DNA Chip Analysis in Diverse Organisms with Unsequenced Genomes.
(2009)
Journal - Molecular biotechnology
Abstract :
Whether for basic research or biotechnology, DNA microarrays have become indispensable tools for studying the transcriptome. Normally, analyses begin with a set of known cDNA sequences to prepare microarray chips specific for a target organism with an extensively sequenced and annotated genome. For many organisms, however, genome programs are not complete or have not been initiated. The present study demonstrates that, whether using homologous or heterologous arrays, the chances of seeing interesting differences are similar. When a specific DNA microarray is not available, the results indicate that a reverse approach based on a heterologous array can be used to probe for interesting differences in gene expression. This may be sufficient in many studies but, if necessary, the genes exhibiting the most significant changes subsequently could be identified by traditional molecular approaches. Such a reverse strategy can provide a convenient and inexpensive approach to probe for significant genetic changes in many diverse studies, to monitor or mine critical biological information for basic or applied research, long before complete sequence data are available.
Ribosomal RNA processing and ribosome biogenesis in eukaryotes.
(2004)
Journal - IUBMB life (England )
Abstract :
In eukaryotes nearly 500 rRNAs, ribosomal proteins, snoRNAs and trans-acting factors contribute to ribosome biogenesis. After more than 30 years of intense research, the incredible complexities of nucleolar function are revealed but details often remain unclear. Here we review this progress and the many intriguing questions which remain.
| ISSN : | 1521-6543 |
|---|
| Mesh Heading : | Active Transport, Cell Nucleus Cell Nucleolus DNA Mutational Analysis Eukaryotic Cells Models, Biological Models, Genetic RNA Processing, Post-Transcriptional RNA, Fungal RNA, Ribosomal RNA, Small Nucleolar Ribosomes Saccharomyces cerevisiae Schizosaccharomyces metabolism metabolism |
|---|
| Mesh Heading Relevant : | metabolism metabolism metabolism chemistry metabolism |
|---|
Polymerase chain reaction-mediated mutagenesis in sequences resistant to homogeneous amplification.
(2001)
Journal - Methods in molecular biology (Clifton, N.J.) (United States )
| ISSN : | 1064-3745 |
|---|
| Mesh Heading : | Base Sequence DNA DNA Primers Indicators and Reagents Molecular Sequence Data Nucleic Acid Amplification Techniques Nucleic Acid Hybridization Polymerase Chain Reaction RNA, Fungal RNA, Ribosomal Sequence Deletion chemistry genetics methods genetics genetics |
|---|
| Mesh Heading Relevant : | Mutagenesis, Site-Directed methods |
|---|
Use of mutant RNAs in studies on yeast 5S rRNA structure and function.
(1991)
Journal - Biochemistry and cell biology = Biochimie et biologie cellulaire (CANADA )
Abstract :
The expression of mutant yeast 5S rRNA genes in vivo is reviewed as a basis for further studies on the structure, function, and regulation of the ribosomal 5S rRNA. Specific base substitutions, insertions, or deletions can result in substantial structural changes which can be detected readily by gel electrophoresis, permitting the assay of mutant RNA synthesis and utilization. Furthermore, the use of high and low copy shuttle vectors, as well as alternate growth conditions, permits a wide adjustment of the mutant RNA concentration. Under optimized conditions more than 80% of the cell's RNA can be replaced with mutant molecules. The application of this strategy to studies on the biosynthesis and structure of the 5S rRNA are demonstrated through recently isolated mutations.
| ISSN : | 0829-8211 |
|---|
| Mesh Heading : | Base Sequence Molecular Sequence Data Mutation Nucleic Acid Conformation RNA, Fungal RNA, Ribosomal, 5S Saccharomyces cerevisiae Transformation, Genetic genetics genetics genetics metabolism |
|---|
| Mesh Heading Relevant : | Mutagenesis, Site-Directed genetics genetics |
|---|
Functional significance of intermediate cleavages in the 3'ETS of the pre-rRNA from Schizosaccharomyces pombe
(2003)
Journal - Nucleic Acids Research
Abstract :
Pathways for the maturation of ribosomal RNAs are complex withnumerous intermediate cleavage sites that are not always conservedclosely in the course of evolution. Both in eukaryotes and bacteriagenetic analyses and in vitro studies have strongly implicatedRNase III-like enzymes in the processing of rRNA precursors.In Schizosacharomyces pombe, for example, the RNase III-likePac1 nuclease has been shown to cleave the free 3'ETS at twoknown intermediate sites but, in the presence of RAC protein,the same RNA also is cleaved at the 3'-end of the 25 S rRNAsequence. In this study normal and mutant 3'ETS sequences weredigested with the Pac1 enzyme to further evaluate its role inrRNA processing. Accurate cleavage at the known intermediateprocessing sites was dependent on the integrity of the helicalstructure at these sites as well as a more distal upper stemregion in the conserved extended hairpin structure of the 3'ETS.The cleavage of mutant 3'ETS sequences also generally correlatedwith the known effects of these mutations on rRNA production,in vivo. One mutant, however, was efficiently processed in vivobut was not a substrate for the Pac1 nuclease, in vitro. Incontrast, in the presence of RAC protein, the same RNA remainedsusceptible to Pac1 nuclease cleavage at the 3'-end of the 25rRNA sequence, indicating that the removal of the 3'ETS doesnot require cleavage at the intermediate sites. These resultssuggest that basic maturation pathways may be less complex thanpreviously reported raising similar questions about other intermediateprocessing sites, which have been identified by analyses oftermini, and/or processing, in vitro.