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Different TL techniques were meticulously tested using the surrogate-based dataset of Wang et al. as the "source" dataset for pre-training and one of the 10 smaller endogenous or functional knockout datasets as the "target" for refining the TL model. It is also worth noticing that CRISPRon outperforms the DeepCRISTL model trained on the dataset of Chari I et al. i on seven of the test datasets (Fig. The genome engineering revolution of the past decade has been fueled by the development of several computational tools for the design of experiments mediated by the CRISPR/Cas9 endonuclease ([3]). [Extracted from the article]

Summary The effectiveness of CRISPR/Cas9-mediated genome editing experiments largely depends on the guide RNA (gRNA) used by the CRISPR/Cas9 system for target recognition and cleavage activation. Careful design is necessary to select a gRNA with high editing efficiency at the on-target site and with minimum off-target potential. Here, we present our webserver for gRNA design with a user-friendly graphical interface, which provides interoperability between our on- and off-target prediction tools, CRISPRon and CRISPRoff, for a complete and streamlined gRNA selection. Availability and implementation The graphical interface uses the Integrative Genomic Viewer (IGV) JavaScript plugin. The backend tools are implemented in Python and C. The CRISPRon and CRISPRoff webservers and command-line tools are freely available at https://rth.dk/resources/crispr. [ABSTRACT FROM AUTHOR]

• The Bacillaceae-1 RNA motif consists of two distinct classes. • Reverse complementary B-1 structure upstream of 16S rRNA has one stable motif. • Intergenic B-1 motifs have high structure diversity and may act as structural switch. Non-coding RNAs are key regulatory players in bacteria. Many computationally predicted non-coding RNAs, however, lack functional associations. An example is the Bacillaceae-1 RNA motif, whose Rfam model consists of two hairpin loops. We find the motif conserved in nine of 13 non-pathogenic strains of the genus Bacillus but only in one pathogenic strain. To elucidate functional characteristics, we studied 118 hits of the Rfam model in 11 Bacillus spp. and found two distinct classes based on the ensemble diversity of their RNA secondary structure and the genomic context concerning the ribosomal RNA (rRNA) cluster. Forty hits are associated with the rRNA cluster, of which all 19 hits upstream flanking of 16S rRNA have a reverse complementary structure of low structural diversity. Fifty-two hits have large ensemble diversity, of which 38 are located between two coding genes. For eight hits in Bacillus subtilis , we investigated public expression data under various conditions and observed either the forward or the reverse complementary motif expressed. Five hits are associated with the rRNA cluster. Four of them are located upstream of the 16S rRNA and are not transcriptionally active, but instead, their reverse complements with low structural diversity are expressed together with the rRNA cluster. The three other hits are located between two coding genes in non-conserved genomic loci. Two of them are independently expressed from their surrounding genes and are structurally diverse. In summary, we found that Bacillaceae-1 RNA motifs upstream flanking of ribosomal RNA clusters tend to have one stable structure with the reverse complementary motif expressed in B. subtilis. In contrast, a subgroup of intergenic motifs has the thermodynamic potential for structural switches. [ABSTRACT FROM AUTHOR]

Obesity is a complex condition that increases the risk of life threatening diseases such as cardiovascular disease and diabetes. Studying the gene regulation of obesity is important for understanding the molecular mechanisms behind the obesity derived diseases and may lead to better intervention and treatment plans. MicroRNAs (miRNAs) are short non-coding RNAs regulating target mRNA by binding to their 3’UTR. They are involved in numerous biological processes and diseases, including obesity. In this study we use a mixed breed pig model designed for obesity studies to investigate differentially expressed miRNAs in subcutaneous adipose tissue by RNA sequencing (RNAseq). Both male and female pigs are included to explore gender differences. The RNAseq study shows that the most highly expressed miRNAs are in accordance with comparable studies in pigs and humans. A total of six miRNAs are differentially expressed in subcutaneous adipose tissue between the lean and obese group of pigs, and in addition gender specific significant differential expression is observed for a number of miRNAs. The differentially expressed miRNAs have been verified using qPCR. The results of these studies in general confirm the trends found by RNAseq. Mir-9 and mir-124a are significantly differentially expressed with large fold changes in subcutaneous adipose tissue between lean and obese pigs. Mir-9 is more highly expressed in the obese pigs with a fold change of 10 and a p-value < 0.001. Mir-124a is more highly expressed in the obese pigs with a fold change of 114 and a p-value < 0.001. In addition, mir-124a is significantly higher expressed in abdominal adipose tissue in male pigs with a fold change of 119 and a p-value < 0.05. Both miRNAs are also significantly higher expressed in the liver of obese male pigs where mir-124a has a fold change of 12 and mir-9 has a fold change of 1.6, both with p-values < 0.05. [ABSTRACT FROM AUTHOR]

