Index Catalog // ScholarsArchive@OSU

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:: reads, BLAT required z78.8 h, which was judged to be unacceptably slow for SBS data sets. FIGURE 1

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:: , 48, and 72 h postinfection (p.i.). Total RNA from uninfected fibroblast cells was included as a

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:: il y c V a li d a te d o r to p p re d ic te d ta rg e ts c M IR N A s w it h v a

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:: harvested at 24, 48, and 72 h postinoculation (hpi) by low-speed centrifugation and resuspended in lysis

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:: . Pruss, X. Ge, R. Marathe, A. C. Mallory, T. H. Smith, and V. B. Vance. 1998. A viral suppressor of gene

Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis

Creator:: Lee, Hanna, Yoo, Seong Jeon, Lee, Jeong Hwan, Kim, Wanhui, Yoo, Seung Kwan, Fitzgerald, Heather, Carrington, James C., and Ahn, Ji Hoon
Abstract:: Flowering is the primary trait affected by ambient temperature changes. Plant microRNAs (miRNAs) are small non-coding RNAs playing an important regulatory role in plant development. In this study, to elucidate the mechanism of flowering-time regulation by small RNAs, we identified six ambient temperature-responsive miRNAs (miR156, miR163, miR169, miR172, miR398 and...
Resource Type:: Article
Full Text:: solidified Murashige and Skoog (MS) medium at 16 or 23�C under long day (LD; 16:8 h, light:dark) conditions

Debilitation of Plant Potyvirus Infectivity by P1 Proteinase-Inactivating Mutations and Restoration by Second-Site Modifications

Creator:: Verchot, Jeanmarie and Carrington, James C.
Abstract:: Tobacco etch virus (TEV) encodes three proteinases that catalyze processing of the genome-encoded polyprotein. The P1 proteinase originates from the N terminus of the polyprotein and catalyzes proteolysis between itself and the helper component proteinase (HC-Pro). Mutations resulting in substitution of a single amino acid, small insertions, or deletions were...
Resource Type:: Article
Full Text:: for 1 h at 258C with commercially prepared wheat germ extract (Promega) in the presence of [35S

Analysis of the VPg-Proteinase (NIa) Encoded by Tobacco Etch Potyvirus: Effects of Mutations on Subcellular Transport, Proteolytic Processing, and Genome Amplification

Creator:: Schadd, Mary C., Haldeman-Chahill, Ruth, Cronin, Stephen, and Carrington, James C.
Abstract:: A mutational analysis was conducted to investigate the functions of the tobacco etch potyvirus VPgproteinase (NIa) protein in vivo. The NIa N-terminal domain contains the VPg attachment site, whereas the C-terminal domain contains a picornavirus 3C-like proteinase. Cleavage at an internal site separating the two domains occurs in a subset...
Resource Type:: Article
Full Text:: method (30). Protoplasts were harvested at 24, 48, and 72 h postinoculation (p.i.), and GUS activity was

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

Identification of MIR390a precursor processing defective mutants in Arabidopsis by direct genome sequencing

Creator:: Cuperus, Josh T., Montgomery, Taiowa A., Fahlgren, Noah, Burke, Russell T., Townsend, Tiffany, Sullivan, Christopher M., and Carrington, James C.
Abstract:: Transacting siRNA (tasiRNA) biogenesis in Arabidopsis is initiated by microRNA (miRNA) –guided cleavage of primary transcripts. In the case of TAS3 tasiRNA formation, ARGONAUTE7 (AGO7)– miR390 complexes interact with primary transcripts at two sites, resulting in recruitment of RNA-DEPENDENT RNA POLYMERASE6 for dsRNA biosynthesis. An extensive screen for Arabidopsis mutants...
Resource Type:: Article
Full Text:: information content of each dataset was used to calculate Shannon's entropy (H) (36, 37), providing measures

ScholarsArchive@OSU

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

Identification and Characterization of Human Cytomegalovirus-Encoded MicroRNAs

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

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

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

Genetic framework for flowering-time regulation by ambient temperature-responsive miRNAs in Arabidopsis

Debilitation of Plant Potyvirus Infectivity by P1 Proteinase-Inactivating Mutations and Restoration by Second-Site Modifications

Analysis of the VPg-Proteinase (NIa) Encoded by Tobacco Etch Potyvirus: Effects of Mutations on Subcellular Transport, Proteolytic Processing, and Genome Amplification

Functional Analysis of Three Arabidopsis ARGONAUTES Using Slicer-Defective Mutants

Identification of MIR390a precursor processing defective mutants in Arabidopsis by direct genome sequencing

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