Genomes and Genes
Summary: A family of RNA-binding proteins that has specificity for MICRORNAS and SMALL INTERFERING RNA molecules. The proteins take part in RNA processing events as core components of RNA-induced silencing complex.
- Seth M, Shirayama M, Gu W, Ishidate T, Conte D, Mello C. The C. elegans CSR-1 argonaute pathway counteracts epigenetic silencing to promote germline gene expression. Dev Cell. 2013;27:656-63 pubmed..elegans adaptively acquires and maintains a transgenerational CSR-1 memory that recognizes and protects self-mRNAs, allowing piRNAs to recognize foreign sequences innately, without the need for prior exposure ..
- Kenesi E, Carbonell A, Lózsa R, Vértessy B, Lakatos L. A viral suppressor of RNA silencing inhibits ARGONAUTE 1 function by precluding target RNA binding to pre-assembled RISC. Nucleic Acids Res. 2017;45:7736-7750 pubmed publisher..Our results describe the negative regulation of RISC, the small RNA containing molecular machine. ..
- Wasserman G, Szymaniak A, Hinds A, Yamamoto K, Kamata H, Smith N, et al. Expression of Piwi protein MIWI2 defines a distinct population of multiciliated cells. J Clin Invest. 2017;127:3866-3876 pubmed publisher..By demonstrating roles for MIWI2 in airway cell identity and pulmonary innate immunity, these studies elucidate unanticipated physiological functions for Piwi proteins in somatic tissues. ..
- Blow N. TO EDIT OR NOT: THE NGAGO STORY. Biotechniques. 2016;61:172-174 pubmed..New genome-editing approaches always receive widespread attention. But in the case of a novel Argonaute-based technique published last spring, attention has been particularly intense. ..
- Goto Y, Kurozumi A, Arai T, Nohata N, Kojima S, Okato A, et al. Impact of novel miR-145-3p regulatory networks on survival in patients with castration-resistant prostate cancer. Br J Cancer. 2017;117:409-420 pubmed publisher..e., MELK, NCAPG, BUB1, and CDK1, in CPRC. These 4 genes significantly predicted survival in patients with PCa. Small RNA sequencing for lethal CRPC and in silico analyses provided novel therapeutic targets for CRPC. ..
- Odokonyero D, Mendoza M, Moffett P, Scholthof H. Tobacco rattle virus (TRV)-Mediated Silencing of Nicotiana benthamiana ARGONAUTES (NbAGOs) Reveals New Antiviral Candidates and Dominant Effects of TRV-NbAGO1. Phytopathology. 2017;107:977-987 pubmed publisherThe objective of this study was to determine the contribution of different ARGONAUTE proteins in Nicotiana benthamiana (NbAGOs) to the defense against silencing sensitive GFP-expressing viral constructs based on Tomato bushy stunt virus (..
- Bisht K, Grill S, Graniel J, Nandakumar J. A lentivirus-free inducible CRISPR-Cas9 system for efficient targeting of human genes. Anal Biochem. 2017;530:40-49 pubmed publisher..In addition to generating inducible knockouts, our technology can be adapted to improve other applications of Cas9, including transcriptional/epigenetic modulation and visualization of cellular DNA loci. ..
- Doxzen K, Doudna J. DNA recognition by an RNA-guided bacterial Argonaute. PLoS ONE. 2017;12:e0177097 pubmed publisher..This structural analysis of MpAgo bound to a hybrid helix advances our understanding of the diversity of target recognition mechanisms by Argonaute proteins.
- Vasiliauskaite L, Vitsios D, Berrens R, Carrieri C, Reik W, Enright A, et al. A MILI-independent piRNA biogenesis pathway empowers partial germline reprogramming. Nat Struct Mol Biol. 2017;24:604-606 pubmed publisher..Here, we demonstrate the existence of a piRNA biogenesis pathway that sustains partial MIWI2 function and reprogramming activity in the absence of MILI. ..
- Luo S, Lu J. Silencing of Transposable Elements by piRNAs in Drosophila: An Evolutionary Perspective. Genomics Proteomics Bioinformatics. 2017;15:164-176 pubmed publisher..The piRNA repression pathway provides us an unparalleled system to study the co-evolutionary process between parasites and host organisms. ..
- ..More generally, this case underscores the need for better informatics tools to allow investigators to analyze the state of a given scientific question at a high-level and to identify possible new research directions. ..
