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https://www.readbyqxmd.com/read/28223504/transcriptome-wide-microrna-and-target-dynamics-in-the-fat-body-during-the-gonadotrophic-cycle-of-aedes-aegypti
#1
Xiufeng Zhang, Emre Aksoy, Thomas Girke, Alexander S Raikhel, Fedor V Karginov
The mosquito Aedes aegypti is a major vector of numerous viral diseases, because it requires a blood meal to facilitate egg development. The fat body, a counterpart of mammalian liver and adipose tissues, is the metabolic center, playing a key role in reproduction. Therefore, understanding of regulatory networks controlling its functions is critical, and the role of microRNAs (miRNAs) in the process is largely unknown. We aimed to explore miRNA expression and potential targets in the female fat body of Ae. aegypti, as well as their changes postblood meal (PBM)...
February 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28223440/idn2-interacts-with-rpa-and-facilitates-dna-double-strand-break-repair-by-homologous-recombination-in-arabidopsis
#2
Mingming Liu, Zhaoqing Ba, Pedro Costa-Nunes, Wei Wei, Lanxia Li, Fansi Kong, Yan Li, Jijie Chai, Olga Pontes, Yijun Qi
Repair of DNA double-strand breaks (DSBs) is critical for the maintenance of genome integrity. We previously showed that DSB-induced small RNAs (diRNAs) facilitate homologous recombination (HR)-mediated DSB repair in Arabidopsis thaliana. Here we show that INVOLVED IN DE NOVO 2 (IDN2), a double-stranded RNA (dsRNA) binding protein involved in small RNA-directed DNA methylation, is required for DSB repair in Arabidopsis. We find that IDN2 interacts with the heterotrimeric replication protein A (RPA) complex...
February 21, 2017: Plant Cell
https://www.readbyqxmd.com/read/28210761/the-evolutionary-loss-of-rnai-key-determinants-in-kinetoplastids-as-a-multiple-sporadic-phenomenon
#3
Andrey V Matveyev, João M P Alves, Myrna G Serrano, Vladimir Lee, Ana M Lara, William A Barton, André G Costa-Martins, Stephen M Beverley, Erney P Camargo, Marta M G Teixeira, Gregory A Buck
We screened the genomes of a broad panel of kinetoplastid protists for genes encoding proteins associated with the RNA interference (RNAi) system using probes from the Argonaute (AGO1), Dicer1 (DCL1), and Dicer2 (DCL2) genes of Leishmania brasiliensis and Crithidia fasciculata. We identified homologs for all the three of these genes in the genomes of a subset of these organisms. However, several of these organisms lacked evidence for any of these genes, while others lacked only DCL2. The open reading frames encoding these putative proteins were structurally analyzed in silico...
February 16, 2017: Journal of Molecular Evolution
https://www.readbyqxmd.com/read/28206606/the-small-non-coding-rna-processing-machinery-of-two-living-fossil-species-lungfish-and-coelacanth-gives-new-insights-into-the-evolution-of-the-argonaute-protein-family
#4
Biscotti Maria Assunta, Canapa Adriana, Forconi Mariko, Gerdol Marco, Pallavicini Alberto, Schartl Manfred, Barucca Marco
No abstract text is available yet for this article.
February 16, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28198592/bone-marrow-derived-mesenchymal-stem-cells-derived-exosomes-promote-survival-of-retinal-ganglion-cells-through-mirna-dependent-mechanisms
#5
Ben Mead, Stanislav Tomarev
The loss of retinal ganglion cells (RGC) and their axons is one of the leading causes of blindness and includes traumatic (optic neuropathy) and degenerative (glaucoma) eye diseases. Although no clinical therapies are in use, mesenchymal stem cells (MSC) have demonstrated significant neuroprotective and axogenic effects on RGC in both of the aforementioned models. Recent evidence has shown that MSC secrete exosomes, membrane enclosed vesicles (30-100 nm) containing proteins, mRNA and miRNA which can be delivered to nearby cells...
