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Human pluripotent stem cells (hPSCs) are uniquely suited to study human development and disease and promise to revolutionize regenerative medicine. These applications rely on robust methods to manipulate gene function in hPSC models. This comprehensive review aims to both empower scientists approaching the field and update experienced stem cell biologists. We begin by highlighting challenges with manipulating gene expression in hPSCs and their differentiated derivatives, and relevant solutions (transfection, transduction, transposition, and genomic safe harbor editing). We then outline how to perform robust constitutive or inducible loss‐, gain‐, and change‐of‐function experiments in hPSCs models, both using historical methods (RNA interference, transgenesis, and homologous recombination) and modern programmable nucleases (particularly CRISPR/Cas9 and its derivatives, i.e., CRISPR interference, activation, base editing, and prime editing). We further describe extension of these approaches for arrayed or pooled functional studies, including emerging single‐cell genomic methods, and the related design and analytical bioinformatic tools. Finally, we suggest some directions for future advancements in all of these areas. Mastering the combination of these transformative technologies will empower unprecedented advances in human biology and medicine. [ABSTRACT FROM AUTHOR]

Inherited information is transmitted to progeny primarily by the genome through the gametes. However, in recent years, epigenetic inheritance has been demonstrated in several organisms, including animals. Although it is clear that certain post‐translational histone modifications, DNA methylation, and noncoding RNAs regulate epigenetic inheritance, the molecular mechanisms responsible for epigenetic inheritance are incompletely understood. This review focuses on the role of small RNAs in transmitting epigenetic information across generations in animals. Examples of documented cases of transgenerational epigenetic inheritance are discussed, from the silencing of transgenes to the inheritance of complex traits, such as fertility, stress responses, infections, and behavior. Experimental evidence supporting the idea that small RNAs are epigenetic molecules capable of transmitting traits across generations is highlighted, focusing on the mechanisms by which small RNAs achieve such a function. Just as the role of small RNAs in epigenetic processes is redefining the concept of inheritance, so too our understanding of the molecular pathways and mechanisms that govern epigenetic inheritance in animals is radically changing. [ABSTRACT FROM AUTHOR]

Diapause is an important overwintering strategy enabling Locusta migratoria to survive under stressed conditions. We identified a novel dual‐specificity kinase gene that is differentially expressed between long and short day‐treated L. migratoria. To determine its function on photoperiodic diapause induction, we cloned the specific gene. Interestingly, phylogenetic analysis shows that this dual‐specificity kinase is of the mycetozoa protein kinase‐like (MPKL) type and may have been transferred horizontally from Mycetozoa to L. migratoria. RNA interference results confirm that MPKL promotes photoperiodic diapause induction of L. migratoria. Furthermore, MPKL significantly inhibits Akt and FOXO (i.e. forkhead box protein O) phosphorylation levels in ovaries, and also enhances reactive oxygen species, superoxide dismutase and catalase activities, whereas peroxidase activity is decreased under both photoperiodic regimes. The findings of the present study offer insight into the molecular mechanism responsible for dual‐specificity kinase‐induced diapause in insects. [ABSTRACT FROM AUTHOR]

MicroRNAs (miRNAs) are small regulatory noncoding RNAs that are generated in the canonical RNA interference (RNAi) pathway. Drosha, DiGeorge syndrome critical region 8 (DGCR8) and Dicer are key players in miRNA biogenesis. Argonaute (Ago) proteins bind to miRNAs and are guided by them to find messenger RNA targets and carry out post‐transcriptional silencing of protein‐coding genes. Recently, emerging evidence suggests that RNAi factors have a range of noncanonical functions that are beyond miRNA biogenesis. These functions pertain to various biological processes, such as development, transcriptional regulation, RNA processing and maintenance of genome integrity. Here, we review recent literature reporting miRNA‐independent, noncanonical functions of Drosha, DGCR8, Dicer and Ago proteins and discuss the importance of these functions. [ABSTRACT FROM AUTHOR]

