39 results match your criteria Silence [Journal]

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Limited evidence for evolutionarily conserved targeting of long non-coding RNAs by microRNAs.

Silence 2013 Aug 20;4(1). Epub 2013 Aug 20.

Department of Medical Biochemistry and Cell Biology, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, SE-405 30, Gothenburg, Sweden.

Background: Long non-coding RNAs (lncRNAs) are emerging as important regulators of cell physiology, but it is yet unknown to what extent lncRNAs have evolved to be targeted by microRNAs. Comparative genomics has previously revealed widespread evolutionarily conserved microRNA targeting of protein-coding mRNAs, and here we applied a similar approach to lncRNAs.

Findings: We used a map of putative microRNA target sites in lncRNAs where site conservation was evaluated based on 46 vertebrate species. Read More

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http://dx.doi.org/10.1186/1758-907X-4-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3751674PMC
August 2013
8 Reads

Analysis of hairpin RNA transgene-induced gene silencing in Fusarium oxysporum.

Silence 2013 Jul 2;4(1). Epub 2013 Jul 2.

Commonwealth Scientific and Industrial Research Organisation Plant Industry, Clunies Ross Street, Canberra ACT 2601, Australia.

Background: Hairpin RNA (hpRNA) transgenes can be effective at inducing RNA silencing and have been exploited as a powerful tool for gene function analysis in many organisms. However, in fungi, expression of hairpin RNA transcripts can induce post-transcriptional gene silencing, but in some species can also lead to transcriptional gene silencing, suggesting a more complex interplay of the two pathways at least in some fungi. Because many fungal species are important pathogens, RNA silencing is a powerful technique to understand gene function, particularly when gene knockouts are difficult to obtain. Read More

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http://dx.doi.org/10.1186/1758-907X-4-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3733888PMC
July 2013
7 Reads

cWords - systematic microRNA regulatory motif discovery from mRNA expression data.

Silence 2013 May 20;4(1). Epub 2013 May 20.

Bioinformatics Centre, Department of Biology, University of Copenhagen, Ole Maaløes Vej 5, Copenhagen N, 2200, Denmark.

Background: Post-transcriptional regulation of gene expression by small RNAs and RNA binding proteins is of fundamental importance in development of complex organisms, and dysregulation of regulatory RNAs can influence onset, progression and potentially be target for treatment of many diseases. Post-transcriptional regulation by small RNAs is mediated through partial complementary binding to messenger RNAs leaving nucleotide signatures or motifs throughout the entire transcriptome. Computational methods for discovery and analysis of sequence motifs in high-throughput mRNA expression profiling experiments are becoming increasingly important tools for the identification of post-transcriptional regulatory motifs and the inference of the regulators and their targets. Read More

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http://dx.doi.org/10.1186/1758-907X-4-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3682869PMC
May 2013
4 Reads

Generation of a luciferase-based reporter for CHH and CG DNA methylation in Arabidopsis thaliana.

Silence 2013 Apr 5;4(1). Epub 2013 Apr 5.

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.

Background: DNA methylation ensures genome integrity and regulates gene expression in diverse eukaryotes. In Arabidopsis, methylation occurs in three sequence contexts: CG, CHG and CHH. The initial establishment of DNA methylation at all three sequence contexts occurs through a process known as RNA-directed DNA methylation (RdDM), in which small RNAs bound by Argonaute4 (AGO4) guide DNA methylation at homologous loci through the de novo methyltransferase DRM2. Read More

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http://dx.doi.org/10.1186/1758-907X-4-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3623655PMC
April 2013
5 Reads

Strand-specific libraries for high throughput RNA sequencing (RNA-Seq) prepared without poly(A) selection.

Silence 2012 Dec 28;3(1). Epub 2012 Dec 28.

Biochemistry and Molecular Pharmacology, and Howard Hughes Medical Institute, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.

Unlabelled:

Background: High throughput DNA sequencing technology has enabled quantification of all the RNAs in a cell or tissue, a method widely known as RNA sequencing (RNA-Seq). However, non-coding RNAs such as rRNA are highly abundant and can consume >70% of sequencing reads. A common approach is to extract only polyadenylated mRNA; however, such approaches are blind to RNAs with short or no poly(A) tails, leading to an incomplete view of the transcriptome. Read More

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http://dx.doi.org/10.1186/1758-907X-3-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3552703PMC
December 2012
3 Reads

MicroRNAs from the same precursor have different targeting properties.