February 15, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28187792/evolution-of-rna-and-dna-guided-antivirus-defense-systems-in-prokaryotes-and-eukaryotes-common-ancestry-vs-convergence
#6
REVIEW
Eugene V Koonin
: Complementarity between nucleic acid molecules is central to biological information transfer processes. Apart from the basal processes of replication, transcription and translation, complementarity is also employed by multiple defense and regulatory systems. All cellular life forms possess defense systems against viruses and mobile genetic elements, and in most of them some of the defense mechanisms involve small guide RNAs or DNAs that recognize parasite genomes and trigger their inactivation...
February 10, 2017: Biology Direct
https://www.readbyqxmd.com/read/28186701/bone-marrow-derived-mesenchymal-stem-cells-derived-exosomes-promote-survival-of-retinal-ganglion-cells-through-mirna-dependent-mechanisms
#7
Ben Mead, Stanislav Tomarev
The loss of retinal ganglion cells (RGC) and their axons is one of the leading causes of blindness and includes traumatic (optic neuropathy) and degenerative (glaucoma) eye diseases. Although no clinical therapies are in use, mesenchymal stem cells (MSC) have demonstrated significant neuroprotective and axogenic effects on RGC in both of the aforementioned models. Recent evidence has shown that MSC secrete exosomes, membrane enclosed vesicles (30-100 nm) containing proteins, mRNA and miRNA which can be delivered to nearby cells...
January 26, 2017: Stem Cells Translational Medicine
https://www.readbyqxmd.com/read/28182654/elli-1-a-novel-germline-protein-modulates-rnai-activity-and-p-granule-accumulation-in-caenorhabditis-elegans
#8
Karolina M Andralojc, Anne C Campbell, Ashley L Kelly, Markus Terrey, Paige C Tanner, Ian M Gans, Michael J Senter-Zapata, Eraj S Khokhar, Dustin L Updike
Germ cells contain non-membrane bound cytoplasmic organelles that help maintain germline integrity. In C. elegans they are called P granules; without them, the germline undergoes partial masculinization and aberrant differentiation. One key P-granule component is the Argonaute CSR-1, a small-RNA binding protein that antagonizes accumulation of sperm-specific transcripts in developing oocytes and fine-tunes expression of proteins critical to early embryogenesis. Loss of CSR-1 complex components results in a very specific, enlarged P-granule phenotype...
February 9, 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28179391/the-nuclear-cap-binding-complex-mediates-meiotic-silencing-by-unpaired-dna
#9
Logan M Decker, Hua Xiao, Erin C Boone, Michael M Vierling, Benjamin S Shanker, Shanika L Kingston, Shannon F Boone, Jackson B Haynes, Patrick K T Shiu
In the filamentous fungus Neurospora crassa, cross walls between individual cells are normally incomplete, making the entire fungal network vulnerable to attack by viruses and selfish DNAs. Accordingly, several genome surveillance mechanisms are maintained to help the fungus to combat these repetitive elements. One of these defense mechanisms is known as meiotic silencing by unpaired DNA (MSUD), which is an RNA silencing system that identifies and silences unpaired genes during meiosis. Utilizing common RNAi proteins such as Dicer and Argonaute, MSUD targets mRNAs homologous to the unpaired sequence to achieve silencing...
February 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28174021/biogenesis-and-function-of-ago-associated-rnas
#10
REVIEW
Iben Daugaard, Thomas Birkballe Hansen
Numerous sophisticated high-throughput sequencing technologies have been developed over the past decade, and these have enabled the discovery of a diverse catalog of small non-coding (nc)RNA molecules that function as regulatory entities by associating with Argonaute (Ago) proteins. MicroRNAs (miRNAs) are currently the best-described class of post-transcriptional regulators that follow a specific biogenesis pathway characterized by Drosha/DGCR8 and Dicer processing. However, more exotic miRNA-like species that bypass particular steps of the canonical miRNA biogenesis pathway continue to emerge, with one of the most recent additions being the agotrons, which escape both Drosha/DGCR8- and Dicer-processing...