Rab5 GTPases are master regulators of early endosome biogenesis and transport. The genome of Saccharomyces cerevisiae encodes three Rab5 proteins: Vps21, the major isoform, Ypt52 and Ypt53. Here, we show that Vps21 is the most abundant Rab5 protein and Ypt53 is the least abundant. In stressed cells, Ypt53 levels increase but never exceed that of Vps21. Its induction requires the transcription factors Crz1 and Gis1. In growing cells, the expression of Ypt53 is suppressed by post-transcriptional mechanisms mediated by the untranslated regions of the YPT53 mRNA. Based on genetic experiments, these sequences appear to stimulate deadenylation, Pat1-activated decapping and Xrn1-mediated mRNA degradation. Once this regulation is bypassed, Ypt53 protein levels surpass Vps21, and Ypt53 is sufficient to maintain endosomal function and cell growth. [ABSTRACT FROM AUTHOR]

The conserved 3′-5′ RNA exonuclease ERI1 is implicated in RNA interference inhibition, 5.8S rRNA maturation and histone mRNA maturation and turnover. The single ERI1 homologue in Drosophila melanogaster Snipper ( Snp) is a 3′-5′ exonuclease, but its in vivo function remains elusive. Here, we report Snp requirement for normal Drosophila development, since its perturbation leads to larval arrest and tissue-specific downregulation results in abnormal tissue development. Additionally, Snp directly interacts with histone mRNA, and its depletion results in drastic reduction in histone transcript levels. We propose that Snp protects the 3′-ends of histone mRNAs and upon its absence, histone transcripts are readily degraded. This in turn may lead to cell cycle delay or arrest, causing growth arrest and developmental perturbations. [ABSTRACT FROM AUTHOR]

Mod5 is a multifunctional protein that modifies a subset of tRNAs in the cytoplasm and is also required for an RNA-mediated form of transcriptional silencing. Previous in vivo studies have shown that the nuclear silencing function of Mod5 does not require that the causative tRNA gene encode a Mod5 substrate, although Mod5 is still required. However, previous data have not directly tested whether Mod5 can directly bind substrate and nonsubstrate RNAs. We herein demonstrate that Mod5 directly binds to both substrate and nonsubstrate RNAs, including a highly structured, non- tRNA sequence (5S- rRNA), consistent with previous in vivo data. Furthermore, we show that some RNAs drastically change the aggregation behavior of Mod5 with implications for tRNA gene-mediated silencing. [ABSTRACT FROM AUTHOR]

Myeloid cell leukemia 1 ( Mcl-1) is an antiapoptotic member of the Bcl-2 family of proteins that when overexpressed is associated with high tumor grade, poor survival, and resistance to chemotherapy. Mcl-1 is amplified in many human cancers, and knockdown of Mcl-1 using RNAi can lead to apoptosis. Thus, Mcl-1 is a promising cancer target. Here, we describe the discovery of picomolar Mcl-1 inhibitors that cause caspase activation, mitochondrial depolarization, and selective growth inhibition. These compounds represent valuable tools to study the role of Mcl-1 in cancer and serve as useful starting points for the discovery of clinically useful Mcl-1 inhibitors. PDB ID codes Comp. 2: ; Comp. 5: . [ABSTRACT FROM AUTHOR]

The role of the RNA-binding protein human antigen R (HuR) in hepatocarcinogenesis is still elusive. By employing short hairpin (sh)RNA-dependent knockdown approach, we demonstrate that lymphotoxin α (LTα) is a target of posttranscriptional gene regulation by HuR in hepatocellular carcinoma (HepG2) cells. Consequently, the increased mRNA decay upon HuR depletion significantly affects lymphotoxin expression at both, the mRNA and protein level. Biotin-pulldown assay showed that HuR specifically interacts with the 3′-untranslated region (3′-UTR) of the LTα mRNA. Furthermore, electrophoretic mobility shift assay (EMSA) implicates that the RNA-binding critically depends on the RNA recognition motif 2 (RRM2) and the hinge region of HuR. [ABSTRACT FROM AUTHOR]