- Brown K, Svendsen J, Tucci R, Montgomery B, Montgomery T. ALG-5 is a miRNA-associated Argonaute required for proper developmental timing in the Caenorhabditis elegans germline. Nucleic Acids Res. 2017;45:9093-9107 pubmed publisher..Our results provide a near-comprehensive analysis of miRNA-Argonaute interactions in C. elegans and reveal a new role for miRNAs in the germline. ..
- Burger K, Schlackow M, Potts M, Hester S, Mohammed S, Gullerova M. Nuclear phosphorylated Dicer processes double-stranded RNA in response to DNA damage. J Cell Biol. 2017;216:2373-2389 pubmed publisher..Collectively, we place Dicer within the context of the DDR by demonstrating a DNA damage-inducible phosphoswitch that causes localized processing of nuclear dsRNA by p-Dicer to promote DNA repair. ..
- Kong R, Xu L, Piao L, Zhang D, Hou T, Chang S. Exploring the RNA-bound and RNA-free human Argonaute-2 by molecular dynamics simulation method. Chem Biol Drug Des. 2017;90:753-763 pubmed publisher..It is speculated that PAZ domain could be a key regulator in hAgo2-mediated miRNA-induced gene regulation. ..
- Ryazansky S, Radion E, Mironova A, Akulenko N, Abramov Y, Morgunova V, et al. Natural variation of piRNA expression affects immunity to transposable elements. PLoS Genet. 2017;13:e1006731 pubmed publisher..that originate from distinct genomic regions termed piRNA clusters and are processed by PIWI-subfamily Argonaute proteins. Here, we explore the variation in the ability to restrain an alien TE in different Drosophila strains...
- Erhard F, Dölken L, Jaskiewicz L, Zimmer R. PARma: identification of microRNA target sites in AGO-PAR-CLIP data. Genome Biol. 2013;14:R79 pubmed publisher..Based on differential PAR-CLIP analysis and comparison to RIP-Chip data, we show that PARma is more accurate than existing approaches. PARma is available from http://www.bio.ifi.lmu.de/PARma. ..
- Rowley M, Rothi M, Böhmdorfer G, Kuciński J, Wierzbicki A. Long-range control of gene expression via RNA-directed DNA methylation. PLoS Genet. 2017;13:e1006749 pubmed publisher..We propose a model, where RdDM prevents the formation of chromosomal interactions between genes and their distant regulatory elements. ..
- Gou L, Kang J, Dai P, Wang X, Li F, Zhao S, et al. Ubiquitination-Deficient Mutations in Human Piwi Cause Male Infertility by Impairing Histone-to-Protamine Exchange during Spermiogenesis. Cell. 2017;169:1090-1104.e13 pubmed publisher..Collectively, our findings identify Piwi as a factor in human infertility and reveal its role in regulating the histone-to-protamine exchange during spermiogenesis. ..
- Sheu Gruttadauria J, Macrae I. Structural Foundations of RNA Silencing by Argonaute. J Mol Biol. 2017;429:2619-2639 pubmed publisherNearly every cell in the human body contains a set of programmable gene-silencing proteins named Argonaute. Argonaute proteins mediate gene regulation by small RNAs and thereby contribute to cellular homeostasis during diverse ..
- Quevillon Huberdeau M, Zeitler D, Hauptmann J, Bruckmann A, Fressigne L, Danner J, et al. Phosphorylation of Argonaute proteins affects mRNA binding and is essential for microRNA-guided gene silencing in vivo. EMBO J. 2017;36:2088-2106 pubmed publisherb>Argonaute proteins associate with microRNAs and are key components of gene silencing pathways. With such a pivotal role, these proteins represent ideal targets for regulatory post-translational modifications...
- Qin J, Tang Z, Ma X, Meng Y. Investigating the regulatory roles of the microRNAs and the Argonaute 1-enriched small RNAs in plant metabolism. Gene. 2017;628:180-189 pubmed publisher..Several functionally conserved subnetworks were identified between the two plant species. Our study provides a basis for studies on metabolism-related sRNAs in plants. ..
- Horvathova I, Voigt F, Kotrys A, Zhan Y, Artus Revel C, Eglinger J, et al. The Dynamics of mRNA Turnover Revealed by Single-Molecule Imaging in Single Cells. Mol Cell. 2017;68:615-625.e9 pubmed publisher..This methodology provides a framework for investigating the entire life history of individual mRNAs from birth to death in single cells...
