the eukaryotic complexity involves the expression and regulation of genes via rna-dna, rna-rna, dna-protein and rna-protein interactions. recently, the role of rna molecules in the regulation of genes in higher organisms has become more evident, especially with the discovery that about 97% of the transcriptional output in higher organisms are represented as noncoding rnas: rrna, snornas, trna, ...

We have investigated the fate of the RNA components of small ribonucleoprotein particles in apoptotic cells. We show that the cytoplasmic Ro ribonucleoprotein-associated Y RNAs are specifically and rapidly degraded during apoptosis via a caspase-dependent mechanism. This is the first study describing the selective degradation of a specific class of small structural RNA molecules in apoptotic ce...

RNase R is a conserved exoribonuclease in the RNase II family that primarily participates in RNA decay in all kingdoms of life. RNase R degrades duplex RNA with a 3' overhang, suggesting that it has RNA unwinding activity in addition to its 3'-to-5' exoribonuclease activity. However, how RNase R coordinates RNA binding with unwinding to degrade RNA remains elusive. Here, we report the crystal s...

Stress-induced Hfq-binding small RNAs of Escherichia coli, SgrS and RyhB, down-regulate the expression of target mRNAs through base-pairing. These small RNAs form ribonucleoprotein complexes with Hfq and RNase E. The regulatory outcomes of the RNase E/Hfq/small RNA-containing ribonucleoprotein complex (sRNP) are rapid degradation of target mRNAs and translational inhibition. Here, we ask to wha...

The immunoglobulin mu heavy chain gene of mouse hybridoma cells is expressed in two forms, microseconds and microns, differing in their use of 3' exons. As for many other mammalian genes, mutations in the mu gene which prematurely terminate translation often have the effect of reducing the amount of these mu RNAs. To test the generality of this relationship, we selected mutant hybridoma cell li...

Small RNA molecules have been found to be specifically associated with posttranscriptional gene silencing (PTGS) in both plants and animals. Here, we find that small sense and antisense RNAs are also involved in PTGS in Neurospora crassa. The accumulation of these RNA molecules depends on the presence of functional qde-1 and qde-3 genes previously shown to be essential for gene silencing, but d...

The RNA exosome is an evolutionarily conserved multi-protein complex involved in the 3' degradation of a variety of RNA transcripts. In the nucleus, the exosome participates in the maturation of structured RNAs, in the surveillance of pre-mRNAs and in the decay of a variety of noncoding transcripts. In the cytoplasm, the exosome degrades mRNAs in constitutive and regulated turnover pathways. Se...

Short interfering RNAs (siRNAs) are double-stranded RNAs of approximately 21-25 nucleotides that have been shown to function as key intermediaries in triggering sequence-specific RNA degradation during posttranscriptional gene silencing in plants and RNA interference in invertebrates. siRNAs have a characteristic structure, with 5'-phosphate/3'-hydroxyl ends and a 2-base 3' overhang on each str...

BACKGROUND MicroRNAs are small non-coding RNAs that post-transcriptionally regulate gene expression and their expression is frequently altered in human diseases, including cancer. To correlate clinically relevant parameters with microRNA expression, total RNA is frequently prepared from samples that were archived for various time periods in frozen tissue banks but, unfortunately, RNA integrity ...

Antisense oligonucleotides (ASOs) are most commonly designed to reduce targeted RNA via RNase H1-dependent degradation, however kinetic parameters for ASO-mediated targeting and subsequent cleavage and degradation of RNA in living cells are poorly understood. In this manuscript we use an inducible minigene system to determine the time course of ASO activity in the cell. Estimates of the time re...