Tetraspanin 1 (TSPAN1) has been reported to be upregulated in gastric cancer (GC). However, whilst TSPAN1 is positively correlated with clinical stage and negatively correlated with survival rates, its function in GC remains elusive. Here we show that expression of TSPAN1 is significantly higher in GC tissues compared to non-cancerous tissues. Furthermore, we demonstrate that RNAi-mediated down-regulation of TSPAN1 expression markedly blocks GC cell proliferation, cell cycle progression and invasive activity. We identified TSPAN1 as a novel target gene of miR-573. Overexpression of miR-573 suppressed proliferation and invasion of GC cells by down-regulation of TSPAN1 expression. Restoration of TSPAN1 rescued the effects of miR-573 overexpression. Therefore, our findings suggest that the miR-573/TSPAN1 axis is important in the control of gastric carcinogenesis. [ABSTRACT FROM AUTHOR]

Smad7 has a key role in apoptosis of mammalian ovarian granulosa cells (GCs), as it antagonizes and fine-tunes transforming growth factor β (TGFβ) signaling. This study demonstrates that miR-92a regulates GC apoptosis in pig ovaries by targeting Smad7 directly. The expression level of miR-92a was down-regulated in atretic porcine follicles, whereas miR-92a expression led to inhibition of GC apoptosis. The Smad7 gene was identified as a direct target of miR-92a using a dual-luciferase reporter assay. Transfection of GCs with miR-92a mimics decreased Smad7 mRNA and protein levels, whereas expression of an miR-92a inhibitor in GCs had the opposite effect. In addition, knockdown of Smad7 prevented GC apoptosis in cells that expressed the miR-92a inhibitor. [ABSTRACT FROM AUTHOR]

The aberrant expression of PSMD10 has important functions in various malignancies. This study showed that PSMD10 was highly expressed and inversely correlated with the expression of miR-605 in intrahepatic cholangiocarcinoma (ICC) specimens. MiR-605 directly targeted and repressed PSMD10 expression. In addition, over-expression of miR-605 inhibited ICC cell progression both in vitro and in vivo. This effect of miR-605 on ICC cells was similar to that of PSMD10 knock-down by RNAi. Moreover, restoration of PSMD10 could reverse the phenotypic alteration caused by miR-605 in ICC cells. These results suggest a new therapeutic strategy in ICC by restoring miR-605, which is regulated by p53. [ABSTRACT FROM AUTHOR]

Rare Caenorhabditis elegans males arise when sex chromosome non-disjunction occurs during meiosis in self-fertilizing hermaphrodites. Non-disjunction is a relatively rare event, and males are typically observed at a frequency of less than one in five hundred wild-type animals. Males are required for genetic crosses and phenotypic analysis, yet current methods to generate large numbers of males can be cumbersome. Here, we identify RNAi reagents (dsRNA-expressing bacteria) with improved effectiveness for eliciting males. Specifically, we used RNAi to systematically reduce the expression of over two hundred genes with meiotic chromosome segregation functions, and we identified a set of RNAi reagents that robustly and reproducibly elicited male progeny. [ABSTRACT FROM AUTHOR]

RNA interference (RNAi) denotes sequence-specific mRNA degradation induced by long double-stranded RNA (dsRNA). RNAi is an ancient eukaryotic defense mechanism against viruses and mobile elements. In mammals, endogenous RNAi was outstripped during evolution by the current innate and acquired immunity. The RNAi apparatus, which remains essentially intact, serves mostly the microRNA pathway, which regulates endogenous gene expression. Remarkably, several recent publications brought the mammalian endogenous RNAi pathway back into the spotlight. Here, I will provide an up-to-date review of the mammalian endogenous RNAi pathway with a focus on its defensive role and overlaps with miRNA and piRNA pathways. [ABSTRACT FROM AUTHOR]