- Dueck A, Meister G. Assembly and function of small RNA - argonaute protein complexes. Biol Chem. 2014;395:611-29 pubmed publisher..The loading of Argonaute proteins with small RNAs is aided by a number of auxiliary factors as well as ATP hydrolysis...
- Kandasamy S, Zhu L, Fukunaga R. The C-terminal dsRNA-binding domain of Drosophila Dicer-2 is crucial for efficient and high-fidelity production of siRNA and loading of siRNA to Argonaute2. RNA. 2017;23:1139-1153 pubmed publisher..This study reveals multifunctions of Dicer-2 CdsRBD and sheds light on the molecular mechanism by which Dicer-2 produces 21-nt siRNAs with a high efficiency and fidelity for efficient RNA silencing. ..
- Koonin E. Evolution of RNA- and DNA-guided antivirus defense systems in prokaryotes and eukaryotes: common ancestry vs convergence. Biol Direct. 2017;12:5 pubmed publisher..This article was reviewed by Mikhail Gelfand and Bojan Zagrovic. ..
- Si H, Cao Y, Zhu H, Li D, Lv Z, Sheng Q, et al. Transposable Element Bm1645 is a Source of BmAGO2-associated Small RNAs that affect its expression in Bombyx mori. BMC Genomics. 2017;18:201 pubmed publisher..Our results suggest Bm1645 functions as a source of small RNAs pool and this pool can produce many BmAGO2-associated small RNAs that regulate TE's expression. ..
- Sheng G, Gogakos T, Wang J, Zhao H, Serganov A, Juranek S, et al. Structure/cleavage-based insights into helical perturbations at bulge sites within T. thermophilus Argonaute silencing complexes. Nucleic Acids Res. 2017;45:9149-9163 pubmed publisher..These structural studies are complemented by cleavage assays that independently monitor the impact of bulges on TtAgo-mediated cleavage reaction. ..
- Carrieri C, Comazzetto S, Grover A, Morgan M, Buness A, Nerlov C, et al. A transit-amplifying population underpins the efficient regenerative capacity of the testis. J Exp Med. 2017;214:1631-1641 pubmed publisher..In summary, the mouse testis has adopted a regenerative strategy to expand stem cell activity by incorporating a transit-amplifying population to the effective stem cell pool, thus ensuring rapid and efficient tissue repair. ..
- Billi A, Freeberg M, Kim J. piRNAs and siRNAs collaborate in Caenorhabditis elegans genome defense. Genome Biol. 2012;13:164 pubmed publisher..Caenorhabditis elegans piRNAs promote genome surveillance by triggering siRNA-mediated silencing of nonself DNA in competition with licensing programs that support endogenous gene expression. ..
- Pitchiaya S, Heinicke L, Park J, Cameron E, Walter N. Resolving Subcellular miRNA Trafficking and Turnover at Single-Molecule Resolution. Cell Rep. 2017;19:630-642 pubmed publisher..Probing single cells for miRNA activity, trafficking, and metabolism promises to facilitate screening for effective miRNA mimics and anti-miRNA drugs. ..
- Qiu Y, Xu Y, Zhang Y, Zhou H, Deng Y, Li X, et al. Human Virus-Derived Small RNAs Can Confer Antiviral Immunity in Mammals. Immunity. 2017;46:992-1004.e5 pubmed publisher..Thus, RNAi can function as an antiviral immunity, which is induced and suppressed by a human virus, in mammals. ..
- Maldonado L, Assis J, Araújo F, Salim A, Macchiaroli N, Cucher M, et al. The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases. BMC Genomics. 2017;18:204 pubmed publisher..Additional cestode genomes need to be sequenced to be able to resolve their phylogeny. ..
- Vagin V, Hannon G, Aravin A. Arginine methylation as a molecular signature of the Piwi small RNA pathway. Cell Cycle. 2009;8:4003-4 pubmed
- Zhou Y, Honda M, Zhu H, Zhang Z, Guo X, Li T, et al. Spatiotemporal sequestration of miR165/166 by Arabidopsis Argonaute10 promotes shoot apical meristem maintenance. Cell Rep. 2015;10:1819-27 pubmed..Thus, this study provides insight into how the spatiotemporal regulation of AGO10-miR165/166 activity affects SAM development. ..
