNA in the Drosophila Genome Reveals a Prominent Location in Development- and Morphogenesis-Related Genes.

Double-stranded DNA is able to form triple-helical structures by accommodating a third nucleotide strand. A nucleic acid triplex occurs according to Hoogsteen rules that predict the stability and affinity of the third strand bound to the Watson-Crick duplex. The "triplex-forming oligonucleotide" (TFO) can be a short sequence of RNA that binds to the major groove of the targeted duplex only when this duplex presents a sequence of purine or pyrimidine bases in one of the DNA strands. Many nuclear proteins are known to bind triplex DNA or DNA:RNA, but their biological functions are unexplored. We identified sequences that are capable of engaging as the "triplex-forming oligonucleotide" in both the pre-lncRNA and pre-mRNA collections of Drosophila melanogaster These motifs were matched against the Drosophila genome in order to identify putative sequences of triplex formation in intergenic regions, promoters, and introns/exons. Most of the identified TFOs appear to be located in the intronic region of the analyzed genes. Computational prediction of the most targeted genes by TFOs originating from pre-lncRNAs and pre-mRNAs revealed that they are restrictively associated with development- and morphogenesis-related gene networks. The refined analysis by Gene Ontology enrichment demonstrates that some individual TFOs present genome-wide scale matches that are located in numerous genes and regulatory sequences. The triplex DNA:RNA computational mapping at the genome-wide scale suggests broad interference in the regulatory process of the gene networks orchestrated by TFO RNAs acting in association simultaneously at multiple sites.

Prediction of miRNA-disease associations with a vector space model.

MicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are associated with diseases contributes to a better understanding of pathogenicity mechanisms. MicroRNAs also represent a tremendous opportunity in biotechnology for early diagnosis. To date, several in silico methods have been developed to address the issue of microRNA-disease association prediction. However, these methods have various limitations. In this study, we investigate the hypothesis that information attached to miRNAs and diseases can be revealed by distributional semantics. Our basic approach is to represent distributional information on miRNAs and diseases in a high-dimensional vector space and to define associations between miRNAs and diseases in terms of their vector similarity. Cross validations performed on a dataset of known miRNA-disease associations demonstrate the excellent performance of our method. Moreover, the case study focused on breast cancer confirms the ability of our method to discover new disease-miRNA associations and to identify putative false associations reported in databases.