Highlights: [•] We design selectively 2′-O-methyl modified 42 and 63bp anti-MDR1-siRNAs. [•] We examine their ability to silence the expression of the target gene and the specificity of their action. [•] We show that 42 and 63bp siRNAs induce more effective RNAi at lower concentrations than classical 21bp siRNA. [•] These siRNAs act in a Dicer-independent mode and are devoid of immunostimulating properties. [Copyright &y& Elsevier]

One of the major challenges in stem cell research is to decipher the controlling mechanisms/genes of stem cell homeostasis. Through an RNAi mediated genetic screen of living animals, we identified an evolutionarily conserved histone acetyltransferase Atac2 as a novel regulator of Drosophila intestinal stem cells (ISCs). Expression of Atac2-RNAi or a dominant negative allele of Atac2 generated more ISCs, while excessive Atac2 or a histone deacetylase inhibitor promoted ISC differentiation without affecting ISC survival or lineage specification. These findings extend our knowledge of epigenetic mechanisms in stem cell regulation. [ABSTRACT FROM AUTHOR]

Highlights: [•] Short heat shock decreased the endocytotic activity of human dendritic cells (DCs). [•] Heat shock-induced robust membrane currents in DCs. [•] These effects were mediated by TRPV2 ion channels. [Copyright &y& Elsevier]

Abstract: The latent ribonuclease RNase L and the interferon-inducible 2′,5′-oligoadenylate synthetase (OAS) have been implicated in the antiviral response against hepatitis C virus (HCV). However, the specific roles of these enzymes against HCV have not been fully elucidated. In this study, a scarce endogenous expression and RNA degrading activity of RNase L in human hepatoma Huh7 cells enabled us to demonstrate the antiviral activity of RNase L against HCV replication through the transient expression of the enzyme. The antiviral potential of specific members of the OAS family was further examined through overexpression and RNA interference approaches. Our data suggested that among the members of the OAS family, OAS1 p46 and OAS3 p100 mediate the RNase l-dependent antiviral activity against HCV. [Copyright &y& Elsevier]

Abstract: T cell activation depends on appropriate and precise regulation of gene expression. Here we find that rapidly translocated RNA-binding protein HuR, forms messenger ribonucleoprotein (mRNP) complexes with transiently expressed mRNAs encoding early-response transcription factors, including c-Fos, c-Jun, and Egr-1. Knockdown and overexpression assays demonstrated that proper posttranscriptional control of Egr-1 expression requires HuR-mediated translation control. Further analysis showed that the Egr-1 3′UTR, which contains AU-rich elements (AREs) and interacts directly with HuR, suppresses reporter gene expression and mediates posttranscriptional regulation of Egr-1 by HuR. These findings underscore an essential role for HuR in regulating early events during T cell activation. [Copyright &y& Elsevier]

Abstract: Protein incorporated later into tight junctions (Pilt), also termed tight junction-associated protein 1 or tight junction protein 4, is a coiled-coil domain-containing protein that was originally identified as a human discs large-interacting protein. In this study, we identified Pilt as an Arf6-binding protein by yeast two-hybrid screening. By immunocytochemical analysis, Pilt was shown to be predominantly localized at the trans-Golgi complex and to exhibit diffuse cytoplasmic distribution in association with endosomes and plasma membrane in NIH3T3 cells. Silencing of endogenous Pilt disrupted the Golgi structure. The present findings suggest the functional involvement of Pilt in the maintenance of the Golgi structure. Structured summary of protein interactions: GM130 and Pilt colocalize by fluorescence microscopy (View interaction) Arf6(Q67L) physically interacts with Pilt by two hybrid (View Interaction: 1, 2) Pilt physically interacts with Arf6(Q67L) by pull down (View interaction) [Copyright &y& Elsevier]