Silence 2012 Sep 27;3(1). Epub 2012 Sep 27.

Faculty of Life Sciences, Michael Smith Building, Oxford Road, University of Manchester, Manchester M13 9PT, UK.

Unlabelled:

Background: The processing of a microRNA results in an intermediate duplex of two potential mature products that derive from the two arms (5' and 3') of the precursor hairpin. It is often suggested that one of the sequences is degraded and the other is incorporated into the RNA-induced silencing complex. However, both precursor arms may give rise to functional levels of mature microRNA and the dominant product may change from species to species, from tissue to tissue, or between developmental stages. Read More

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http://dx.doi.org/10.1186/1758-907X-3-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503882PMC
September 2012
3 Reads

RNA: methods and protocols - a new series.

Authors:
Phillip D Zamore

Silence 2012 Jun 7;3(1). Epub 2012 Jun 7.

Howard Hughes Medical Institute and Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation Street, Worcester, MA, 01605, USA.

This month, Silence launches a new series on methods and protocols to study silencing pathways and analyze nucleic acids and proteins. Read More

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http://dx.doi.org/10.1186/1758-907X-3-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3420260PMC
June 2012
6 Reads

Development of a luciferase-based reporter of transcriptional gene silencing that enables bidirectional mutant screening in Arabidopsis thaliana.

Silence 2012 Jun 7;3(1). Epub 2012 Jun 7.

Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.

Unlabelled:

Background: Cytosine methylation is an important chromatin modification that maintains genome integrity and regulates gene expression through transcriptional gene silencing. Major players in de novo methylation guided by siRNAs (known as RNA-directed DNA methylation, or RdDM), maintenance methylation, and active demethylation have been identified in Arabidopsis. However, active demethylation only occurs at a subset of RdDM loci, raising the question of how the homeostasis of DNA methylation is achieved at most RdDM loci. Read More

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http://dx.doi.org/10.1186/1758-907X-3-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3548752PMC
June 2012
9 Reads

Application of RNA silencing to plant disease resistance.

Silence 2012 May 31;3(1). Epub 2012 May 31.

State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.

To reduce the losses caused by plant pathogens, plant biologists have adopted numerous methods to engineer resistant plants. Among them, RNA silencing-based resistance has been a powerful tool that has been used to engineer resistant crops during the last two decades. Based on this mechanism, diverse approaches were developed. Read More

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http://dx.doi.org/10.1186/1758-907X-3-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503840PMC
May 2012
4 Reads

Reducing ligation bias of small RNAs in libraries for next generation sequencing.

Silence 2012 May 30;3(1). Epub 2012 May 30.

School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.

Background: The use of nucleic acid-modifying enzymes has driven the rapid advancement in molecular biology. Understanding their function is important for modifying or improving their activity. However, functional analysis usually relies upon low-throughput experiments. Read More

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http://dx.doi.org/10.1186/1758-907X-3-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3489589PMC
May 2012
19 Reads

Target gene expression levels and competition between transfected and endogenous microRNAs are strong confounding factors in microRNA high-throughput experiments.

Silence 2012 Feb 10;3. Epub 2012 Feb 10.

Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Prinsesse Kristinsgt, 1, NO-7491 Trondheim, Norway.

Background: MicroRNA (miRNA) target genes tend to have relatively long and conserved 3' untranslated regions (UTRs), but to what degree these characteristics contribute to miRNA targeting is poorly understood. Different high-throughput experiments have, for example, shown that miRNAs preferentially regulate genes with both short and long 3' UTRs and that target site conservation is both important and irrelevant for miRNA targeting.

Results: We have analyzed several gene context-dependent features, including 3' UTR length, 3' UTR conservation, and messenger RNA (mRNA) expression levels, reported to have conflicting influence on miRNA regulation. Read More

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http://dx.doi.org/10.1186/1758-907X-3-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3293725PMC
February 2012
3 Reads

Noncoding RNA localisation mechanisms in chromatin regulation.

Silence 2012 Jan 31;3(1). Epub 2012 Jan 31.

Division of Infection and Immunity and UCL Cancer Institute, University College London, 72 Huntley Street, London, WC1E 6BT, UK.