February 4, 2017: Trends in Genetics: TIG
https://www.readbyqxmd.com/read/28165496/small-rna-directed-epigenetic-programming-of-embryonic-stem-cell-cardiac-differentiation
#11
Hossein Ghanbarian, Nicole Wagner, Jean-François Michiels, François Cuzin, Kay-Dietrich Wagner, Minoo Rassoulzadegan
Microinjection of small noncoding RNAs in one-cell embryos was reported in several instances to result in transcriptional activation of target genes. To determine the molecular mechanisms involved and to explore whether such epigenetic regulations could play a role in early development, we used a cell culture system as close as possible to the embryonic state. We report efficient cardiac differentiation of embryonic stem (ES) cells induced by small non-coding RNAs with sequences of Cdk9, a key player in cardiomyocyte differentiation...
February 6, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28165224/programmable-dna-guided-artificial-restriction-enzymes
#12
Behnam Enghiad, Huimin Zhao
Restriction enzymes are essential tools for recombinant DNA technology that have revolutionized modern biological research. However, they have limited sequence specificity and availability. Here we report a Pyrococcus furiosus Argonaute (PfAgo) based platform for generating artificial restriction enzymes (AREs) capable of recognizing and cleaving DNA sequences at virtually any arbitrary site and generating defined sticky ends of varying length. Short DNA guides are used to direct PfAgo to target sites for cleavage at high temperatures (>87 °C) followed by reannealing of the cleaved single stranded DNAs...
February 6, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28163933/analysis-of-argonaute-complex-bound-mrnas-in-du145-prostate-carcinoma-cells-reveals-new-mirna-target-genes
#13
Jaroslaw Szczyrba, Volker Jung, Michaela Beitzinger, Elke Nolte, Sven Wach, Martin Hart, Sandra Sapich, Marc Wiesehöfer, Helge Taubert, Gunther Wennemuth, Norbert Eichner, Thomas Stempfl, Bernd Wullich, Gunter Meister, Friedrich A Grässer
Posttranscriptional gene regulation by microRNAs (miRNAs) contributes to the induction and maintenance of prostate carcinoma (PCa). To identify mRNAs enriched or removed from Ago2-containing RISC complexes, these complexes were immunoprecipitated from normal prostate fibroblasts (PNFs) and the PCa line DU145 and the bound mRNAs were quantified by microarray. The analysis of Ago complexes derived from PNFs or DU145 confirmed the enrichment or depletion of a variety of mRNAs already known from the literature to be deregulated...
2017: Prostate Cancer
https://www.readbyqxmd.com/read/28159471/microrna-211-and-autophagy-related-gene-14-signaling-regulate-osteoblast-like-cell-differentiation-of-human-induced-pluripotent-stem-cells
#14
Nobuaki Ozeki, Naoko Hase, Taiki Hiyama, Hideyuki Yamaguchi, Rie Kawai-Asano, Kazuhiko Nakata, Makio Mogi
MicroRNAs (miRNAs) have been the subject of recent attention as key regulatory factors in cell differentiation. In the current study, to explore the early signaling cascade of osteogenic differentiation of human induced pluripotent stem (hiPS) cells, we investigated miR-211 regulation and autophagy-related gene (Atg) signaling in osteogenic differentiation. In addition to reciprocal strong induction of miR-211 expression in differentiated cells following osteogenic differentiation, we found abundant Argonaute 3 bound to miR-211⊡ There were also dramatic increases in the mRNA and protein levels of Atg14 together with increases in the amount of autophagosomes as well as autophagic fluxes...
January 31, 2017: Experimental Cell Research
https://www.readbyqxmd.com/read/28148824/biochemical-and-genetic-functional-dissection-of-the-p38-viral-suppressor-of-rna-silencing
#15
Taichiro Iki, Marie-Aude Tschopp, Olivier Voinnet
Phytoviruses encode viral suppressors of RNA-silencing (VSRs) to counteract the plant antiviral silencing response, which relies on virus-derived small interfering (si)RNAs processed by Dicer RNaseIII enzymes and subsequently loaded into ARGONAUTE (AGO) effector proteins. Here, a tobacco cell-free system was engineered to recapitulate the key steps of antiviral RNA-silencing and, in particular, the most upstream double-stranded (ds)RNA processing reaction, not kinetically investigated thus far in the context of plant VSR studies...