Background Annotating mammalian genomes for noncoding RNAs (ncRNAs) is nontrivial since far from all ncRNAs are known and the computational models are resource demanding. Currently, the human genome holds the best mammalian ncRNA annotation, a result of numerous efforts by several groups. However, a more direct strategy is desired for the increasing number of sequenced mammalian genomes of which some, such as the pig, are relevant as disease models and production animals. Results We present a comprehensive annotation of structured RNAs in the pig genome. Combining sequence and structure similarity search as well as class specific methods, we obtained a conservative set with a total of 3,391 structured RNA loci of which 1,011 and 2,314, respectively, hold strong sequence and structure similarity to structured RNAs in existing databases. The RNA loci cover 139 cis-regulatory element loci, 58 lncRNA loci, 11 conflicts of annotation, and 3,183 ncRNA genes. The ncRNA genes comprise 359 miRNAs, 8 ribozymes, 185 rRNAs, 638 snoRNAs, 1,030 snRNAs, 810 tRNAs and 153 ncRNA genes not belonging to the here fore mentioned classes. When running the pipeline on a local shuffled version of the genome, we obtained no matches at the highest confidence level. Additional analysis of RNA-seq data from a pooled library from 10 different pig tissues added another 165 miRNA loci, yielding an overall annotation of 3,556 structured RNA loci. This annotation represents our best effort at making an automated annotation. To further enhance the reliability, 571 of the 3,556 structured RNAs were manually curated by methods depending on the RNA class while 1,581 were declared as pseudogenes. We further created a multiple alignment of pig against 20 representative vertebrates, from which RNAz predicted 83,859 dec novo RNA loci with conserved RNA structures. 528 of the RNAz predictions overlapped with the homology based annotation or novel miRNAs. We further present a substantial synteny analysis which includes 1,004 lineage specific dec novo RNA loci and 4 ncRNA loci in the known annotation specific for Laurasiatheria (pig, cow, dolphin, horse, cat, dog, hedgehog). Conclusions We have obtained one of the most comprehensive annotations for structured ncRNAs of a mammalian genome, which is likely to play central roles in both health modelling and production. The core annotation is available in Ensembl 70 and the complete annotation is available at http://rth.dk/ resources/rnannotator/susscr102/version1.02. [ABSTRACT FROM AUTHOR]

Background: MicroRNAs (miRNAs) are a class of non-protein-coding genes that play a crucial regulatory role in mammalian development and disease. Whereas a large number of miRNAs have been annotated at the structural level during the latest years, functional annotation is sparse. Actinobacillus pleuropneumoniae (APP) causes serious lung infections in pigs. Severe damage to the lungs, in many cases deadly, is caused by toxins released by the bacterium and to some degree by host mediated tissue damage. However, understanding of the role of microRNAs in the course of this infectious disease in porcine is still very limited. Results: In this study, the RNA extracted from visually unaffected and necrotic tissue from pigs infected with Actinobacillus pleuropneumoniae was subjected to small RNA deep sequencing. We identified 169 conserved and 11 candidate novel microRNAs in the pig. Of these, 17 were significantly up-regulated in the necrotic sample and 12 were down-regulated. The expression analysis of a number of candidates revealed microRNAs of potential importance in the innate immune response. MiR-155, a known key player in inflammation, was found expressed in both samples. Moreover, miR-664-5p, miR-451 and miR-15a appear as very promising candidates for microRNAs involved in response to pathogen infection. Conclusions: This is the first study revealing significant differences in composition and expression profiles of miRNAs in lungs infected with a bacterial pathogen. Our results extend annotation of microRNA in pig and provide insight into the role of a number of microRNAs in regulation of bacteria induced immune and inflammatory response in porcine lung. [ABSTRACT FROM AUTHOR]