Abstract: We previously identified the peroxin PEX13 in Trypanosoma brucei. Although lacking some features considered typical of PEX13s, it appeared functional in the biogenesis of glycosomes, the peroxisome-like organelles of trypanosomatids. Here we report the identification of a very different trypanosomatid PEX13, not containing the commonly encountered PEX13 SH3 domain but having other typical features. It is readily detected with the jackhmmer database search program, but not with PSI-BLAST. This is the first time different PEX13 isoforms are reported in a single organism. We show that this PEX13.2, like the PEX13.1 previously described, is associated with glycosomes and that its depletion by RNA interference affects the biogenesis of the organelles and viability of trypanosomes. The features considered typical of PEX13s are discussed. Structured summary of protein interactions: Pex19 physically interacts with Pex13.2 by two hybrid (View interaction) Pex13.1 physically interacts with Pex13.2 by two hybrid (View interaction) [Copyright &y& Elsevier]

Abstract: Gonadotropin-releasing hormone (GnRH) regulates the synthesis and secretion of follicle-stimulating hormone (FSH) by stimulating the transcription of Fshβ gene. Our iTRAQ quantitative proteomics result showed that the abundance of α-actinin4 (ACTN4) increased in the nuclei of LβT2 cells upon GnRH induction. Using RNA interference, reverse transcription and real-time PCR, luciferase and transient transfection assays, we proved that ACTN4 is involved in the regulation of mouse Fshβ gene (mFshβ) transcription and its C-terminal calmodulin (CaM)-like domain is crucial for this process. Our study suggests that ACTN4 nuclear translocation mediates GnRH stimulation of mFshβ gene transcription. [Copyright &y& Elsevier]

Abstract: MicroRNAs are small non-coding RNAs that modulate gene expression at post-transcriptional level, playing a crucial role in cell differentiation and development. Recently, some reports have shown that a limited number of mammalian microRNAs also display antiviral effects. This article summarizes the data in the field paying a special attention to the conservation of the microRNA target sequences in the viral populations. This issue is relevant both for the evaluation of the biological significance of the antiviral effects and for the development of microRNA-based strategies for antiviral intervention. [Copyright &y& Elsevier]

Abstract: Vector-mediated delivery of short-hairpin RNA (shRNA) to regulate gene expression holds a great therapeutic promise. We hypothesize that gene expression can be autoregulated with RNA interference. We used inducible nitric oxide synthase (iNOS) as a gene model to test this hypothesis. Lipopolysaccharide dose-dependently increased iNOS in rat aortic smooth muscle cells and the nitrite production from these cells. These increases were attenuated in cells transfected with plasmids containing code for iNOS shRNA whose expression was controlled by an iNOS promoter. The production of shRNA was lipopolysaccharide dose-dependent. The lipopolysaccharide-induced iNOS expression in rat C6 glioma cells also was attenuated by transfection with plasmids containing the iNOS shRNA code. These results provide proof-of-concept evidence for using RNA interference technique to achieve autoregulation of gene expression. [Copyright &y& Elsevier]

Abstract: The thermodynamic properties of siRNA duplexes are important for their silencing activity. siRNAs with high thermodynamic stability of both the central part of the duplex and in the whole, usually display low silencing activity. Destabilization of the central part of the siRNA duplex could increase its silencing activity. However, mismatches located in the central part of the duplex could substantially decrease the amount of RNAi efficacy, hindering active RISC formation and function. In this study, we examined the impact of duplex destabilization by nucleotide substitutions in the central part (7–10nt counting from the 5′-end of the antisense strand) of the nuclease-resistant siRNA on its silencing activity. [Copyright &y& Elsevier]

Abstract: MicroRNA profiling of diseased/non-diseased tissue has identified expression signatures associated with a wide range of pathogenic conditions including malignancy. For example, colon cancer is associated with the under expression of miRNA-143 yet the molecular etiology of under expression is unknown. The K-Ras oncogene is a target of miRNA-143. Here, we show that the ecotropic viral integration site 1 oncoprotein (Evi1) is a transcriptional suppressor of the miRNA-143 gene. We find an indirect relationship between miRNA-143 and Evi1 expression. A complex molecular axis linking Evi1, miRNA-143 is operational in human colon cancer. [Copyright &y& Elsevier]