- Rashpa R, Vazquez Pianzola P, Colombo M, Hernández G, Beuchle D, Berger F, et al. Cbp80 is needed for the expression of piRNA components and piRNAs. PLoS ONE. 2017;12:e0181743 pubmed publisher..This shows that Cbp80 plays an important role in the production and localization of the protein components of the piRNA pathway and it seems to be less important for the production and export of the piRNA precursor transcripts. ..
- Luna J, Barajas J, Teng K, Sun H, Moore M, Rice C, et al. Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer. Mol Cell. 2017;67:400-410.e7 pubmed publisher..Upregulation of several common mouse and human targets, most notably BCL9, predicted survival in HCC patients. These results broadly define the molecular consequences of miR-122 downregulation in hepatocellular carcinoma. ..
- Li Y, Li S, Luo Y, Liu Y, Yu N. LncRNA PVT1 Regulates Chondrocyte Apoptosis in Osteoarthritis by Acting as a Sponge for miR-488-3p. DNA Cell Biol. 2017;36:571-580 pubmed publisher..Collectively, this study revealed that lncRNA PVT1 regulated the apoptosis of chondrocytes by acting as a sponge for miR-488-3p in OA. PVT1 may be considered a new therapeutic target for the treatment of OA. ..
- Rojas Ríos P, Chartier A, Pierson S, Simonelig M. Aubergine and piRNAs promote germline stem cell self-renewal by repressing the proto-oncogene Cbl. EMBO J. 2017;36:3194-3211 pubmed publisher..This study reveals the role of piRNAs and PIWI proteins in controlling stem cell homeostasis via translational repression and highlights piRNAs as major post-transcriptional regulators in key developmental decisions. ..
- Wang X, Chang L, Wang H, Su A, Wu Z. Dcp1a and GW182 Induce Distinct Cellular Aggregates and Have Different Effects on microRNA Pathway. DNA Cell Biol. 2017;36:565-570 pubmed publisher..Our results suggest that overexpressed Dcp1a and GW182 can form different cytoplasmic aggregates and play distinct biological roles in the miRNA pathway. ..
- Wenda J, Homolka D, Yang Z, Spinelli P, Sachidanandam R, Pandey R, et al. Distinct Roles of RNA Helicases MVH and TDRD9 in PIWI Slicing-Triggered Mammalian piRNA Biogenesis and Function. Dev Cell. 2017;41:623-637.e9 pubmed publisher..In contrast, ATPase activity of TDRD9 is dispensable for piRNA biogenesis but is essential for transposon silencing and male fertility. Our work implicates distinct RNA helicases in specific steps along the nuclear piRNA pathway. ..
- Honda S, Kawamura T, Loher P, Morichika K, Rigoutsos I, Kirino Y. The biogenesis pathway of tRNA-derived piRNAs in Bombyx germ cells. Nucleic Acids Res. 2017;45:9108-9120 pubmed publisher..Our study advances the understanding of biogenesis mechanisms and the genesis of specific expression profiles for tRNA-derived ncRNAs. ..
- Pan S, Yang X, Jia Y, Li R, Zhao R. Microvesicle-shuttled miR-130b reduces fat deposition in recipient primary cultured porcine adipocytes by inhibiting PPAR-g expression. J Cell Physiol. 2014;229:631-9 pubmed publisher..We also showed that MV-shuttled miRNA-130b inhibited adipogenesis and lipogenesis, and reduced fat deposition in recipient adipocytes by targeting PPAR-g. ..
- Kamel W, Akusjarvi G. An Ago2-associated capped transcriptional start site small RNA suppresses adenovirus DNA replication. RNA. 2017;23:1700-1711 pubmed publisher..Collectively, our results suggest that this novel sRNA may serve a regulatory function controlling viral genome replication during a lytic and/or persistent adenovirus infection in its natural host. ..
- Daugaard I, Hansen T. Biogenesis and Function of Ago-Associated RNAs. Trends Genet. 2017;33:208-219 pubmed publisher..We review here the current knowledge and most recent discoveries relating to alternative functions and biogenesis strategies for Ago-associated RNAs in mammals. ..
- Khin N, Lowe J, Jensen L, Burgio G. No evidence for genome editing in mouse zygotes and HEK293T human cell line using the DNA-guided Natronobacterium gregoryi Argonaute (NgAgo). PLoS ONE. 2017;12:e0178768 pubmed publisher..Together our findings indicate that we failed to edit using NgAgo. ..