An important challenge in biology has been to understand how cell-type-specific expression programs are orchestrated through regulated access to chromatin. Knowledge of the interaction between noncoding RNAs (ncRNAs) and chromatin regulators has the potential to help answer such questions, but how ncRNAs target chromatin regulators to specific sites in the genome is not well understood. Recently, Jeon and Lee proposed that DNA-binding proteins act as a bridge between ncRNAs and their target sites in chromatin. Read More

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http://dx.doi.org/10.1186/1758-907X-3-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3284870PMC
January 2012
2 Reads

Inhibition of microRNA function by antimiR oligonucleotides.

Silence 2012 Jan 9;3(1). Epub 2012 Jan 9.

Santaris Pharma, Kogle Allé 6, DK-2970 Hørsholm, Denmark.

MicroRNAs (miRNAs) have emerged as important post-transcriptional regulators of gene expression in many developmental and cellular processes. Moreover, there is now ample evidence that perturbations in the levels of individual or entire families of miRNAs are strongly associated with the pathogenesis of a wide range of human diseases. Indeed, disease-associated miRNAs represent a new class of targets for the development of miRNA-based therapeutic modalities, which may yield patient benefits unobtainable by other therapeutic approaches. Read More

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http://dx.doi.org/10.1186/1758-907X-3-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3306207PMC
January 2012
55 Reads

The dose can make the poison: lessons learned from adverse in vivo toxicities caused by RNAi overexpression.

Authors:
Dirk Grimm

Silence 2011 Oct 26;2. Epub 2011 Oct 26.

Cluster of Excellence CellNetworks, Department of Infectious Diseases, Virology, University of Heidelberg, BioQuant BQ0030, Room 502a, Im Neuenheimer Feld 267, D-69120 Heidelberg, Germany.

For the past five years, evidence has accumulated that vector-mediated robust RNA interference (RNAi) expression can trigger severe side effects in small and large animals, from cytotoxicity and accelerated tumorigenesis to organ failure and death. The recurring notions in these studies that a critical parameter is the strength of RNAi expression and that Exportin-5 and the Argonaute proteins are rate-limiting mammalian RNAi, strongly imply dose-dependent saturation of the endogenous miRNA pathway as one of the underlying mechanisms. This minireview summarizes the relevant work and data leading to this intriguing model and highlights potential avenues by which to alleviate RNAi-induced toxicities in future clinical applications. Read More

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http://dx.doi.org/10.1186/1758-907X-2-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234190PMC
October 2011
1 Read

Helicobacter pylori interferes with an embryonic stem cell micro RNA cluster to block cell cycle progression.

Silence 2011 Oct 25;2(1). Epub 2011 Oct 25.

Univ, Bordeaux, ARNA Laboratory, F-33000, Bordeaux, France.

Background: MicroRNAs, post-transcriptional regulators of eukaryotic gene expression, are implicated in host defense against pathogens. Viruses and bacteria have evolved strategies that suppress microRNA functions, resulting in a sustainable infection. In this work we report that Helicobacter pylori, a human stomach-colonizing bacterium responsible for severe gastric inflammatory diseases and gastric cancers, downregulates an embryonic stem cell microRNA cluster in proliferating gastric epithelial cells to achieve cell cycle arrest. Read More

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http://dx.doi.org/10.1186/1758-907X-2-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3212895PMC
October 2011
31 Reads

Noncoding RNAs and cancer.

Silence 2011 Sep 29;2(1). Epub 2011 Sep 29.

Cancer Research UK Viral Oncology Group, UCL Cancer Institute, University College London, Paul O'Gorman Building, 72 Huntley Street, London, WC1E 6BT, UK.

The study of miRNAs and other noncoding RNAs has revolutionised our understanding of gene expression regulation during cancer development and progression, creating one of the fastest-growing research fields in cancer with realistic therapeutic potential. The 2011 Non-coding RNAs and Cancer Symposium hosted by the University College London Cancer Institute focused on the function and regulation of noncoding RNAs during oncogenesis. Read More

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http://dx.doi.org/10.1186/1758-907X-2-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205004PMC
September 2011
24 Reads

Posttranslational modification of Argonautes and their role in small RNA-mediated gene regulation.

Silence 2011 Sep 26;2. Epub 2011 Sep 26.

