Biomedical subjects

William S Marshall

Publications and source records attributed to William S Marshall.

10 recordsLinked to original sources

PubMed2006

Off-target effects by siRNA can induce toxic phenotype.

Although recent microarray studies have provided evidence of RNA interference (RNAi)-mediated off-target gene modulation, little is known about whether these changes induce observable phenotypic outcomes. Here we show that a fraction of randomly selected small inhibitory RNAs (siRNAs) can induce changes in cell viability in a target-independent fashion. The observed toxicity requires an intact RNAi pathway and can be eliminated by the addition of chemical modifications that reduce off-target effects. Furthermore, an analysis of toxic and nontoxic duplexes identifies a strong correlation between the toxicity and the presence of a 4-base-pair motif (UGGC) in the RISC-entering strand of toxic siRNA. This article provides further evidence of siRNA-induced off-target effects generating a measurable phenotype and also provides an example of how such undesirable phenotypes can be mitigated by addition of chemical modifications to the siRNA.

Base Sequence↗

PubMed2006

Induction of the interferon response by siRNA is cell type- and duplex length-dependent.

Long (27-29-bp dsRNA) Dicer-dependent substrates have been identified as potent mediators of RNAi-induced gene knockdown in HEK293 and HeLa cells. As the lengths of these molecules are reported to be below the threshold generally regarded as necessary for induction of the mammalian interferon (IFN) response, these long siRNA are being considered as RNAi substrates in both research and therapeutic settings. In this report, we demonstrate that >23-bp dsRNA can influence cell viability and induce a potent IFN response (highlighted by a strong up-regulation of the dsRNA receptor, Toll-like receptor 3) in a cell type-specific manner. This finding suggests that the length threshold for siRNA induction of the IFN response is not fixed but instead varies significantly among different cell types. Given the diversity of cell types that comprise whole organisms, these findings suggest great care should be taken when considering length variations of dsRNA molecules for RNAi experimentation, especially in therapeutic applications.

Cell Survival↗

PubMed2006

3' UTR seed matches, but not overall identity, are associated with RNAi off-targets.

Off-target gene silencing can present a notable challenge in the interpretation of data from large-scale RNA interference (RNAi) screens. We performed a detailed analysis of off-targeted genes identified by expression profiling of human cells transfected with small interfering RNA (siRNA). Contrary to common assumption, analysis of the subsequent off-target gene database showed that overall identity makes little or no contribution to determining whether the expression of a particular gene will be affected by a given siRNA, except for near-perfect matches. Instead, off-targeting is associated with the presence of one or more perfect 3' untranslated region (UTR) matches with the hexamer or heptamer seed region (positions 2-7 or 2-8) of the antisense strand of the siRNA. These findings have strong implications for future siRNA design and the application of RNAi in high-throughput screening and therapeutic development.

3' Untranslated Regions↗

PubMed2005

Crystal structure of a luteoviral RNA pseudoknot and model for a minimal ribosomal frameshifting motif.

To understand the role of structural elements of RNA pseudoknots in controlling the extent of -1-type ribosomal frameshifting, we determined the crystal structure of a high-efficiency frameshifting mutant of the pseudoknot from potato leaf roll virus (PLRV). Correlations of the structure with available in vitro frameshifting data for PLRV pseudoknot mutants implicate sequence and length of a stem-loop linker as modulators of frameshifting efficiency. Although the sequences and overall structures of the RNA pseudoknots from PLRV and beet western yellow virus (BWYV) are similar, nucleotide deletions in the linker and adjacent minor groove loop abolish frameshifting only with the latter. Conversely, mutant PLRV pseudoknots with up to four nucleotides deleted in this region exhibit nearly wild-type frameshifting efficiencies. The crystal structure helps rationalize the different tolerances for deletions in the PLRV and BWYV RNAs, and we have used it to build a three-dimensional model of the PRLV pseudoknot with a four-nucleotide deletion. The resulting structure defines a minimal RNA pseudoknot motif composed of 22 nucleotides capable of stimulating -1-type ribosomal frameshifts.

Base Sequence↗

PubMed2005

The contributions of dsRNA structure to Dicer specificity and efficiency.

Dicer processes long double-stranded RNA (dsRNA) and pre-microRNAs to generate the functional intermediates (short interfering RNAs and microRNAs) of the RNA interference pathway. Here we identify features of RNA structure that affect Dicer specificity and efficiency. The data presented show that various attributes of the 3' end structure, including overhang length and sequence composition, play a primary role in determining the position of Dicer cleavage in both dsRNA and unimolecular, short hairpin RNA (shRNA). We also demonstrate that siRNA end structure affects overall silencing functionality. Awareness of these new features of Dicer cleavage specificity as it is related to siRNA functionality provides a more detailed understanding of the RNAi mechanism and can shape the development of hairpins with enhanced functionality.

Base Sequence↗

PubMed2005

Mechanistic insights aid computational short interfering RNA design.