Abstract: This study describes the first application of unlocked nucleic acid (UNA)-modified small interfering RNAs (siRNAs) directed against a medically relevant target, the coxsackievirus B3. We systematically analyzed the impact of different siRNA modification patterns and observed good compatibility of the introduction of UNA with the maintenance of high antiviral activity. Additionally, the polarity of an siRNA was successfully reversed by modulating the relative stability of the termini with locked nucleic acid (LNA) and UNA as shown in a reporter assay. The potency of the reversed siRNA against the full-length target was, however, too low to inhibit the infectious virus. Altogether, combined modification of siRNAs with LNA und UNA provides a promising approach to alter and improve properties of an siRNA. [Copyright &y& Elsevier]

Abstract: MicroRNA (miRNA) are a class of non-coding RNA that suppress gene expression by degradation or translational inhibition of target RNA. Several miRNA have been shown to target oncogenes and recently miRNA-125b was shown to translationally and transcriptionally inhibit the p53 gene. Here, we show that an additional isomer of miRNA-125 (miRNA-125a) translationally arrests mRNA of the p53 tumor suppressor gene. The basis of this activity is the high degree of sequence homology between the seed sequence of miR-125a and the 3′-UTR of p53. Our findings add miRNA-125a to the growing list of miRNA with oncogenic targets. [Copyright &y& Elsevier]

Abstract: The prion protein PrP has a key role in transmissible spongiform encephalopathies but its biological function remains largely unknown. Recently, a related protein, Shadoo, was discovered. Its biological properties and brain distribution partially overlap that of PrP. We report that the Shadoo-encoding gene knockdown in PrP-knockout mouse embryos results in a lethal phenotype, occurring between E8 and E11, not observed on the wild-type genetic background. It reveals that these two proteins play a shared, crucial role in mammalian embryogenesis, explaining the lack of severe phenotype in PrP-knockout mammals, an appreciable step towards deciphering the biological role of this protein family. [Copyright &y& Elsevier]

Abstract: Superoxide dismutase 1 (SOD1) is an important antioxidant previously shown to impact life span in Drosophila. We examined the consequences of manipulating Sod1 expression throughout the body or in the nervous system or musculature on life span and age-related locomotor impairment (ARLI) in Drosophila. Ubiquitous overexpression of SOD1 extended life span but did not substantially forestall ARLI, whereas ubiquitous knock-down of Sod1 shortened life span and accelerated ARLI. Interestingly, neither overexpression of Sod1 nor expression of Sod1 RNAi in the nervous system or muscle altered life span or ARLI. Our studies suggest that the control of reactive oxygen species by SOD1 in tissues other than the nervous system and musculature support life span and ARLI in Drosophila. [Copyright &y& Elsevier]

Abstract: Substantial progress in functional genomic and proteomic technologies has opened new perspectives in biomedical research. The sequence of the human genome has been mostly determined and opened new visions on its complexity and regulation. New technologies, like RNAi and protein arrays, allow gathering knowledge beyond single gene analysis. Increasingly, biological processes are studied with systems biological approaches, where qualitative and quantitative data of the components are utilized to model the respective processes, to predict effects of perturbations, and to then refine these models after experimental testing. Here, we describe the potential of applying functional genomics and proteomics, taking the ERBB family of growth-factor receptors as an example to study the signaling network and its impact on cancer. [Copyright &y& Elsevier]

Abstract: Mammalian X-chromosome inactivation is controlled by a multilayered silencing pathway involving both short and long non-coding RNAs, which differentially recruit the epigenetic machinery to establish chromatin asymmetries. In response to developmentally regulated small RNAs, dicer, a key effector of RNA interference, locally silences Xist on the active X-chromosome and establishes the heterochromatin conformation along the silent X-chromosome. The 1.6kb RepA RNA initiates silencing by targeting the PRC2 polycomb complex to the inactive X-chromosome. In addition, the nuclear microenvironment is implicated in the initiation and maintenance of X-chromosome asymmetries. Here we review new findings involving these various RNA species in terms of understanding Xist gene regulation and the establishment of X-chromosome inactivation. [Copyright &y& Elsevier]

