MicroRNAs (miRNAs) are small regulatory RNAs that serve fundamental biological roles across eukaryotic species. We describe a new method for high-throughput miRNA detection. The technique is termed the RNA-primed, array-based Klenow enzyme (RAKE) assay, because it involves on-slide application of the Klenow fragment of DNA polymerase I to extend unmodified miRNAs hybridized to immobilized DNA probes. We used RAKE to study human cell lines and brain tumors. We show that the RAKE assay is sensitive and specific for miRNAs and is ideally suited for rapid expression profiling of all known miRNAs. RAKE offers unique advantages for specificity over northern blots or other microarray-based expression profiling platforms. Furthermore, we demonstrate that miRNAs can be isolated and profiled from formalin-fixed paraffin-embedded tissue, which opens up new opportunities for analyses of small RNAs from archival human tissue. The RAKE assay is theoretically versatile and may be used for other applications, such as viral gene profiling.
The winged helix transcription factors, hepatocyte nuclear factors 3␣, -, and -␥ (HNF-3, encoded by the Foxa1, -a2, and -a3 genes, respectively), are expressed early in embryonic endoderm and play important roles in the regulation of gene expression in liver and pancreas. Foxa1 has been shown to be required for glucagon secretion in the pancreas, whereas Foxa2 is critical for the regulation of insulin secretion in pancreatic -cells. Here we address the role of Foxa3 in the maintenance of glucose homeostasis. Mice homozygous for a null mutation in Foxa3 appear normal under fed conditions. However, when fasted, Foxa3 ؊/؊ mice have a significantly lower blood glucose compared with control mice. The fasting hypoglycemia in Foxa3 ؊/؊ mice could not be attributed to defects in pancreatic hormone secretion, ketone production, or hepatic glycogen breakdown. Surprisingly, mRNA levels for several gluconeogenic enzymes were up-regulated appropriately in fasted Foxa3 ؊/؊ mice, despite the fact that the corresponding genes had been shown to be activated by FOXA proteins in vitro. However, the mRNA for the plasma membrane glucose transporter GLUT2 was decreased by 64% in the fasted and 93% in the fed state, suggesting that efflux of newly synthesized glucose is limiting in Foxa3 ؊/؊ hepatocytes. Thus, Foxa3 is the dominating transcriptional regulator of GLUT2 expression in hepatocytes in vivo. In addition, we investigated the hepatic transcription factor network in Foxa3 ؊/؊ mice and found that the normal activation of HNF-4␣, HNF-1␣, and PGC-1 induced by fasting is attenuated in mice lacking Foxa3.Recent studies suggest that no single transcription factor on its own controls hepatocyte differentiation and metabolism. Instead, a transcription factor network including HNF-3␣, 1
Over the past 5 years, microarrays have greatly facilitated large-scale analysis of gene expression levels. Although these arrays were not specifically geared to represent tissues and pathways known to be affected by diabetes, they have been used in both type 1 and type 2 diabetes research. To prepare a tool that is particularly useful in the study of type 1 diabetes, we have assembled a nonredundant set of 3,400 clones representing genes expressed in the mouse pancreas or pathways known to be affected by diabetes. We have demonstrated the usefulness of this clone set by preparing a cDNA glass microarray, the PancChip, and using it to analyze pancreatic gene expression from embryonic day 14.5 through adulthood in mice. The clone set and corresponding array are useful resources for diabetes research.
The Endocrine Pancreas Consortium was formed in late 1999 to derive and sequence cDNA libraries enriched for rare transcripts expressed in the mammalian endocrine pancreas. Over the past 3 years, the Consortium has generated 20 cDNA libraries from mouse and human pancreatic tissues and deposited >150,000 sequences into the public expressed sequence tag databases. A special effort was made to enrich for cDNAs from the endocrine pancreas by constructing libraries from isolated islets. In addition, we constructed a library in which fetal pancreas from Neurogenin 3 null mice, which consists of only exocrine and duct cells, was subtracted from fetal wild-type pancreas to enrich for the transcripts from the endocrine compartment. Sequence analysis showed that these clones cluster into 9,464 assembly groups (approximating unique transcripts) for the mouse and 13,910 for the human sequences. Of these, >4,300 were unique to Consortium libraries. We have assembled a core clone set containing one cDNA for each assembly group for the mouse and have constructed the corresponding microarray, termed "PancChip 4.0," which contains >9,000 nonredundant elements. We show that this PancChip is highly enriched for genes expressed in the endocrine pancreas. The mouse and human clone sets and corresponding arrays will be important resources for diabetes research. Diabetes 52:1604 -1610, 2003 D espite recent progress in -cell biology and diabetes research, tools for the treatment of diabetes have not changed fundamentally. Although it is now clear that islet transplantation is a valuable therapeutic approach, this solution is severely limited by the shortage of islet tissue. Over the past decade, significant advances have been made toward identifying the hierarchy of transcription factors that govern pancreatic development (1). In addition, it has been shown that embryonic stem cells can be differentiated in vitro toward insulin-producing cells, although the issue remains controversial (2-4). Despite these discoveries, major obstacles to the isolation, expansion, and differentiation of pancreatic endocrine stem and/or progenitor cells exist, including a lack of appropriate cell surface antibodies for sorting of progenitor cell populations and an only rudimentary understanding of the lineage of -cells during development and regeneration of the pancreas.To accelerate the progress toward the identification of endocrine precursor cells and factors that regulate the development and differentiation of -cells, the National Institute of Diabetes and Digestive and Kidney Diseases sponsored a program entitled "Functional Genomics of the Developing Endocrine Pancreas" in 1999. The Endocrine Pancreas Consortium was created in response to this program to construct and sequence cDNA libraries derived from multiple stages of pancreatic development. Its purpose was to provide the public expressed sequence tag (EST) databases with sequences from mouse and human endocrine pancreas to discover novel transcripts that could be incorporated into custom m...
In this report we evaluate three methods for labeling nucleic acids to be hybridized to a cDNA microarray: direct labeling, indirect amino-allyl labeling, and the dendrimer labeling method (Genisphere). The dendrimer method requires the smallest quantity of sample, 2.5 microg of total RNA compared with 20 microg with the direct or indirect methods. Therefore, we wanted to know whether the performance of the dendrimer method is comparable to the other methods, or whether significant information is lost. Performance can be considered in terms of sensitivity, dynamic range, and reproducibility of the quantitative signals for gene intensity. We compared the three labeling methods by generating three sets of eight self-to-self hybridizations using the same total RNA sample in all cases ("replicate study"). In our analysis, we controlled for the effects of print-tip and background subtraction biases. We also performed a smaller study, namely, a dilution series study with five dilution points per labeling method, to evaluate one aspect of predictive ability. From the replicate study, the dendrimer method appeared to perform as well, and often better, with respect to reproducibility and ability to detect expression. However, in the dilution series study, this method was outperformed by the other two in terms of predictive ability and did not perform very well. These findings are helping to guide our decisions on what labeling method to use for subsequent studies, based on the purpose of a specific study and its limitations in terms of available material.
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