RNA Biology, Department of Biology, Swiss Federal Institute of Technology Zurich, LFW D18,1 Universitätstrasse 2, 8092, Zürich, Switzerland.

Shortly after their discovery, repertoires of miRNA were identified, together with proteins involved in their biogenesis and action. It is now obvious that miRNA-mediated gene regulation itself is regulated at multiple levels. Identifying the regulatory mechanisms that underpin small RNA homeostasis by modulation of their biogenesis and action has become a key issue, which can be partly resolved by identifying mediators of Argonautes turnover. Read More

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http://dx.doi.org/10.1186/1758-907X-2-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3199228PMC
September 2011
1 Read

A 5'-uridine amplifies miRNA/miRNA* asymmetry in Drosophila by promoting RNA-induced silencing complex formation.

Silence 2011 Jun 7;2. Epub 2011 Jun 7.

Laboratoire de Biologie Moléculaire Eucaryote, 118 route de Narbonne, Université Toulouse III Paul Sabatier (UPS), F-31000 Toulouse, France.

Background: MicroRNA (miRNA) are diverse in sequence and have a single known sequence bias: they tend to start with uridine (U).

Results: Our analyses of fly, worm and mouse miRNA sequence data reveal that the 5'-U is recognized after miRNA production. Only one of the two strands can be assembled into Argonaute protein from a single miRNA/miRNA* molecule: in fly embryo lysate, a 5'-U promotes miRNA loading while decreasing the loading of the miRNA*. Read More

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http://dx.doi.org/10.1186/1758-907X-2-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3127740PMC
June 2011
3 Reads

Off-target effects dominate a large-scale RNAi screen for modulators of the TGF-β pathway and reveal microRNA regulation of TGFBR2.

Silence 2011 Mar 14;2. Epub 2011 Mar 14.

Computational Biology Program, Memorial Sloan-Kettering Cancer Center, New York, NY, USA.

Background: RNA interference (RNAi) screens have been used to identify novel components of signal-transduction pathways in a variety of organisms. We performed a small interfering (si)RNA screen for novel members of the transforming growth factor (TGF)-β pathway in a human keratinocyte cell line. The TGF-β pathway is integral to mammalian cell proliferation and survival, and aberrant TGF-β responses have been strongly implicated in cancer. Read More

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http://silencejournal.biomedcentral.com/articles/10.1186/175
Publisher Site
http://dx.doi.org/10.1186/1758-907X-2-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3068080PMC
March 2011
18 Reads

Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experiments.

Silence 2011 Feb 28;2(1). Epub 2011 Feb 28.

Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA.

Prior to the advent of new, deep sequencing methods, small RNA (sRNA) discovery was dependent on Sanger sequencing, which was time-consuming and limited knowledge to only the most abundant sRNA. The innovation of large-scale, next-generation sequencing has exponentially increased knowledge of the biology, diversity and abundance of sRNA populations. In this review, we discuss issues involved in the design of sRNA sequencing experiments, including choosing a sequencing platform, inherent biases that affect sRNA measurements and replication. Read More

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http://dx.doi.org/10.1186/1758-907X-2-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3055805PMC
February 2011
7 Reads

Effect of small interfering RNA 3'-end overhangs on chemosensitivity to thymidylate synthase inhibitors.

Silence 2011 Jan 19;2(1). Epub 2011 Jan 19.

VACT Healthcare System, VACT Cancer Center, West Haven, CT, USA.

Background: Small interfering RNAs (siRNAs) are double-stranded RNAs that effectively inhibit expression of its complimentary target mRNA. Standard siRNAs contain two nucleotide overhangs on their 3' end. While these overhangs are usually comprised of deoxythymidines (dT), it has been shown that any nucleotide can be used on the 3' end without affecting RNAi silencing. Read More

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http://dx.doi.org/10.1186/1758-907X-2-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3035029PMC
January 2011
6 Reads

MicroR159 regulation of most conserved targets in Arabidopsis has negligible phenotypic effects.

Silence 2010 Oct 28;1(1):18. Epub 2010 Oct 28.

Research School of Biology, Australian National University, Canberra, Australian Capital Territory, Australia.