Recent reports on new types of reactions and bonding using uranium coordination complexes have marked uranium as an effective candidate for small molecule activation and potentially as a key participant in catalytic processes. This review discusses the advantages of employing uranium in coordination chemistry, with emphasis on the importance of ligand design and the promotion of unusual chemical transformations by steric pressure. The activation of industrially relevant C1 feedstocks such as CO and CO2by uranium complexes with their exemplary abilities to stabilize highly reactive charge-separated complexes are highlighted in this article. Spectroscopic and DFT studies are also presented, demonstrating the important methods that are utilized for investigating the electronic properties of these uranium complexes. [ABSTRACT FROM AUTHOR]

Abstract: The use of density functional theory (DFT) as a means of providing otherwise inaccessible parameters of ligand-field theory (LFT) is discussed. This application of DFT strengthens both models: it revitalizes ligand-field theory by helping it relieving its permanent burden of over-parameterization, especially when applied to low-symmetry chemical systems, while LFT simultaneously provides a conceptual framework on which the plentiful numerical data from DFT computations can be reduced to familiar values of familiar parameters. The revived LFT contains information that cannot be extracted from DFT, but which, in principle, can be projected back on to DFT, thus providing the complete energy matrix of the partially filled d q configuration. Application to two kinds of chemical systems will be described: electronically strongly anisotropic nitride complexes and tetrahedral d2 systems. In the former applications, focus is on the ligand field, its symmetry partition, and its additivity. In the d2 systems, the focus is on extracting repulsion parameters, but also parameters of the angular overlap model will be discussed. Structural and spectroscopic studies corroborated by DFT computations demonstrate that complexes containing the {Cr(N)}2+ moiety coordinated to weak auxiliary ligands are better considered as perturbed linear systems than axially compressed octahedral systems. Average-of-configuration (AOC) computations on the tetrahedral systems, analysed by using two electronic interaction models, the Slater–Condon–Shortley model and the Parametrical Multiplet Term model, both formulated in terms of mutually orthogonal, barycentered coefficient operators, illuminate two-electron interactions. Thereby the quantitative influence of the individual parameters associated with these operators becomes the novelty of the analysis. The SCS model has D terms and E terms, where D is Jørgensen''s spin-pairing energy parameter and E is proportional to the Racah parameter B. The PMT model has four terms, two D terms and two E terms, and can be used to free the SCS model, which is the superior model for comparing with experiments, from small unwanted parts of the DFT-computational results. For CrIVX4 in T d symmetry, the results were as a new illustration deprived of their ligand-field contribution and the remaining “molecular atom” analysed in the PMT model, whereas for the VIIIX4 − complexes, distorted to D 2d symmetry, the results were described with four PMT parameters, all following the nephelauxetic series, and three AOM parameters, whose computed values provide support to the concept of linear ligation. [Copyright &y& Elsevier]