RNA interference is widely recognized for its utility as a functional genomics tool. In the absence of reliable target site selection tools, however, the impact of RNA interference (RNAi) may be diminished. The primary determinants of silencing are influenced by highly coordinated RNA-protein interactions that occur throughout the RNAi process, including short interfering RNA (siRNA) binding and unwinding followed by target recognition, cleavage, and subsequent product release. Recently developed strategies for identification of functional siRNAs reveal that thermodynamic and siRNA sequence-specific properties are crucial to predict functional duplexes (Khvorova et al., 2003; Reynolds et al., 2004; Schwarz et al., 2003). Additional assessments of siRNA specificity reveal that more sophisticated sequence comparison tools are also required to minimize potential off-target effects (Jackson et al., 2003; Semizarov et al., 2003). This chapter reviews the biological basis for current computational design tools and how best to utilize and assess their predictive capabilities for selecting functional and specific siRNAs.

Algorithms↗

PubMed2005

RNA oligonucleotide synthesis via 5'-silyl-2'-orthoester chemistry.

Rapid, reliable, and cost-efficient methods of ribonucleic acid (RNA) oligonucleotide synthesis are in demand owing to an increasing awareness of critical structural, functional, and regulatory roles of RNA throughout biology. The most promising area of growth and development is in RNA interference as an emerging technology for facilitating research in drug discovery and therapeutic intervention. Traditional methods of RNA synthesis, which are based on 2'-silyl protection strategies derived from deoxyribonucleic acid (DNA) synthesis strategies, are limited in their ability to produce oligos of sufficient purity and length for high-throughput applications. The more recently developed 5'-silyl-2'-acetoxy ethyl orthoester chemistry (2'-ACE trade mark ), circumvents several limitations of the 2'-silyl approaches. A clear improvement in RNA synthesis technology, 2'-ACE results in faster coupling rates, higher yields, greater purity, and superior ease of handling. Another advantage of the 2'-ACE protecting group strategy is that the molecules can be produced in an intermediately protected form that is soluble in aqueous solutions but resistant to nuclease attack. The chemistry can be scaled up or down and is flexible enough to allow for the incorporation of modifying groups if desired. A detailed description of the 2'-ACE protocol and procedures for end product analysis are presented.

Electrophoresis, Polyacrylamide Gel↗

PubMed2004

Rational siRNA design for RNA interference.

Short-interfering RNAs suppress gene expression through a highly regulated enzyme-mediated process called RNA interference (RNAi). RNAi involves multiple RNA-protein interactions characterized by four major steps: assembly of siRNA with the RNA-induced silencing complex (RISC), activation of the RISC, target recognition and target cleavage. These interactions may bias strand selection during siRNA-RISC assembly and activation, and contribute to the overall efficiency of RNAi. To identify siRNA-specific features likely to contribute to efficient processing at each step, we performed a systematic analysis of 180 siRNAs targeting the mRNA of two genes. Eight characteristics associated with siRNA functionality were identified: low G/C content, a bias towards low internal stability at the sense strand 3'-terminus, lack of inverted repeats, and sense strand base preferences (positions 3, 10, 13 and 19). Further analyses revealed that application of an algorithm incorporating all eight criteria significantly improves potent siRNA selection. This highlights the utility of rational design for selecting potent siRNAs and facilitating functional gene knockdown studies.

Animals↗

PubMed2004

Recent advances in the high-speed solid phase synthesis of RNA.

Development of rapid and reliable RNA synthesis strategies is fueled by the emergence of critical functional and regulatory roles for RNA, including RNA interference. Traditional methods are based on 5'-dimethoxytrityl-2'-silyl protection strategies which are derivatives of highly successful DNA synthesis methods. These approaches are limited in their ability to rapidly produce oligos of sufficient purity and length for genomic and pharmaceutical applications. Recently, new protection chemistries have been developed that circumvent the many limitations of 2'-silyl protection. The 5'-silyl-2'-bis(acetoxyethoxy)methyl strategy is the most notable, as it provides dramatic improvements--faster coupling rates, higher yields, greater product purity and superior post-synthetic ease-of-handling--affording a reliable high-speed chemical RNA synthesis technology.

Combinatorial Chemistry Techniques↗

PubMed2003

Rapid regulation of NaCl secretion by estuarine teleost fish: coping strategies for short-duration freshwater exposures.

This review summarizes the mechanism of Cl(-) active secretion and its regulation in estuarine teleost fish. Small estuarine fish such as the killifish, Fundulus heteroclitus, forage in shallow water following advancing tides and are exposed regularly to very dilute microenvironments. Using the killifish opercular epithelium and related teleost membranes containing mitochondria-rich cells, the regulation includes a reduction of active Cl(-) secretion and passive diffusive ion loss in a three-stage process spanning approximately 30 min. There is a combination of sympathetic neural reflex mediated by alpha(2)-adrenoceptors operating via intracellular inositol tris phosphate and intracellular Ca(2+) and a cellular hypotonic shock response, followed by covering over of ion-secreting cells by pavement cells. This effectively minimizes salt loss in dilute media. The upregulation of salt secretion on return to full strength seawater may be via hormones (arginine vasotocin and urotensin I) and neurotransmitter (vasoactive intestinal polypeptide) in combination with hypertonic shock. A hypothetical model includes involvement of protein kinase A and C and protein phosphatases 1 and 2A in regulation of the NKCC1 cotransporter on the basolateral side and protein kinase A regulation of the CFTR-like apical anion channel.

Adaptation, Physiological↗