Exogenous and endogenous dsRNAs perceived by plant Dicer-like 4 protein in the RNAi-depleted cellular context

[1]  Mohammad-javad Sanaei,et al.  The role of noncoding RNAs in metabolic reprogramming of cancer cells , 2023, Cellular & Molecular Biology Letters.

[2]  S. Ding,et al.  Mammalian viral suppressors of RNA interference. , 2022, Trends in biochemical sciences.

[3]  V. Pantaleo,et al.  Regulation of plant antiviral defense genes via host RNA-silencing mechanisms , 2021, Virology journal.

[4]  M. Fawzy,et al.  Association of cyclin-dependent kinase inhibitor 2B antisense RNA 1 gene expression and rs2383207 variant with breast cancer risk and survival , 2021, Cellular & molecular biology letters.

[5]  P. D. Nagy,et al.  Tombusviruses orchestrate the host endomembrane system to create elaborate membranous replication organelles. , 2021, Current opinion in virology.

[6]  V. Pantaleo,et al.  Endogenous activated small interfering RNAs in virus‐infected Brassicaceae crops show a common host gene‐silencing pattern affecting photosynthesis and stress response , 2020, The New phytologist.

[7]  Hongwei Guo,et al.  The diversity of post-transcriptional gene silencing mediated by small silencing RNAs in plants. , 2020, Essays in biochemistry.

[8]  Hong Zhang,et al.  Plant 22-nt siRNAs mediate translational repression and stress adaptation , 2020, Nature.

[9]  Rafał Bartoszewski,et al.  Editorial focus: understanding off-target effects as the key to successful RNAi therapy , 2019, Cellular & Molecular Biology Letters.

[10]  T. Fukuhara,et al.  Long DCL4-substrate dsRNAs efficiently induce RNA interference in plant cells , 2019, Scientific Reports.

[11]  B. Meyers,et al.  24-nt reproductive phasiRNAs are broadly present in angiosperms , 2019, Nature Communications.

[12]  Yang Li,et al.  Small RNA-based antimicrobial immunity , 2018, Nature Reviews Immunology.

[13]  J. van der Oost,et al.  Ethyl acetate production by the elusive alcohol acetyltransferase from yeast. , 2017, Metabolic engineering.

[14]  S. Liuni,et al.  A fuzzy method for RNA-Seq differential expression analysis in presence of multireads , 2016, BMC Bioinformatics.

[15]  Annemarthe G. van der Veen,et al.  Inactivation of the type I interferon pathway reveals long double‐stranded RNA‐mediated RNA interference in mammalian cells , 2016, The EMBO journal.

[16]  Måns Magnusson,et al.  MultiQC: summarize analysis results for multiple tools and samples in a single report , 2016, Bioinform..

[17]  W. Huber,et al.  Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 , 2014, Genome Biology.

[18]  Xianbing Wang,et al.  Virus infection triggers widespread silencing of host genes by a distinct class of endogenous siRNAs in Arabidopsis , 2014, Proceedings of the National Academy of Sciences.

[19]  L. Aravind,et al.  New perspectives on the diversification of the RNA interference system: insights from comparative genomics and small RNA sequencing , 2014, Wiley interdisciplinary reviews. RNA.

[20]  Anton Glieder,et al.  Carbon source dependent promoters in yeasts , 2014, Microbial Cell Factories.

[21]  L. Steinmetz,et al.  Gene regulation by antisense transcription , 2013, Nature Reviews Genetics.

[22]  V. Pantaleo,et al.  AGO/RISC-mediated antiviral RNA silencing in a plant in vitro system , 2013, Nucleic acids research.

[23]  Colin N. Dewey,et al.  RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome , 2011, BMC Bioinformatics.

[24]  Marcel Martin Cutadapt removes adapter sequences from high-throughput sequencing reads , 2011 .

[25]  A. Fukudome,et al.  Specific requirement of DRB4, a dsRNA-binding protein, for the in vitro dsRNA-cleaving activity of Arabidopsis Dicer-like 4. , 2011, RNA.

[26]  Frederick P. Roth,et al.  Reconstitution of human RNA interference in budding yeast , 2011, Nucleic acids research.

[27]  N. Friedman,et al.  Strand-specific RNA sequencing reveals extensive regulated long antisense transcripts that are conserved across yeast species , 2010, Genome Biology.

[28]  C. Sullivan,et al.  Unique Functionality of 22 nt miRNAs in Triggering RDR6-Dependent siRNA Biogenesis from Target Transcripts in Arabidopsis , 2010, Nature Structural &Molecular Biology.

[29]  Vincent Moulton,et al.  Structural and Functional Analysis of Viral siRNAs , 2010, PLoS pathogens.

[30]  J. M. Lee,et al.  The telomere-specific non-LTR retrotransposons SART1 and TRAS1 are suppressed by Piwi subfamily proteins in the silkworm, Bombyx mori , 2009, Cellular & Molecular Biology Letters.

[31]  B. Schulz,et al.  Replication of Tomato bushy stunt virus RNA in a plant in vitro system. , 2009, Virology.

[32]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[33]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[34]  Todd Blevins,et al.  Evolution of Arabidopsis MIR genes generates novel microRNA classes , 2008, Nucleic acids research.

[35]  P. D. Nagy Yeast as a model host to explore plant virus-host interactions. , 2008, Annual review of phytopathology.

[36]  Xuemei Chen,et al.  DICER-LIKE2 Plays a Primary Role in Transitive Silencing of Transgenes in Arabidopsis , 2008, PloS one.

[37]  Anuj Kumar,et al.  Unconventional Genomic Architecture in the Budding Yeast Saccharomyces cerevisiae Masks the Nested Antisense Gene NAG1 , 2008, Eukaryotic Cell.