Sterically pressured mid- to high-valent uranium complexes with an aryloxide substituted triazacyclononane ligand scaffold, [(([supR]ArO)[sub3−], were studied for carbon dioxide activation and transformation chemistry. The high valent uranium(V) imido species [(([supR=ArO)[sub3]tacn)U(NR)] (R = [supt]Bu, R' = 2,4,6-trimethylphenyl (2=[supt]Bu); R = Ad, R' = 2,4,6-trimethyiphenyl (2-Ad); R = [supt]Bu, R' = phenyl (3=[supt]Bu)) were synthesized and spectroscopically characterized. X-ray crystallography of the tert-butyl mesityl imido derivative, 2=[supt]BU, reveals coordination of a bent imido fragment with a relatively long U-N bond distance of 2.05 Å. The mesityl imido complexes reacted with carbon dioxide, readily extruding free isocyanate to produce uranium(V) terminal oxo species, [((RArO)3tacn)U(O)] (R = [supt]Bu (4−[supt]Bu), Ad (4-Ad)), presumably through multiple bond metathesis via a uranium(V) carbimate intermediate. Using the smaller phenyl imido fragment in 3−[supt]Bu slowed isocyanate loss, allowing the uranium(V) carbimate intermediate to undergo a second metathesis reaction, ultimately producing the diphenyl ureate derivative, [(([suptBU]ArO)[sub3]tacn)U(NPh[sub2])CO] (5Bu). Single crystal X-ray diffraction studies were carried out on both uranium(V) terminal oxo complexes and revealed short U-a bonds (1.85 A) indicative of a formal UO triple bond. The electronic structure of the oxo U(V) complexes was investigated by electronic absorption and EPR spectroscopies as well as SQUID magnetization and DFT studies, which indicated that their electronic properties are highly unusual. To obtain insight into the reactivity of CO2 with U-N bonds, the reaction of the uranium(lV) amide species, [((RArO)3tacn)U(NHMe5)] (R = [supt]Bu (6tBU), Ad (6-Ad) with carbon dioxide was investigated. These reactions produced the uranium(lV) carbamate complexes, [(([supR]ArO)[sub3]tacn)U(CO[sub2]NHMes)] (R = [supt]Bu (7=[supt]Bu), Ad (7ϟ Ad)), resulting from insertion of carbon dioxide into U-N(amide) bonds. The molecular structures of the synthesized uranium carbamate complexes highlight the different reactivities due to the steric pressure introduced by the alkyl derivatized tris(aryloxide) triazacyclononane ligand. The sterically open tert-butyl derivative creates a monodentate η[sup1]-O bound carbamate species, while the sterically more bulky adamantyl- substituted compound forces a bidentate ,κ[sup2]-O,O coordination mode of the carbamate ligand. [ABSTRACT FROM AUTHOR]

The reaction of [((t-BuArO)3tacn)UIII] (1) with 4,4′-di-tert-butylbenzophenone affords a unique isolable U(IV) ketyl radical species [((t-BuArO)3tacn)UIV(OC•t-BuPh2)] (2) supported by XRD data, magnetization measurements, and DFT calculations. Isolation and full characterization of the corresponding diphenyl methoxide complex [((t-BuArO)3tacn)UIV(OCHt-BuPh2)] (3) is also presented. The one-electron reduction of benzophenone by [((AdArO)3tacn)UIII] (4) leads to a purple U(IV) ketyl radical intermediate [((AdArO)3tacn)UIV(OC•Ph2)] (5). This species is highly reactive, and attempts at isolation were unsuccessful and resulted in methoxide complex [((AdArO)tacn)3UIV(OCHPh2)] (6) from H abstraction and dinuclear paracoupled complex [((AdArO)3tacn)UIV(OCPhPh-CPh2O)UIV((AdArO)3tacn)] (7). [ABSTRACT FROM AUTHOR]

With tetragonal distortions of tetrahedral d² complexes as examples, nonadditive and additive ligand fields are compared computationally, using Kohn-Sham density functional theory (KS-DFT) and ligand-field theory to obtain 45 linear, parametrical equations. For each complex, a ‘data’ reduction from three nonadditive-field parameters to two parameters of the additive field occurs. The complexes VX4- and CrX4 (where X = F, Cl, Br, I) provide the two-dimensional spectrochemical series of the σ and π AOM parameters, which are known semiempirically for the halide ligands. The same parametrical results can be obtained from the Kohn-Sham orbital energies of the ‘average of configuration’ computation. [ABSTRACT FROM AUTHOR]