Background: A current challenge of microRNA (miRNA) research is the identification of biologically relevant miRNA:target gene relationships. In plants, high miRNA:target gene complementarity has enabled accurate target predictions, and slicing of target mRNAs has facilitated target validation through rapid amplification of 5' cDNA ends (5'-RACE) analysis. Together, these approaches have identified more than 20 targets potentially regulated by the deeply conserved miR159 family in Arabidopsis, including eight MYB genes with highly conserved miR159 target sites. Read More

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http://dx.doi.org/10.1186/1758-907X-1-18DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2988730PMC
October 2010
2 Reads

A structural-based statistical approach suggests a cooperative activity of PUM1 and miR-410 in human 3'-untranslated regions.

Silence 2010 Sep 22;1(1):17. Epub 2010 Sep 22.

Department of Computer Sciences, Technion - Israel Institute of Technology, Technion City, Haifa 32000, Israel.

Background: Micro (mi)RNAs comprise a large family of small non-coding RNAs that are thought to regulate a large fraction of protein-coding genes. Generally, miRNAs downregulate messenger (m)RNA expression by binding to the 3' untranslated regions (UTRs) of the RNA molecules. An important factor for binding specificity is the matching in the seed region. Read More

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http://dx.doi.org/10.1186/1758-907X-1-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2955683PMC
September 2010
2 Reads

In vivo quantification of formulated and chemically modified small interfering RNA by heating-in-Triton quantitative reverse transcription polymerase chain reaction (HIT qRT-PCR).

Silence 2010 Aug 23;1(1):16. Epub 2010 Aug 23.

Alnylam Pharmaceuticals, Cambridge, MA, USA.

Background: While increasing numbers of small interfering RNA (siRNA) therapeutics enter into clinical trials, the quantification of siRNA from clinical samples for pharmacokinetic studies remains a challenge. This challenge is even more acute for the quantification of chemically modified and formulated siRNAs such as those typically required for systemic delivery.

Results: Here, we describe a novel method, heating-in-Triton quantitative reverse transcription PCR (HIT qRT-PCR) that improves upon the stem-loop RT-PCR technique for the detection of formulated and chemically modified siRNAs from plasma and tissue. Read More

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http://dx.doi.org/10.1186/1758-907X-1-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2939650PMC
August 2010
19 Reads

An endogenous F-box protein regulates ARGONAUTE1 in Arabidopsis thaliana.

Silence 2010 Jul 12;1(1):15. Epub 2010 Jul 12.

Department of Biology, University of Pennsylvania, Philadelphia PA 19104, USA.

ARGONAUTE1 (AGO1) mediates microRNA- and small interfering RNA-directed posttranscriptional gene silencing in Arabidopsis thaliana. Mutant alleles of SQUINT (SQN) slightly reduce AGO1 activity and have weak effects on shoot morphology. A screen for mutations that suppress the sqn phenotype produced loss-of-function mutations in the F-box gene FBW2. Read More

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http://dx.doi.org/10.1186/1758-907X-1-15DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2914764PMC
July 2010
2 Reads

A status report on RNAi therapeutics.

Silence 2010 Jul 8;1(1):14. Epub 2010 Jul 8.

Alnylam Pharmaceuticals Inc,, 300 Third Street, Cambridge, MA 02142, USA.

Fire and Mello initiated the current explosion of interest in RNA interference (RNAi) biology with their seminal work in Caenorhabditis elegans. These observations were closely followed by the demonstration of RNAi in Drosophila melanogaster. However, the full potential of these new discoveries only became clear when Tuschl and colleagues showed that 21-22 bp RNA duplexes with 3" overhangs, termed small interfering (si)RNAs, could reliably execute RNAi in a range of mammalian cells. Read More

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http://dx.doi.org/10.1186/1758-907X-1-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2908561PMC
July 2010
6 Reads

RNA silencing in plants: Flash report!

Silence 2010 Jun 30;1(1):13. Epub 2010 Jun 30.

Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK.

Earlier this year plant scientists met in Santa Fe, New Mexico at the Keystone Symposium "RNA Silencing Mechanisms in Plants". Sessions included small RNA biogenesis and signalling, development and stress responses, small RNA-directed DNA methylation, and interaction with pathogens. This report highlights some of the prominent and recurring themes at the meeting and emerging arenas of future research. Read More

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http://dx.doi.org/10.1186/1758-907X-1-13DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2902426PMC
June 2010
3 Reads

Naturally occurring variations in sequence length creates microRNA isoforms that differ in argonaute effector complex specificity.

