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The structures of RNA molecules are often important for their function and regulation, yet there are no experimental techniques for genome-scale measurement of RNA structure. Here we describe a novel strategy termed parallel analysis of RNA structure (PARS), which is based on deep sequencing fragments of RNAs that were treated with structure-specific(More)
The complete nucleotide sequence of the maize chlorotic mottle virus (MCMV) genome has been determined to be 4437 nucleotides. The viral genome has four long open reading frames (ORFs) which could encode polypeptides of 31.6, 50, 8.9 and 25.1 kd. If the termination codons, for the polypeptides encoded by the 50 and 8.9 kd ORFs are suppressed, readthrough(More)
The Ti plasmid sequences (T DNA) maintained in four unorganized crown gall tumor lines were defined by using restriction endonucleases and molecular hybridization techniques. Each tumor line contains a "core" T DNA which is apparently responsible for maintaining the transformed state; the core T DNA is colinear with the Ti plasmid and contains the Ti(More)
High-throughput RNA sequencing enables quantification of transcripts (both known and novel), exon/exon junctions and fusions of exons from different genes. Discovery of gene fusions-particularly those expressed with low abundance- is a challenge with short- and medium-length sequencing reads. To address this challenge, we implemented an RNA-Seq mapping(More)
Maize chlorotic mottle virus (MCMV) is a 30-nm icosahedral plant virus composed of a single 25-kDa capsid protein component and a 4.4-kb single-stranded, positive-sense genomic RNA. Northern blot hybridization analysis detected a single 3'-terminal 1.1-kb subgenomic RNA in infected plants. Virion RNA directs the synthesis of several polypeptides in a rabbit(More)
Abnormalities of genomic methylation patterns are lethal or cause disease, but the cues that normally designate CpG dinucleotides for methylation are poorly understood. We have developed a new method of methylation profiling that has single-CpG resolution and can address the methylation status of repeated sequences. We have used this method to determine the(More)
RNA structural transitions are important in the function and regulation of RNAs. Here, we reveal a layer of transcriptome organization in the form of RNA folding energies. By probing yeast RNA structures at different temperatures, we obtained relative melting temperatures (Tm) for RNA structures in over 4000 transcripts. Specific signatures of RNA Tm(More)
A full-length cDNA clone (pMCM41) was constructed to contain the exact 5' end of MCMV behind a T7 RNA polymerase promoter and a Smal site at the 3' end. Uncapped RNA synthesized from pMCM41 has the exact 3' end of viral RNA (vRNA) but is missing the cap found on vRNA. This RNA was infectious in protoplasts from black Mexican sweet (BMS) maize (Zea mays)(More)
Massively parallel, tag-based sequencing systems, such as the SOLiD system, hold the promise of revolutionizing the study of whole genome gene expression due to the number of data points that can be generated in a simple and cost-effective manner. We describe the development of a 5'-end transcriptome workflow for the SOLiD system and demonstrate the(More)
The Ti plasmid sequences (T-DNA) from the octopine-producing crown gall tumor A6S/2 were isolated by molecular cloning, using the bacteriophage lambda vector Charon 4A. Analysis of the cloned DNA segments indicates that the Ti plasmid sequences are covalently joined to plant nuclear DNA. These data demonstrate that genetic recombination between a eukaryote(More)