The Amsterdam Density Functional (ADF) package has been used to constrain Kohn-Sham DFT in such a fashion that a transition from KS-DFT to ligand-field theory in the form of the parametrical d[sup q] model is completely well-defined. A relationship is established between the strong-field approximation of the parametrical d² model for the tetrahedral complexes VCl[sup -, sub 4] and VBr[sup -, sub 4] and certain fixed-orbital ADF-computed energies. In this way values for all the parameters of the d² model may be computed, thus allowing the ADF results to be expressed in terms of a KS-DFT energy matrix that can be diagonalized. This means that the KS-DFT deficiency with regard to computation of nondiagonal elements has been overcome and the KS-DFT eigenenergies have become available through the KS-DFT mimicking of the ligand-field plus repulsion model. By using mutually orthogonal strong-field energy matrices, the mimicking has been further elucidated. The computed values for the empirical parameters of VCl[sup -, sub 4]- and VBr[sup -, sub 4] are in good agreement with experimental data. The spectrochemical and the nephelauxetic series have been computed by including the remaining halide complexes and the quantitatively special position of F[sup -] among the halides corroborated for both series. [ABSTRACT FROM AUTHOR]

The nephelauxetic phenomenon is reviewed. So is the newest formulation of the Slater–Condon–Shortley model (SCS) for the multiplet term energies of atomic dq ions. This model is expressed as a sum of products of empirical parameters and their associated coefficient operators. The orthogonal-operators formalism is used by choosing Jørgensen''s spin-pairing energy parameter D as one of the repulsion parameters when the other parameter required by the SCS model is the Racah parameter B. By restricting the coefficient operators further so as to make them orthonormal, B changes into the new parameter E=(21/4)B. D accounts for the energy separation of eigenstates with different spin and/or seniority, E for the final separation into the spatially different eigenstates. The numerical values of D and E exhibit directly the relative contributions of D and E to the average configurational splitting. The parameter set {D, E} is equivalent to the SCS set {F2, F4} as well as to the Racah set {C, B} even though these sets are not associated with orthogonal operators so that cross products, as for instance CB, enter the expressions for the average configurational splitting. Moreover, neither conventional parameter set provides a visualizable interpretation of the energetic functioning of its parameters upon the eigenstate energy separations. The symmetry problem of the two-electron part of Kohn–Sham DFT is discussed in the framework of the SCS model. With the future perspective of mimicking ligand-field theory and, in particular, of dealing with the full nephelauxetic phenomenon non-empirically, the atomic part of the phenomenon is handled by calculation of the parameters D and E successfully for numerous gaseous ions with 3dq configurations. The Amsterdam Density Functional package (ADF) has been used in a two-step procedure. First, all the Kohn–Sham self-consistent field d-orbitals of the 3dq configurations as well as all the inner core orbitals were determined using population numbers of q/10 for all the 3d-spin–orbitals, that is, by doing the average-of-configuration calculation. Secondly, all these orbitals were frozen in all the subsequent calculations on the same system. Here density distributions of α and β electrons were defined by integer occupation numbers of d-spin–orbitals corresponding to single Slater determinants. On grounds of principle, complex orbitals were found not to be usable. The ADF energy associated with a real determinant was—apart from an additive constant—taken to correspond to the expectation value of the interelectronic repulsion operator acting on the dq part of this determinant. A characteristic property of the method is that the energy is expressed by a sum over contributions from the Coulomb and the exchange-correlation functional. It has turned out that for real d-orbitals both of these terms independently obey the symmetry restrictions as well as the special SCS restrictions of the dq assumption. However, the two functionals are not commensurable. They give different parametric results. Nevertheless, by averaging the total energy results from using a gradient-corrected (GC) set of functionals over the configuration dq, values for the SCS parameters that are better than those of Hartree–Fock calculations are obtained. In the local density approximation (LDA) the exchange-correlation functionals were found to provide the same energy for all real Slater determinants with the same value for MS, which means that the exchange-correlation part of the energy corresponds to B=E=0. However, the Coulomb functional invariably exaggerates the values of the E parameter so that LDA functionals end up giving fairly reasonable values of E, as well as D. We have obtained a complete bridge between KS-DFT in the form of ADF and the atomic part of ligand-field theory. [Copyright &y& Elsevier]