Silence 2010 Jun 9;1(1):12. Epub 2010 Jun 9.

Department of Biochemistry, School of Molecular and Systems Medicine, University of Alberta, Edmonton, T6G 2H7, Canada.

Background: Micro(mi)RNAs are short RNA sequences, ranging from 16 to 35 nucleotides (miRBase; http://www.mirbase.org). Read More

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http://silencejournal.biomedcentral.com/articles/10.1186/175
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http://dx.doi.org/10.1186/1758-907X-1-12DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2901367PMC
June 2010
4 Reads

How do miRNAs mediate translational repression?

Authors:
Shuo Gu Mark A Kay

Silence 2010 May 7;1(1):11. Epub 2010 May 7.

Departments of Pediatrics and Genetics, Stanford University, Stanford, CA 94305, USA.

Micro(mi)RNAs regulate gene expression by what are believed to be related but separate mechanistic processes. The relative contribution that each process plays, their mechanistic overlap, and the degree by which they regulate complex genetic networks is still being unraveled. One process by which miRNAs inhibit gene expression occurs through translational repression. Read More

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http://dx.doi.org/10.1186/1758-907X-1-11DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881910PMC
May 2010
5 Reads

Specificity and functionality of microRNA inhibitors.

Silence 2010 Apr 1;1(1):10. Epub 2010 Apr 1.

Dharmacon Products, Thermo Fisher Scientific, 2650 Crescent Drive, Suite 100 Lafayette, CO 80026, USA.

Background: Micro(mi)RNAs regulate gene expression through translational attenuation and messenger (m)RNA degradation, and are associated with differentiation, homeostasis and disease. Natural miRNA target recognition is determined primarily by perfect complementarity in a seed region (nucleotide positions 2 to 7) with additional interactions contributing in a sequence- and target-specific manner. Synthetic miRNA target analogs, which are fully complementary, chemically modified oligonucleotides, have been used successfully to inhibit miRNA function. Read More

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http://dx.doi.org/10.1186/1758-907X-1-10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864222PMC
April 2010
7 Reads

Inhibiting miRNA in Caenorhabditis elegans using a potent and selective antisense reagent.

Silence 2010 Apr 1;1(1). Epub 2010 Apr 1.

Departments of Cell Biology and of Biochemistry, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd, Dallas, TX 75390-9039, USA.

Background: Antisense reagents can serve as efficient and versatile tools for studying gene function by inhibiting nucleic acids in vivo. Antisense reagents have particular utility for the experimental manipulation of the activity of microRNAs (miRNAs), which are involved in the regulation of diverse developmental and physiological pathways in animals. Even in traditional genetic systems, such as the nematode Caenorhabditis elegans, antisense reagents can provide experimental strategies complementary to mutational approaches. Read More

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http://dx.doi.org/10.1186/1758-907X-1-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864223PMC
April 2010
4 Reads

Riding in silence: a little snowboarding, a lot of small RNAs.

Silence 2010 Mar 15;1(1). Epub 2010 Mar 15.

Department of Biochemistry and Molecular Pharmacology, Massachusetts Medical School, 364 Plantation Street, Worcester, MA 01605, USA.

The recent symposium, RNA silencing: Mechanism, Biology and Applications, organized by Phillip D. Zamore (University of Massachusetts Medical School) and Beverly Davidson (University of Iowa), and held in Keystone, Colorado, brought together scientists working on diverse aspects of RNA silencing, a field that comprises a multitude of gene regulatory pathways guided by microRNAs, small interfering RNAs and PIWI-interacting RNAs. Read More

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http://dx.doi.org/10.1186/1758-907X-1-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2851661PMC
March 2010
2 Reads

Development of the human cancer microRNA network.

Silence 2010 Feb 2;1(1). Epub 2010 Feb 2.

Machine Intelligence Unit, Indian Statistical Institute, Kolkata, India.

Background: MicroRNAs are a class of small noncoding RNAs that are abnormally expressed in different cancer cells. Molecular signature of miRNAs in different malignancies suggests that these are not only actively involved in the pathogenesis of human cancer but also have a significant role in patients survival. The differential expression patterns of specific miRNAs in a specific cancer tissue type have been reported in hundreds of research articles. Read More

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http://dx.doi.org/10.1186/1758-907X-1-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835996PMC
February 2010
10 Reads

Expression patterns of intronic microRNAs in Caenorhabditis elegans.