Abstract: In short hairpin RNA (shRNA) transgenic mice, the tissue difference in gene silencing efficiency and oversaturation of microRNA (miRNA) pathway have not been well assessed. We studied these problems in our previously-reported anti-copper/zinc superoxide dismutase (SOD1) shRNA transgenic mice. Although there was a tissue difference (liver and skeletal muscle, >95%; central nervous system and lung, ∼80%), the target gene silencing was systemic and our anti-SOD1 shRNA transgenic mice recapitulated the SOD1-null mice. Neither endogenous miRNAs nor their target gene levels were altered, indicating the preservation of endogenous miRNA pathways. We think that the shRNA transgenic mice can be utilized for gene analysis. [Copyright &y& Elsevier]

Abstract: Short-hairpin RNAs (shRNAs) inhibit gene expression by RNA interference. Here, we report on the inhibition, by baculovirus-based vector-derived shRNAs, of core-protein expression in full-length hepatitis C virus (HCV) replicon cells. shRNAs were designed to target the highly conserved core region of the HCV genome. In particular, the core-shRNA452 containing nucleotides 452–472, as the target in the HCV core gene, dramatically inhibited the expression of the HCV core protein in replicon cells. Furthermore, HCV core-protein expression was inhibited more strongly by the vesicular stomatitis virus glycoprotein (VSV-G)-pseudotyped baculovirus vector than by the wild-type baculovirus vector. [Copyright &y& Elsevier]

Abstract: This study describes a strategy to develop LNA-modified small interfering RNA (siRNAs) against the highly structured 5′ UTR of coxsackievirus B3 (CVB-3), which is an attractive target site due to its high degree of conservation. Accessible sites were identified based on structural models and RNase H assays with DNA oligonucleotides. Subsequently, LNA gapmers, siRNAs, siLNAs and small internally segmented interfering RNA (sisiLNAs) were designed against sites, which were found to be accessible in the in vitro assays, and tested in reporter assays and experiments with the infectious virus. The best siLNA improved viability of infected cells by 92% and exerted good antiviral activity in plaque reduction assays. [Copyright &y& Elsevier]

Abstract: Dicers are associated with double-stranded RNA-binding proteins (dsRBPs) in animals. In the plant, Arabidopsis, there are four dicer-like (DCL) proteins and five potential dsRBPs. These DCLs act redundantly and hierarchically. However, we show there is little or no redundancy or hierarchy amongst the DRBs in their DCL interactions. DCL1 operates exclusively with DRB1 to produce micro (mi)RNAs, DCL4 operates exclusively with DRB4 to produce trans-acting (ta) siRNAs and 21nt siRNAs from viral RNA. DCL2 and DCL3 produce viral siRNAs without requiring assistance from any dsRBP. DRB2, DRB3 and DRB5 appear unnecessary for mi-, tasi-, viral si-, or heterochromatinising siRNA production but act redundantly in a developmental pathway. [Copyright &y& Elsevier]

Abstract: Disabled-2 (DAB2) is an adaptor protein implicated in signal transduction pathways and in protein traffic regulation. Here, we show that DAB2 is highly expressed in human endothelial cells. DAB2 silencing in endothelial cells by lentiviral-mediated small hairpin RNA expression affects cell migration and differentiation into capillary-like structures while increasing cell proliferation and viability. DAB2 knockdown causes activation of the Src-FAK signal pathway, extracellular-signal regulated kinase and c-Jun NH2-terminal kinase activation, and inhibition of p38 phosphorylation. In DAB2 silenced endothelial cells, pharmacological inhibition of Src with its specific inhibitor PP2 abolishes focal adhesion kinase activation and restores differentiation of endothelial cells. These results suggest that DAB2, via Src and focal adhesion signaling, plays a role in human endothelial cell function. [Copyright &y& Elsevier]

Abstract: Cellular levels of the phosphoinositide PtdIns5P are regulated by agonist stimulation, but the mechanisms controlling turnover of this lipid, and the subcellular location of the regulated PtdIns5P pool(s), remain poorly understood. Here we show that enhanced tyrosine phosphorylation robustly increases cellular PtdIns5P levels. Moreover, unlike PtdIns5P production enhanced by cell stress, we show that this pool of PtdIns5P is specifically regulated by the inositol lipid kinase PIP4K2a. [Copyright &y& Elsevier]

