Translating Ribosome Affinity Purification (TRAP) and Bioinformatic RNA-Seq Analysis in Post-metamorphic Xenopus laevis.

Recent technical advances provide the ability to isolate and purify mRNAs from genetically distinct cell types so as to provide a broader view of gene expression as they relate to gene networks. These tools allow the genome of organisms undergoing different developmental or diseased states and environmental or behavioral conditions to be compared. Translating ribosome affinity purification (TRAP), a method using transgenic animals expressing a ribosomal affinity tag (ribotag) that targets ribosome-bound mRNAs, allows for the rapid isolation of genetically distinct populations of cells.

Resting metabolic rate, abdominal fat pad and liver metabolic gene expression in female rats provided a snacking diet from weaning to adulthood.

Our female rat model with continuous, ad libitum access to snacks and chow from weaning to adulthood closely mimics human feeding behavior from childhood onwards. It causes weight gain, enlarged abdominal fat pads, reduced insulin sensitivity and leptin resistance without an increase in total caloric intake. Our current study investigated if this change in energy partitioning is due to a decrease in resting metabolic rate (RMR).

High-fat high-sugar diet induces polycystic ovary syndrome in a rodent model.

Obesity has been linked with a host of metabolic and reproductive disorders including polycystic ovary syndrome (PCOS). While a clear association exists between obesity and PCOS, the exact nature of this relationship remains unexplained. The primary symptoms of PCOS include hyperandrogenism, anovulation, and polycystic ovaries.

Complex gene expression in the dragline silk producing glands of the Western black widow (Latrodectus hesperus).

Background: Orb-web and cob-web weaving spiders spin dragline silk fibers that are among the strongest materials known. Draglines are primarily composed of MaSp1 and MaSp2, two spidroins (spider fibrous proteins) expressed in the major ampullate (MA) silk glands. Prior genetic studies of dragline silk have focused mostly on determining the sequence of these spidroins, leaving other genetic aspects of silk synthesis largely uncharacterized.

Diverse environmental stresses elicit distinct responses at the level of pre-mRNA processing in yeast.

Gene expression in eukaryotic cells is profoundly influenced by the post-transcriptional processing of mRNAs, including the splicing of introns in the nucleus and both nuclear and cytoplasmic degradation pathways. These processes have the potential to affect both the steady-state levels and the kinetics of changes to levels of intron-containing transcripts. Here we report the use of a splicing isoform-specific microarray platform to investigate the effects of diverse stress conditions on pre-mRNA processing.

An introduction to microarray data analysis and visualization.

Microarray experiments offer a potential wealth of information but also present a significant data analysis challenge. A typical microarray data analysis project involves many interconnected manipulations of the raw experimental values, and each stage of the analysis challenges the experimenter to make decisions regarding the proper selection and usage of a variety of statistical techniques. In this chapter, we will provide an overview of each of the major stages of a typical yeast microarray project.

A genetic interaction map of RNA-processing factors reveals links between Sem1/Dss1-containing complexes and mRNA export and splicing.

We used a quantitative, high-density genetic interaction map, or E-MAP (Epistatic MiniArray Profile), to interrogate the relationships within and between RNA-processing pathways. Due to their complexity and the essential roles of many of the components, these pathways have been difficult to functionally dissect. Here, we report the results for 107,155 individual interactions involving 552 mutations, 166 of which are hypomorphic alleles of essential genes.

Genome-wide search for yeast RNase P substrates reveals role in maturation of intron-encoded box C/D small nucleolar RNAs.

Ribonuclease P (RNase P) is an essential endonuclease responsible for the 5'-end maturation of precursor tRNAs. Bacterial RNase P also processes precursor 4.5S RNA, tmRNA, 30S preribosomal RNA, and several reported protein-coding RNAs.

Rapid, transcript-specific changes in splicing in response to environmental stress.

While the core splicing machinery is highly conserved between budding yeast and mammals, the absence of alternative splicing in Saccharomyces cerevisiae raises the fundamental question of why introns have been retained in approximately 5% of the 6000 genes. Because ribosomal protein-encoding genes (RPGs) are highly overrepresented in the set of intron-containing genes, we tested the hypothesis that splicing of these transcripts would be regulated under conditions in which translation is impaired. Using a microarray-based strategy, we find that, within minutes after the induction of amino acid starvation, the splicing of the majority of RPGs is specifically inhibited.

Transcript specificity in yeast pre-mRNA splicing revealed by mutations in core spliceosomal components.

Appropriate expression of most eukaryotic genes requires the removal of introns from their pre-messenger RNAs (pre-mRNAs), a process catalyzed by the spliceosome. In higher eukaryotes a large family of auxiliary factors known as SR proteins can improve the splicing efficiency of transcripts containing suboptimal splice sites by interacting with distinct sequences present in those pre-mRNAs. The yeast Saccharomyces cerevisiae lacks functional equivalents of most of these factors; thus, it has been unclear whether the spliceosome could effectively distinguish among transcripts.