Silence 2010 Feb 1;1(1). Epub 2010 Feb 1.

Hubrecht Institute, Royal Netherlands Academy of Arts and Sciences and University Medical Center Utrecht, Uppsalalaan 8, 3584CT Utrecht, The Netherlands.

Background: MicroRNAs (miRNA) are an abundant and ubiquitous class of small RNAs that play prominent roles in gene regulation. A significant fraction of miRNA genes reside in the introns of the host genes in the same orientation and are thought to be co-processed from the host gene mRNAs and thus depend on the host gene promoter for their expression. However, several lines of evidence for independent expression of intronic miRNAs exist in the literature but the extent of this independence remains unclear. Read More

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http://dx.doi.org/10.1186/1758-907X-1-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835999PMC
February 2010
6 Reads

Aptamer-targeted cell-specific RNA interference.

Silence 2010 Feb 1;1(1). Epub 2010 Feb 1.

Division of Molecular and Cellular Biology, Beckman Research Institute of City of Hope, City of Hope, Duarte, CA 91010, USA.

This potent ability of small interfering (si)RNAs to inhibit the expression of complementary RNA transcripts is being exploited as a new class of therapeutics for a variety of diseases. However, the efficient and safe delivery of siRNAs into specific cell populations is still the principal challenge in the clinical development of RNAi therapeutics. With the increasing enthusiasm for developing targeted delivery vehicles, nucleic acid-based aptamers targeting cell surface proteins are being explored as promising delivery vehicles to target a distinct disease or tissue in a cell-type-specific manner. Read More

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http://dx.doi.org/10.1186/1758-907X-1-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835998PMC
February 2010
4 Reads

Solution structure of the Drosha double-stranded RNA-binding domain.

Silence 2010 Jan 12;1(1). Epub 2010 Jan 12.

Laboratory of Structural Biology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, NC, USA.

Background: Drosha is a nuclear RNase III enzyme that initiates processing of regulatory microRNA. Together with partner protein DiGeorge syndrome critical region 8 (DGCR8), it forms the Microprocessor complex, which cleaves precursor transcripts called primary microRNA to produce hairpin precursor microRNA. In addition to two RNase III catalytic domains, Drosha contains a C-terminal double-stranded RNA-binding domain (dsRBD). Read More

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http://dx.doi.org/10.1186/1758-907X-1-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2836000PMC
January 2010
4 Reads

How to slice: snapshots of Argonaute in action.

Authors:
James S Parker

Silence 2010 Jan 12;1(1). Epub 2010 Jan 12.

Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK.

Argonaute is the principal protein component of the mechanisms of RNA silencing, providing anchor sites for the small guide RNA strand and the 'slicer' activity for cleavage of target mRNAs or short passenger RNA strands. Argonaute is the core constituent of the silencing effector complexes RISC (RNA-induced silencing complex) and the RITS complex (RNA-induced initiation of transcriptional gene silencing complex), interacting directly or indirectly with Dicer proteins, R2D2/Loquacious/TRBP and GW182 family proteins in the former, and Chp1 and Tas3 in the latter. In a breakthrough series of papers, Patel et al. Read More

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http://dx.doi.org/10.1186/1758-907X-1-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835997PMC
January 2010
5 Reads

Welcome to silence.

Silence 2010 Jan 12;1(1). Epub 2010 Jan 12.

Editors-in-Chief, Silence, BioMed Central, London, UK.

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http://dx.doi.org/10.1186/1758-907X-1-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2835995PMC
January 2010
2 Reads

microRNA as a new immune-regulatory agent in breast milk.

Silence 2010 Mar 1;1(1). Epub 2010 Mar 1.

Section for Studies on Metastasis, National Cancer Center Research Institute, 1-1, Tsukiji 5-chome, Chuo-ku, Tokyo 104-0045, Japan.

Background: Breast milk is a complex liquid that provides nutrition to the infant and facilitates the maturation of the infant's immune system. Recent studies indicated that microRNA (miRNA) exists in human body fluid. Because miRNAs are known to regulate various immune systems, we hypothesized that human breast milk contains miRNAs that may be important for the development of the infant's immune system. Read More

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http://dx.doi.org/10.1186/1758-907X-1-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2847997PMC
March 2010
20 Reads
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