Self-contained structured domains of RNA sequences have often distinct molecular functions. Determining the boundaries of structured domains of a non-coding RNA (ncRNA) is needed for many ncRNA gene finder programs that predict RNA secondary structures in aligned genomes because these methods do not necessarily provide precise information about the boundaries or the location of the RNA structure inside the predicted ncRNA. Even without having a structure prediction, it is of interest to search for structured domains, such as for finding common RNA motifs in RNA-protein binding assays. The precise definition of the boundaries are essential for downstream analyses such as RNA structure modelling, e.g., through covariance models, and RNA structure clustering for the search of common motifs. Such efforts have so far been focused on single sequences, thus here we present a comparison for boundary definition between single sequence and multiple sequence alignments. We also present a novel approach, named RNAbound, for finding the boundaries that are based on probabilities of evolutionarily conserved base pairings. We tested the performance of two different methods on a limited number of Rfam families using the annotated structured RNA regions in the human genome and their multiple sequence alignments created from 14 species. The results show that multiple sequence alignments improve the boundary prediction for branched structures compared to single sequences independent of the chosen method. The actual performance of the two methods differs on single hairpin structures and branched structures. For the RNA families with branched structures, including transfer RNA (tRNA) and small nucleolar RNAs (snoRNAs), RNAbound improves the boundary predictions using multiple sequence alignments to median differences of −6 and −11.5 nucleotides (nts) for left and right boundary, respectively (window size of 200 nts). [ABSTRACT FROM AUTHOR]

Yield improvements in cell factories can potentially be obtained by fine-tuning the regulatory mechanisms for gene candidates. In pursuit of such candidates, we performed RNA-sequencing of two α-amylase producing Bacillus strains and predict hundreds of putative novel non-coding transcribed regions. Surprisingly, we found among hundreds of non-coding and structured RNA candidates that non-coding genomic regions are proportionally undergoing the highest changes in expression during fermentation. Since these classes of RNA are also understudied, we targeted the corresponding genomic regions with CRIPSRi knockdown to test for any potential impact on the yield. From differentially expression analysis, we selected 53 non-coding candidates. Although CRISPRi knockdowns target both the sense and the antisense strand, the CRISPRi experiment cannot link causes for yield changes to the sense or antisense disruption. Nevertheless, we observed on several instances with strong changes in enzyme yield. The knockdown targeting the genomic region for a putative antisense RNA of the 3′ UTR of the skfA-skfH operon led to a 21% increase in yield. In contrast, the knockdown targeting the genomic regions of putative antisense RNAs of the cytochrome c oxidase subunit 1 (ctaD) , the sigma factor sigH , and the uncharacterized gene yhfT decreased yields by 31 to 43%. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) are covalently closed circular non-coding RNAs. Due to their structure, circRNAs are more stable and have longer half-lives than linear RNAs making them good candidates for disease biomarkers. Despite the scientific relevance of these molecules, the study of circRNAs in non-model organisms is still in its infancy. Here, we analyse total RNA-seq data to identify circRNAs in sheep from peripheral blood mononuclear cells (PBMCs) and parietal lobe cortex. Out of 2510 and 3403 circRNAs detected in parietal lobe cortex and in PBMCs, a total of 1379 novel circRNAs were discovered. Remarkably, around 63% of all detected circRNAs were found to be completely homologous to a circRNA annotated in human. Functional enrichment analysis was conducted for both tissues based on GO terms and KEGG pathways. The enriched terms suggest an important role of circRNAs from encephalon in synaptic functions and the involvement of circRNAs from PBMCs in basic immune system functions. In addition to this, we investigated the role of circRNAs in repetitive vaccination experiments via differential expression analysis and did not detect any significant relationship. At last, our results support both the miRNA sponge and the miRNA shuttle functions of CDR1-AS in sheep brain. To our knowledge, this is the first study on circRNA annotation in sheep PBMCs or parietal lobe cortex samples. [ABSTRACT FROM AUTHOR]

