Index Catalog // ScholarsArchive@OSU

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:: Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.
Abstract:: Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...
Resource Type:: Article
Full Text:: . Sullivan 1,2 , Jason S. Cumbie 1,2 , Scott A. Givan 1,2 , James C. Carrington 1,2* 1 Center for Genome

Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

Creator:: Carbonell, Alberto, Fahlgren, Noah, Garcia-Ruiz, Hernan, Gilbert, Kerrigan B., Montgomery, Taiowa A., Nguyen, Tammy, Cuperus, Josh T., and Carrington, James C.
Abstract:: In RNA-directed silencing pathways, ternary complexes result from small RNA-guided ARGONAUTE (AGO) associating with target transcripts. Target transcripts are often silenced through direct cleavage (slicing), destabilization through slicer-independent turnover mechanisms, and translational repression. Here, wild-type and active-site defective forms of several Arabidopsis thaliana AGO proteins involved in posttranscriptional silencing were...
Resource Type:: Article
Full Text:: Kerrigan B. Gilbert,a Taiowa A. Montgomery,b,1 Tammy Nguyen,b Josh T. Cuperus,b,2 and James C. Carringtona

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Creator:: Fahlgren, Noah, Howell, Miya D., Kasschau, Kristin D., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., Law, Theresa F., Grant, Sarah R., Dangl, Jeffrey L., and Carrington, James C.
Abstract:: In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep...
Resource Type:: Article
Full Text:: Y 9 (2 0 6 ) 2 (5 1 ) C C -N B S -L R R A t1 g 5 1 4 8 0 (1 )d , A t5 g 4 3 7 4 0

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

Creator:: Fahlgren, Noah, Bollmann, Stephanie R., Kasschau, Kristin D., Cuperus, Josh T., Press, Caroline M., Sullivan, Christopher M., Chapman, Elisabeth J., Hoyer, J. Steen, Gilbert, Kerrigan B., Grunwald, Niklaus J., and Carrington, James C.
Abstract:: In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora...
Resource Type:: Article
Full Text:: , Elisabeth J. Chapman2¤b, J. Steen Hoyer1, Kerrigan B. Gilbert1, Niklaus J. Grünwald3*, James C

Complementation of tobacco etch potyvirus mutants by active RNA polymerase expressed in transgenic cells

Creator:: Li, Xiao Hua and Carrington, James C.
Abstract:: A genetic complementation system was developed in which tobacco etch virus (TEV) polymerase (NIb)- expressing transgenic plants or protoplasts were inoculated with NIb-defective TEV mutants. A β-glucuronidase (GUS) reporter gene integrated into the genomes of parental and four mutant viruses was used to assay RNA amplification. Two mutants (termed VNN...
Resource Type:: Article
Full Text:: sequence, respectively; one (aD/b) con- tained a mutation debilitating the NIb N-terminal cleavage site

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Creator:: Fahlgren, Noah, Sullivan, Christopher M., Kasschau, Krisitin D., Chapman, Elisabeth J., Cumbie, Jason S., Montgomery, Taiowa A., Gilbert, Sunny D., Dasenko, Mark, Backman, Tyler W. H., Givan, Scott A., and Carrington, James C.
Abstract:: The advent of high-throughput sequencing (HTS) methods has enabled direct approaches to quantitatively profile small RNA populations. However, these methods have been limited by several factors, including representational artifacts and lack of established statistical methods of analysis. Furthermore, massive HTS data sets present new problems related to data processing and...
Resource Type:: Article
Full Text:: ,1,2 KRISTIN D. KASSCHAU,1,2 ELISABETH J. CHAPMAN,1,2,3 JASON S. CUMBIE,1,2 TAIOWA A. MONTGOMERY,1,2

Autocatalytic Processing of the Potyvirus Helper Component Proteinase in Escherichia coli and In Vitro

Creator:: Carrington, James C., Freed, Deon D., and Sanders, Tatia C.
Abstract:: The virus-encoded proteins of tobacco etch virus (TEV), a plant potyvirus, arise by proteolytic processing of a large polyprotein precursor. The TEV genome codes for two proteinases, a 49-kilodalton proteinase and helper component proteinase (HC-Pro), which cleave the polyprotein at specific sites. The only known cleavage event catalyzed by HC-Pro...
Resource Type:: Article
Full Text:: processing half-time of approximately 100 s. The processing kinetics of HC-Pro expressed in vitro by cell

Identification and Characterization of Human Cytomegalovirus-Encoded MicroRNAs

Creator:: Grey, Finn, Antoniewicz, Andy, Allen, Edwards, Saugstad, Julie, McShea, Andy, Carrington, James C., and Nelson, Jay
Abstract:: MicroRNAs (miRNAs) are an extensive class of noncoding genes that regulate gene expression through posttranscriptional repression. Given the potential for large viral genomes to encode these transcripts, we examined the human cytomegalovirus AD169 genome for miRNAs using a bioinformatics approach. We identified 406 potential stem-loops, of which 110 were conserved...
Resource Type:: Article
Full Text:: suppressor of RNA silencing. Immunity 22:607–619. 2. Cai, X., S. Lu, Z. Zhang, C. M. Gonzalez, B. Damania

Host-Specific Involvement of the HC Protein in the Long-Distance Movement of Potyviruses

Creator:: Sáenz, Pilar, Salvador, Beatriz, Simón-Mateo, Carmen, Kasschau, Kristin D., Carrington, James C., and García, Juan Antonio
Abstract:: Plum pox virus (PPV) is a member of the Potyvirus genus that, in nature, infects trees of the Prunus genus. Although PPV infects systemically several species of the Nicotiana genus, such as N. clevelandii and N. benthamiana, and replicates in the inoculated leaves of N. tabacum, it is unable to...
Resource Type:: Article
Full Text:: promoter. Plants. The tobacco transgenic line U6-B transformed with a cDNA fragment from the 5� end of the

Evidence that the Potyvirus P1 Proteinase Functions in trans as an Accessory Factor for Genome Amplification

Creator:: Verchot, Jeanmarie and Carrington, James C.
Abstract:: The tobacco etch potyvirus (TEV) polyprotein is proteolytically processed by three viral proteinases (NIa, HC-Pro, and P1). While the NIa and HC-Pro proteinases each provide multiple functions essential for viral infectivity, the role of the P1 proteinase beyond its autoproteolytic activity is understood poorly. To determine if P1 is necessary...
Resource Type:: Article
Full Text:: helicases. Nature (London) 333:22–23. 36. Horsch, R. B., J. E. Fry, N. L. Hoffmann, D. Eichholtz, S. G

ScholarsArchive@OSU

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

Complementation of tobacco etch potyvirus mutants by active RNA polymerase expressed in transgenic cells

Computational and analytical framework for small RNA profiling by high-throughput sequencing

Autocatalytic Processing of the Potyvirus Helper Component Proteinase in Escherichia coli and In Vitro

Identification and Characterization of Human Cytomegalovirus-Encoded MicroRNAs

Host-Specific Involvement of the HC Protein in the Long-Distance Movement of Potyviruses

Evidence that the Potyvirus P1 Proteinase Functions in trans as an Accessory Factor for Genome Amplification

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