February 1, 2017: RNA
https://www.readbyqxmd.com/read/28146558/genome-wide-exonic-small-interference-rna-mediated-gene-silencing-regulates-sexual-reproduction-in-the-homothallic-fungus-fusarium-graminearum
#16
Hokyoung Son, Ae Ran Park, Jae Yun Lim, Chanseok Shin, Yin-Won Lee
Various ascomycete fungi possess sex-specific molecular mechanisms, such as repeat-induced point mutations, meiotic silencing by unpaired DNA, and unusual adenosine-to-inosine RNA editing, for genome defense or gene regulation. Using a combined analysis of functional genetics and deep sequencing of small noncoding RNA (sRNA), mRNA, and the degradome, we found that the sex-specifically induced exonic small interference RNA (ex-siRNA)-mediated RNA interference (RNAi) mechanism has an important role in fine-tuning the transcriptome during ascospore formation in the head blight fungus Fusarium graminearum...
February 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28145468/the-srnaome-mining-revealed-existence-of-unique-signature-small-rnas-derived-from-5-8srrna-from-piper-nigrum-and-other-plant-lineages
#17
Srinivasan Asha, E V Soniya
Small RNAs derived from ribosomal RNAs (srRNAs) are rarely explored in the high-throughput data of plant systems. Here, we analyzed srRNAs from the deep-sequenced small RNA libraries of Piper nigrum, a unique magnoliid plant. The 5' end of the putative long form of 5.8S rRNA (5.8SLrRNA) was identified as the site for biogenesis of highly abundant srRNAs that are unique among the Piperaceae family of plants. A subsequent comparative analysis of the ninety-seven sRNAomes of diverse plants successfully uncovered the abundant existence and precise cleavage of unique rRF signature small RNAs upstream of a novel 5' consensus sequence of the 5...
February 1, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28130299/identification-and-functional-analysis-of-dicer-and-argonaute-genes-involved-in-rna-interference-in-the-entomopathogenic-fungus-metarhizium-robertsii
#18
Huimin Meng, Zhangxun Wang, Yulong Wang, Hong Zhu, Bo Huang
RNA interference (RNAi) is a gene silencing mechanism that plays an important role in gene regulation in a number of eukaryotic organisms. Two core components, Dicer and Argonaute, are central in the RNAi machinery. However, the physiological roles of Dicer and Argonaute in the entomopathogenic fungus Metarhizium robertsii remained unclear. Here, the roles of genes encoding Dicers (Mrdcl1 and Mrdcl2) and Argonautes (Mrago1 and Mrago2) in M.robertsii were investigated. The results showed that the Dicer protein MrDCL2 and Argonaute protein MrAGO1 are the major components of the RNAi process occurring in M...
January 27, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28122825/endogenous-rnai-pathways-are-required-in-neurons-for-dauer-formation-in-caenorhabditis-elegans
#19
Pallavi S Bharadwaj, Sarah E Hall
Animals can adapt to unfavorable environments through changes in physiology or behavior. In the nematode, C. elegans, environmental conditions perceived early in development determine whether the animal enters either the reproductive cycle or enters into an alternative diapause stage named dauer. Here, we show that endogenous RNAi pathways play a role in dauer formation in crowding (high pheromone), starvation, and high temperature conditions. Disruption of the Mutator proteins or the nuclear Argonaute CSR-1 result in differential dauer-deficient phenotypes that are dependent upon the experienced environmental stress...
January 25, 2017: Genetics
https://www.readbyqxmd.com/read/28119422/non-canonical-targets-destabilize-micrornas-in-human-argonautes
#20
June Hyun Park, Sang-Yoon Shin, Chanseok Shin
Although much is known about microRNA (miRNA) biogenesis and the mechanism by which miRNAs regulate their targets, little is known about the regulation of miRNA stability. Mature miRNAs are stabilized by binding to Argonaute (Ago) proteins, the core components of the RNA-induced silencing complex (RISC). Recent studies suggest that interactions between miRNAs and their highly complementary target RNAs promote release of miRNAs from Ago proteins, and this in turn can lead to destabilization of miRNAs. However, the physiological triggers of miRNA destabilization with molecular mechanisms remain largely unknown...
January 24, 2017: Nucleic Acids Research
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