- Hyams Y, Paz G, Rabinowitz C, Rinkevich B. Insights into the unique torpor of Botrylloides leachi, a colonial urochordate. Dev Biol. 2017;428:101-117 pubmed publisher..Considering the evolutionary perspectives to hibernation we propose linkages to the disposable-soma theory. ..
- Gainetdinov I, Skvortsova Y, Kondratieva S, Funikov S, Azhikina T. Two modes of targeting transposable elements by piRNA pathway in human testis. RNA. 2017;23:1614-1625 pubmed publisher..e., pachytene piRNA cluster primary transcripts), we ascertain that these are a specific set of lincRNAs that both possess distinguishing epigenetic features and are expressed exclusively in testis. ..
- Wang C, Gupta P, Fressigne L, Bossé G, Wang X, Simard M, et al. TEG-1 CD2BP2 controls miRNA levels by regulating miRISC stability in C. elegans and human cells. Nucleic Acids Res. 2017;45:1488-1500 pubmed publisher..Together, these data demonstrate that TEG-1 CD2BP2 stabilizes miRISC and mature miRNAs, maintaining them at levels necessary to properly regulate target gene expression. ..
- Choi J, Kim K, Jeon J, Wu J, Song H, Asiegbu F, et al. funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi. BMC Genomics. 2014;15 Suppl 9:S14 pubmed publisher..It could serve as a versatile genomics workbench for key components of RNAi. ..
- Tyc K, Nabih A, Wu M, Wedeles C, Sobotka J, Claycomb J. The Conserved Intron Binding Protein EMB-4 Plays Differential Roles in Germline Small RNA Pathways of C. elegans. Dev Cell. 2017;42:256-270.e6 pubmed publisher..These data suggest that EMB-4 could contribute to a molecular signature that distinguishes the targets of these two germline small RNA pathways. ..
- Elkayam E, Faehnle C, Morales M, Sun J, Li H, Joshua Tor L. Multivalent Recruitment of Human Argonaute by GW182. Mol Cell. 2017;67:646-658.e3 pubmed publisher..Finally, we show that hGW182 can recruit up to three copies of hAgo via its three GW motifs. This may explain the observed cooperativity in miRNA-mediated gene silencing. ..
- Lee H, Jung S, Hwang H, Kang D, De S, Dudekula D, et al. WIG1 is crucial for AGO2-mediated ACOT7 mRNA silencing via miRNA-dependent and -independent mechanisms. Nucleic Acids Res. 2017;45:6894-6910 pubmed publisher..Altogether, our data indicate that WIG1 governs the miRNA-dependent and the miRNA-independent recruitment of AGO2 to lower the stability of and suppress the translation of ACOT7 mRNA. ..
- Tassetto M, Kunitomi M, Andino R. Circulating Immune Cells Mediate a Systemic RNAi-Based Adaptive Antiviral Response in Drosophila. Cell. 2017;169:314-325.e13 pubmed publisher..Thus, similar to vertebrates, insects use immune cells to generate immunological memory in the form of stable vDNAs that generate systemic immunity, which is mediated by the vsRNA-containing exosomes. ..
- Rios C, Warren D, Olson B, Abbott A. Functional analysis of microRNA pathway genes in the somatic gonad and germ cells during ovulation in C. elegans. Dev Biol. 2017;426:115-125 pubmed publisher..These data identify specific steps in the process of ovulation that require miRNA pathway gene activity in the somatic gonad cells. ..
- Javidi Parsijani P, Niu G, Davis M, Lu P, Atala A, Lu B. No evidence of genome editing activity from Natronobacterium gregoryi Argonaute (NgAgo) in human cells. PLoS ONE. 2017;12:e0177444 pubmed publisher..Our data show that NgAgo is not a robust genome editing tool, although it may have such activity under other conditions. ..
- Flamand M, Gan H, Mayya V, Gunsalus K, Duchaine T. A non-canonical site reveals the cooperative mechanisms of microRNA-mediated silencing. Nucleic Acids Res. 2017;45:7212-7225 pubmed publisher..Our results delineate multiple cooperative mechanisms in miRNA-mediated silencing and further support the consideration of target site cooperation as a fundamental characteristic of miRNA function. ..