Biomedical subjects

Oystein Røsok

Publications and source records attributed to Oystein Røsok.

3 recordsLinked to original sources

PubMed2006

Computational prediction of microRNAs encoded in viral and other genomes.

We present an overview of selected computational methods for microRNA prediction. It is especially aimed at viral miRNA detection. As the number of microRNAs increases and the range of genomes encoding miRNAs expands, it seems that these small regulators have a more important role than has been previously thought. Most microRNAs have been detected by cloning and Northern blotting, but experimental methods are biased towards abundant microRNAs as well as being time-consuming. Computational detection methods must therefore be refined to serve as a faster, better, and more affordable method for microRNA detection. We also present data from a small study investigating the problems of computational miRNA prediction. Our findings suggest that the prediction of microRNA precursor candidates is fairly easy, while excluding false positives as well as exact prediction of the mature microRNA is hard. Finally, we discuss possible improvements to computational microRNA detection.

Journal Article↗

PubMed2005

Systematic search for natural antisense transcripts in eukaryotes (review).

The availability of several complete genome sequences and large numbers of expressed sequences, has led to the development of bioinformatic strategies for large-scale predictions of natural antisense transcripts. In the past two years, this has given at least 1,600 human pairs and 2,500 murine pairs of natural antisense transcripts. However, due to limitations in bioinformatic search tools, experimental validation of the predicted antisense transcripts is crucial. This has been performed only for a small fraction of the large number of predicted natural antisense transcripts. Additionally, bioinformatic approaches will not allow systematic identification of natural antisense transcripts in specific cell or tissue types. More recently, an experimental approach for identification of sense-antisense transcript pairs has been developed. The principle of the strategy is based upon the selection of double-stranded cDNAs as a result of hybridization between first-strand cDNAs that should be generated in the presence of actinomycin D. This experimental strategy allows systematic analysis of sense and antisense partners in any cell or tissue type.

Animals↗

PubMed2004

Profiling microRNA expression using sensitive cDNA probes and filter arrays.

MicroRNAs (miRNAs) are small noncoding RNAs (approximately 22 nucleotides) that have recently emerged as important regulators of gene expression in both plants and animals. With few exceptions, however, the target genes and the expression levels of most miRNAs are unknown. Here we show that direct random-primed cDNA synthesis on either chemically synthesized small RNAs (21-22 nucleotides) or gel-purified mature miRNAs from human cells can produce specific and sensitive full-length cDNA probes. Using oligonucleotide filter arrays, we demonstrate that the internally labeled cDNA probes are sensitive for detecting differential miRNA expression between untreated and O-tetradecanoylphorbol-13-acetate (TPA)-treated HL60 cells. The present study should facilitate a high-throughput analysis of miRNA expression between samples.

DNA Probes↗