The synthesis of a potentially redox active tripodal ligand containing a thri(aryloxide) functionalized mesitylene anchor, ((tBu'ArOH)3mes) (1), and its metatation with low-valent uranium to form [((tBu ArO)3mes)U] (1-U) is reported. The results from characterization by X-ray crystallography, spectroscopic studies, and computational analysis, as well as initial reactivity studies, support a+3 uranium oxidation state. Comparison to the previously synthesized complex, [((tBuArO)3tacn)U] (2-U), featuring the . redox-innocent Irtazacyctononane anchor reveals that changing the anchor from the flexible friazacydononane to a rigid mesilyl fragment increases the structural flexibility of the arylotdde substituents in complexes ott. The synthesis and crystal structures of uranium(IV) amide complexes of 1-U and 2-U are discussed. [ABSTRACT FROM AUTHOR]

Circular RNAs (circRNAs) are increasingly recognized to play crucial roles in post-transcriptional gene regulation including functioning as microRNA (miRNA) sponges or as wide-spread regulators, for example in stem cell differentiation. It is therefore highly relevant to identify if a transcript of interest can also function as a circRNA. Here, we present a user-friendly web server that predicts if coding and noncoding RNAs have circRNA isoforms and whether circRNAs are expressed in stem cells. The predictions are made by random forest models using sequence-derived features as input. The output scores are converted to fractiles, which are used to assess the circRNA and stem cell potential. The performances of the three models are reported as the area under the receiver operating characteristic (ROC) curve and are 0.82 for coding genes, 0.89 for long noncoding RNAs (lncRNAs) and 0.72 for stem cell expression. We present WebCircRNA for quick evaluation of human genes and transcripts for their circRNA potential, which can be essential in several contexts. [ABSTRACT FROM AUTHOR]

The innate immune system is paramount in the response to and clearance of influenza A virus (IAV) infection in non-immune individuals. Known factors include type I and III interferons and antiviral pathogen recognition receptors, and the cascades of antiviral and pro- and anti-inflammatory gene expression they induce. MicroRNAs (miRNAs) are increasingly recognized to participate in post-transcriptional modulation of these responses, but the temporal dynamics of how these players of the antiviral innate immune response collaborate to combat infection remain poorly characterized. We quantified the expression of miRNAs and protein coding genes in the lungs of pigs 1, 3, and 14 days after challenge with swine IAV (H1N2). Through RT-qPCR we observed a 400-fold relative increase in IFN-λ3 gene expression on day 1 after challenge, and a strong interferon-mediated antiviral response was observed on days 1 and 3 accompanied by up-regulation of genes related to the pro-inflammatory response and apoptosis. Using small RNA sequencing and qPCR validation we found 27 miRNAs that were differentially expressed after challenge, with the highest number of regulated miRNAs observed on day 3. In contrast, the number of protein coding genes found to be regulated due to IAV infection peaked on day 1. Pulmonary miRNAs may thus be aimed at fine-tuning the initial rapid inflammatory response after IAV infection. Specifically, we found five miRNAs (ssc-miR-15a, ssc-miR-18a, ssc-miR-21, ssc-miR-29b, and hsa-miR-590-3p)–four known porcine miRNAs and one novel porcine miRNA candidate–to be potential modulators of viral pathogen recognition and apoptosis. A total of 11 miRNAs remained differentially expressed 14 days after challenge, at which point the infection had cleared. In conclusion, the results suggested a role for miRNAs both during acute infection as well as later, with the potential to influence lung homeostasis and susceptibility to secondary infections in the lungs of pigs after IAV infection. [ABSTRACT FROM AUTHOR]