Abstract: To test for redox regulation of anion channels in erythroid cells, we exposed K562 cells to oxidants and measured changes in transmembrane Cl− currents using patch-clamp, and in intracellular Cl− content using the Cl− selective dye MQAE. Oxidation with tert-butylhydroperoxide or H2O2 produced a plasma membrane anion permeability with a permselectivity of >lactate− >gluconate−. The permeability increase was paralleled by insertion of ClC-3 protein into the plasma membrane as evident from immunofluorescence microscopy and surface biotinylation. Down-regulation of ClC-3 protein by RNA interference as assessed by immunoblotting decreased the oxidation-stimulated permeability. In conclusion, oxidation induces surface expression of ClC-3 and activation of a ClC-3-dependent anion permeability in K562 cells. [Copyright &y& Elsevier]

Abstract: We performed genome wide gene expression analysis on L4 stage Caenorhabditis elegans rrf-3(pk1426) and eri-1(mg366) mutant strains to study the effects caused by loss of their encoded proteins, which are required for the accumulation of endogenous secondary siRNAs. Mutant rrf-3 and eri-1 strains exhibited 72 transcripts that were co-over-expressed and 4 transcripts co-under-expressed (>2-fold, P <0.05) compared to N2 wild type strain. Ontology analysis indicated these transcripts were over represented for protein phosphorylation and sperm function genes. These results provide additional support for the hypothesis that RRF-3 and ERI-1 act together in the endo-siRNA pathway, and furthermore suggests their involvement in additional biological processes. [Copyright &y& Elsevier]

Abstract: RNA-dependent transcriptional silencing (RdTS) has been reported to operate even in human cell lines. It is tempting to speculate that RdTS plays a role in retroviral gene silencing, considering that retroviral RNA transcripts harbor a U3 promoter sequence that is a potentially good source of double-stranded RNAs. To test this possibility, we constructed several model HeLaS3 cell lines expressing GFP driven by murine leukaemia virus (MLV)-long terminal repeat (LTR) and introduced a series of shRNAs that target the U3 region of the MLV-LTR. However, transcriptional gene silencing was not induced in most instances, in spite of the fact that processed shRNA was found in cellular nuclei, indicating that RdTS does not contribute to MLV gene silencing in host cells. [Copyright &y& Elsevier]

Abstract: We studied the role of the bursicon gene in wing expansion. First, we investigated its expression at different developmental stages in the silkworm, Bombyx mori. Bursicon gene was expressed at low levels in larvae, high levels in pupae, and low levels again in adults. Then, we injected the double-stranded bursicon RNA into B. mori pupae to test RNA interference. The level of bursicon mRNA was reduced significantly in pupae, and a deficit in wing expansion was observed in adults. In addition, the differential display reverse transcription polymerase chain reaction (DD-RT-PCR) was used to reveal differences in the expression of transcripts in response to the inhibition of bursicon. In conclusion, bursicon plays a key role in the stereotyped behavioral program involved in wing expansion. [Copyright &y& Elsevier]

Abstract: In rodents a high-fructose diet induces metabolic derangements similar to those in metabolic syndrome. Previously we suggested that in mouse liver an unidentified nuclear protein binding to the sterol regulatory element (SRE)-binding protein-1c (SREBP-1c) promoter region plays a key role for the response to high-fructose diet. Here, using MALDI-TOF MASS technique, we identified an X-chromosome-linked RNA binding motif protein (RBMX) as a new candidate molecule. In electrophoretic mobility shift assay, anti-RBMX antibody displaced the bands induced by fructose-feeding. Overexpression or suppression of RBMX on rat hepatoma cells regulated the SREBP-1c promoter activity. RBMX may control SREBP-1c expression in mouse liver in response to high-fructose diet. [Copyright &y& Elsevier]