[38]  I. MacRae,et al.  Ribonuclease revisited: structural insights into ribonuclease III family enzymes. , 2007, Current opinion in structural biology.

[39]  T. Fukuhara,et al.  The dsRNA-binding protein DRB4 interacts with the Dicer-like protein DCL4 in vivo and functions in the trans-acting siRNA pathway , 2007, Plant Molecular Biology.

[40]  B. Vojtesek,et al.  Endoplasmic reticulum stress and apoptosis , 2006, Cellular & Molecular Biology Letters.

[41]  Jinsong Bao,et al.  Hierarchical Action and Inhibition of Plant Dicer-Like Proteins in Antiviral Defense , 2006, Science.

[42]  V. Pantaleo,et al.  Cytological analysis of Saccharomyces cerevisiae cells supporting cymbidium ringspot virus defective interfering RNA replication. , 2006, The Journal of general virology.

[43]  R. Poethig,et al.  A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. , 2005, Genes & development.

[44]  Edwards Allen,et al.  DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[45]  David P. Bartel,et al.  Partially Redundant Functions of Arabidopsis DICER-like Enzymes and a Role for DCL4 in Producing trans-Acting siRNAs , 2005, Current Biology.

[46]  Adam M. Gustafson,et al.  microRNA-Directed Phasing during Trans-Acting siRNA Biogenesis in Plants , 2005, Cell.

[47]  Jianbo Chen,et al.  Alternate, virus-induced membrane rearrangements support positive-strand RNA virus genome replication. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[48]  V. Pantaleo,et al.  The p36 and p95 replicase proteins of Carnation Italian ringspot virus cooperate in stabilizing defective interfering RNA. , 2004, The Journal of general virology.

[49]  Albert Sickmann,et al.  The proteome of Saccharomyces cerevisiae mitochondria , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[50]  Marjori Matzke,et al.  Evidence for Nuclear Processing of Plant Micro RNA and Short Interfering RNA Precursors1[w] , 2003, Plant Physiology.

[51]  Michael Zuker,et al.  Mfold web server for nucleic acid folding and hybridization prediction , 2003, Nucleic Acids Res..

[52]  Sherif Abou Elela,et al.  Sequence dependence of substrate recognition and cleavage by yeast RNase III. , 2003, Journal of molecular biology.

[53]  J. Baker,et al.  The overlapping RNA-binding domains of p33 and p92 replicase proteins are essential for tombusvirus replication. , 2003, Virology.

[54]  Z. Bánfalvi,et al.  Low temperature inhibits RNA silencing‐mediated defence by the control of siRNA generation , 2003, The EMBO journal.

[55]  V. Pantaleo,et al.  Replication of Carnation Italian Ringspot Virus Defective Interfering RNA in Saccharomyces cerevisiae , 2003, Journal of Virology.

[56]  B. Reinhart,et al.  MicroRNAs in plants. , 2002, Genes & development.

[57]  Tom H. Pringle,et al.  The human genome browser at UCSC. , 2002, Genome research.

[58]  S. Eddy Computational Genomics of Noncoding RNA Genes , 2002, Cell.

[59]  C. Hornyik,et al.  Short Defective Interfering RNAs of Tombusviruses Are Not Targeted but Trigger Post-Transcriptional Gene Silencing against Their Helper Virus Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.010366. , 2002, The Plant Cell Online.

[60]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[61]  V. Kushnirov Rapid and reliable protein extraction from yeast , 2000, Yeast.

[62]  Yian-Biao Zhang,et al.  The VRG4 Gene Is Required for GDP-mannose Transport into the Lumen of the Golgi in the Yeast, Saccharomyces cerevisiae * , 1997, The Journal of Biological Chemistry.

[63]  P. Ahlquist,et al.  Brome mosaic virus helicase- and polymerase-like proteins colocalize on the endoplasmic reticulum at sites of viral RNA synthesis , 1996, Journal of virology.

[64]  P. Ahlquist,et al.  Complete replication of an animal virus and maintenance of expression vectors derived from it in Saccharomyces cerevisiae. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[65]  Sherif Abou Elela,et al.  RNase III Cleaves Eukaryotic Preribosomal RNA at a U3 snoRNP-Dependent Site , 1996, Cell.

[66]  T. Dalmay,et al.  The replication of cymbidium ringspot tombusvirus defective interfering-satellite RNA hybrid molecules , 1992, Virology.

[67]  H. Vaucheret,et al.  Respective contributions of Arabidopsis DCL2 and DCL4 to RNA silencing. , 2015, The Plant journal : for cell and molecular biology.

[68]  Thomas R. Gingeras,et al.  STAR: ultrafast universal RNA-seq aligner , 2013, Bioinform..

[69]  Elliot J. Lefkowitz,et al.  Virus taxonomy: classification and nomenclature of viruses , 2012 .

[70]  Jeffrey P. Mower,et al.  RNAi in Budding Yeast , 2009, Science.

[71]  Kazuo Shinozaki,et al.  Specific interactions between Dicer-like proteins and HYL1/DRB- family dsRNA-binding proteins in Arabidopsis thaliana , 2004, Plant Molecular Biology.

[72]  L. Rubino,et al.  Expression of a plant virus non-structural protein in Saccharomyces cerevisiae causes membrane proliferation and altered mitochondrial morphology. , 2000, The Journal of general virology.

[73]  A. Covarrubias,et al.  Construction of a CUP1 promoter-based vector to modulate gene expression in Saccharomyces cerevisiae. , 1996, Gene.

[74]  G. Martelli,et al.  Molecular biology of tombusviridae. , 1994, Advances in virus research.