Alzheimer's disease (AD) is a progressive and irreversible brain disorder, which can occur either sporadically, due to a complex combination of environmental, genetic, and epigenetic factors, or because of rare genetic variants in specific genes (familial AD, or fAD). A key hallmark of AD is the accumulation of amyloid beta (Aβ) and Tau hyperphosphorylated tangles in the brain, but the underlying pathomechanisms and interdependencies remain poorly understood. Here, we identify and characterise gene expression changes related to two fAD mutations (A79V and L150P) in the Presenilin-1 (PSEN1) gene. We do this by comparing the transcriptomes of glutamatergic forebrain neurons derived from fAD-mutant human induced pluripotent stem cells (hiPSCs) and their individual isogenic controls generated via precision CRISPR/Cas9 genome editing. Our analysis of Poly(A) RNA-seq data detects 1111 differentially expressed coding and non-coding genes significantly altered in fAD. Functional characterisation and pathway analysis of these genes reveal profound expression changes in constituents of the extracellular matrix, important to maintain the morphology, structural integrity, and plasticity of neurons, and in genes involved in calcium homeostasis and mitochondrial oxidative stress. Furthermore, by analysing total RNA-seq data we reveal that 30 out of 31 differentially expressed circular RNA genes are significantly upregulated in the fAD lines, and that these may contribute to the observed protein-coding gene expression changes. The results presented in this study contribute to a better understanding of the cellular mechanisms impacted in AD neurons, ultimately leading to neuronal damage and death. • Extracellular matrix components are altered in fAD neurons compared to controls • Merging GENCODE and FANTOM-CAT annotations improves lncRNA identification in RNA-seq • CircRNAs are predominantly upregulated in fAD neurons compared to controls • Competing endogenous RNAs may contribute to gene expression modulation in fAD [ABSTRACT FROM AUTHOR]

Protein association networks can be inferred from a range of resources including experimental data, literature mining and computational predictions. These types of evidence are emerging for non-coding RNAs (ncRNAs) aswell. However, integration of ncRNAs into protein association networks is challenging due to data heterogeneity. Here, we present a database of ncRNA-RNA and ncRNA-protein interactions and its integration with the STRING database of protein-protein interactions. These ncRNA associations cover four organisms and have been established from curated examples, experimental data, interaction predictions and automatic literaturemining. RAIN uses an integrative scoring scheme to assign a confidence score to each interaction. We demonstrate that RAIN outperforms the underlying microRNA-target predictions in inferring ncRNA interactions. RAIN can be operated through an easily accessibleweb interface and all interaction data can be downloaded. [ABSTRACT FROM AUTHOR]

Recent experimental and computational progress has revealed a large potential for RNA structure in the genome. This has been driven by computational strategies that exploit multiple genomes of related organisms to identify common sequences and secondary structures. However, these computational approaches have two main challenges: they are computationally expensive and they have a relatively high false discovery rate (FDR). Simultaneously, RNA 3D structure analysis has revealed modules composed of non-canonical base pairs which occur in non-homologous positions, apparently by independent evolution. These modules can, for example, occur inside structural elements which in RNA 2D predictions appear as internal loops. Hence one question is if the use of such RNA 3D information can improve the prediction accuracy of RNA secondary structure at a genome-wide level. Here, we use RNAz in combination with 3D module prediction tools and apply them on a 13-way vertebrate sequence-based alignment. We find that RNA 3D modules predicted by metaRNAmodules and JAR3D are significantly enriched in the screened windows compared to their shuffled counterparts. The initially estimated FDR of 47.0% is lowered to below 25% when certain 3D module predictions are present in the window of the 2D prediction. We discuss the implications and prospects for further development of computational strategies for detection of RNA 2D structure in genomic sequence. [ABSTRACT FROM AUTHOR]

For 10,000?years pigs and humans have shared a close and complex relationship. From domestication to modern breeding practices, humans have shaped the genomes of domestic pigs. Here we present the assembly and analysis of the genome sequence of a female domestic Duroc pig (Sus scrofa) and a comparison with the genomes of wild and domestic pigs from Europe and Asia. Wild pigs emerged in South East Asia and subsequently spread across Eurasia. Our results reveal a deep phylogenetic split between European and Asian wild boars ?1 million years ago, and a selective sweep analysis indicates selection on genes involved in RNA processing and regulation. Genes associated with immune response and olfaction exhibit fast evolution. Pigs have the largest repertoire of functional olfactory receptor genes, reflecting the importance of smell in this scavenging animal. The pig genome sequence provides an important resource for further improvements of this important livestock species, and our identification of many putative disease-causing variants extends the potential of the pig as a biomedical model. [ABSTRACT FROM AUTHOR]