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Silence

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https://www.readbyqxmd.com/read/23962258/limited-evidence-for-evolutionarily-conserved-targeting-of-long-non-coding-rnas-by-micrornas
#1
Babak Alaei-Mahabadi, Erik Larsson
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...
2013: Silence
https://www.readbyqxmd.com/read/23819794/analysis-of-hairpin-rna-transgene-induced-gene-silencing-in-fusarium-oxysporum
#2
Ulrike Schumann, Neil A Smith, Kemal Kazan, Michael Ayliffe, Ming-Bo Wang
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...
2013: Silence
https://www.readbyqxmd.com/read/23688306/cwords-systematic-microrna-regulatory-motif-discovery-from-mrna-expression-data
#3
Simon H Rasmussen, Anders Jacobsen, Anders Krogh
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...
2013: Silence
https://www.readbyqxmd.com/read/23561294/generation-of-a-luciferase-based-reporter-for-chh-and-cg-dna-methylation-in-arabidopsis-thaliana
#4
Thanh Theresa Dinh, Michael O'Leary, So Youn Won, Shengben Li, Lorena Arroyo, Xigang Liu, Andrew Defries, Binglian Zheng, Sean R Cutler, Xuemei Chen
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. Once established, DNA methylation at each of the three sequence contexts is maintained through different mechanisms...
2013: Silence
https://www.readbyqxmd.com/read/23016695/micrornas-from-the-same-precursor-have-different-targeting-properties
#5
Antonio Marco, Jamie I Macpherson, Matthew Ronshaugen, Sam Griffiths-Jones
UNLABELLED: HASH(0x4b2ea38) 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...
September 27, 2012: Silence
https://www.readbyqxmd.com/read/22647250/reducing-ligation-bias-of-small-rnas-in-libraries-for-next-generation-sequencing
#6
Karim Sorefan, Helio Pais, Adam E Hall, Ana Kozomara, Sam Griffiths-Jones, Vincent Moulton, Tamas Dalmay
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. Here we present a method for functional analysis of nucleic acid-modifying enzymes using next generation sequencing. FINDINGS: We demonstrate that sequencing data of libraries generated by RNA ligases can reveal novel secondary structure preferences of these enzymes, which are used in small RNA cloning and library preparation for NGS...
May 30, 2012: Silence
https://www.readbyqxmd.com/read/22292981/noncoding-rna-localisation-mechanisms-in-chromatin-regulation
#7
Aditi Kanhere, Richard G Jenner
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...
January 31, 2012: Silence
https://www.readbyqxmd.com/read/23273270/strand-specific-libraries-for-high-throughput-rna-sequencing-rna-seq-prepared-without-poly-a-selection
#8
Zhao Zhang, William E Theurkauf, Zhiping Weng, Phillip D Zamore
UNLABELLED: HASH(0x4899500) 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...
2012: Silence
https://www.readbyqxmd.com/read/22676652/rna-methods-and-protocols-a-new-series
#9
Phillip D Zamore
This month, Silence launches a new series on methods and protocols to study silencing pathways and analyze nucleic acids and proteins.
2012: Silence
https://www.readbyqxmd.com/read/22676624/development-of-a-luciferase-based-reporter-of-transcriptional-gene-silencing-that-enables-bidirectional-mutant-screening-in-arabidopsis-thaliana
#10
So Youn Won, Shengben Li, Binglian Zheng, Yuanyuan Zhao, Dongming Li, Xin Zhao, Huilan Yi, Lei Gao, Thanh Theresa Dinh, Xuemei Chen
UNLABELLED: HASH(0x4b63c80) 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...
2012: Silence
https://www.readbyqxmd.com/read/22650989/application-of-rna-silencing-to-plant-disease-resistance
#11
Cheng-Guo Duan, Chun-Han Wang, Hui-Shan Guo
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. In this review, we focus on the application of RNA silencing to produce plants that are resistant to plant viruses such as RNA and DNA viruses, viroids, insects, and the recent expansion to fungal pathogens...
2012: Silence
https://www.readbyqxmd.com/read/22325809/target-gene-expression-levels-and-competition-between-transfected-and-endogenous-micrornas-are-strong-confounding-factors-in-microrna-high-throughput-experiments
#12
Takaya Saito, Pål Sætrom
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...
2012: Silence
https://www.readbyqxmd.com/read/22230293/inhibition-of-microrna-function-by-antimir-oligonucleotides
#13
Jan Stenvang, Andreas Petri, Morten Lindow, Susanna Obad, Sakari Kauppinen
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...
2012: Silence
https://www.readbyqxmd.com/read/22029761/the-dose-can-make-the-poison-lessons-learned-from-adverse-in-vivo-toxicities-caused-by-rnai-overexpression
#14
Dirk Grimm
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...
2011: Silence
https://www.readbyqxmd.com/read/22027184/helicobacter-pylori-interferes-with-an-embryonic-stem-cell-micro-rna-cluster-to-block-cell-cycle-progression
#15
Cédric Belair, Jessica Baud, Sandrine Chabas, Cynthia M Sharma, Jörg Vogel, Cathy Staedel, Fabien Darfeuille
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...
2011: Silence
https://www.readbyqxmd.com/read/21958754/noncoding-rnas-and-cancer
#16
Ohad Yogev, Dimitris Lagos
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.
2011: Silence
https://www.readbyqxmd.com/read/21943311/posttranslational-modification-of-argonautes-and-their-role-in-small-rna-mediated-gene-regulation
#17
Michael Johnston, Gyorgy Hutvagner
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. An emerging theme in the control of Argonaute stability and activity is through posttranslational modifications, which are the focus of this review...
2011: Silence
https://www.readbyqxmd.com/read/21649885/a-5-uridine-amplifies-mirna-mirna-asymmetry-in-drosophila-by-promoting-rna-induced-silencing-complex-formation
#18
Hervé Seitz, Jogender S Tushir, Phillip D Zamore
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*. CONCLUSION: We suggest that recognition of the 5'-U enhances Argonaute loading by a mechanism distinct from its contribution to weakening base pairing at the 5'-end of the prospective miRNA and, as recently proposed in Arabidopsis and in humans, that it improves miRNA precision by excluding incorrectly processed molecules bearing other 5'-nt...
2011: Silence
https://www.readbyqxmd.com/read/21401928/off-target-effects-dominate-a-large-scale-rnai-screen-for-modulators-of-the-tgf-%C3%AE-pathway-and-reveal-microrna-regulation-of-tgfbr2
#19
Nikolaus Schultz, Dina R Marenstein, Dino A De Angelis, Wei-Qing Wang, Sven Nelander, Anders Jacobsen, Debora S Marks, Joan Massagué, Chris Sander
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. RESULTS: We assayed how strongly single siRNAs targeting each of 6,000 genes affect the nuclear translocation of a green fluorescent protein (GFP)-SMAD2 reporter fusion protein...
2011: Silence
https://www.readbyqxmd.com/read/21356093/experimental-design-preprocessing-normalization-and-differential-expression-analysis-of-small-rna-sequencing-experiments
#20
Kevin P McCormick, Matthew R Willmann, Blake C Meyers
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...
2011: Silence
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