In a similar fashion to transcription factors, non-coding RNAs can be essential regulators of gene expression. The largest class of non-coding RNAs is the microRNAs. These approximately 22 nt double-stranded RNA molecules can repress translation or target mRNA degradation. There has been a surge of research in the past year stimulated by the recent availability of specialized techniques, both i...

RNA degradation is among the most fundamental processes that occur in living cells. The continuous decay of RNA molecules is associated not only with nucleotide turnover, but also with transcript maturation and quality control. The efficiency of RNA decay is ensured by a broad spectrum of both specific and non-specific ribonucleases. Some of these ribonucleases participate mainly in processing ...

Several models (animal caliciviruses, poliovirus 1 [PV1], and F-specific RNA bacteriophages) are usually used to predict inactivation of nonculturable viruses. For the same UV fluence, viral inactivation observed in the literature varies from 0 to 5 logs according to the models and the methods (infectivity versus molecular biology). The lack of knowledge concerning the mechanisms of inactivatio...

The molecular mechanism of mRNA degradation in the chloroplast consists of sequential events including endonucleolytic cleavage, the addition of poly(A)-rich sequences to the endonucleolytic cleavage products, and exonucleolytic degradation by polynucleotide phosphorylase (PNPase). In Escherichia coli, polyadenylation is performed mainly by poly(A)-polymerase (PAP) I or by PNPase in its absence...

Lysosomes are thought to be the major intracellular compartment for the degradation of macromolecules. We recently identified a novel type of autophagy, RNautophagy, where RNA is directly taken up by lysosomes in an ATP-dependent manner and degraded. However, the mechanism of RNA translocation across the lysosomal membrane and the physiological role of RNautophagy remain unclear. In the present...

Illumina BeadArrays are among the most popular and reliable platforms for gene expression profiling. However, little external scrutiny has been given to the design, selection and annotation of BeadArray probes, which is a fundamental issue in data quality and interpretation. Here we present a pipeline for the complete genomic and transcriptomic re-annotation of Illumina probe sequences, also ap...

The 50-30 exoribonucleases have important functions in RNA processing, RNA degradation, RNA interference, transcription, and other cellular processes. The Xrn1 and Xrn2/Rat1 family of enzymes are the best characterized 50-30 exoribonucleases, and there has been significant recent progress in the understanding of their structure and function. Especially, the first structural information on Rat1 ...

Estimation of postmortem interval (PMI) is a key issue in the field of forensic pathology. With the availability of quantitative analysis of RNA levels in postmortem tissues, several studies have assessed the postmortem degradation of constitutively expressed RNA species to estimate PMI. However, conventional RNA quantification as well as biochemical and physiological changes employed thus far ...

Background: RNA interference (RNAi) is the mechanism of gene silencing-mediated messenger RNA degradation by small interference RNA (siRNA), which becomes a powerful tool for in vivo research, especially in the areas of cancer. In this research, the potential use of an expression vector as a specific siRNA producing tool for silencing of Bcr-abl in K562 cell line has been investigated. Methods:...

Polyethylene glycol (PEG)-based hydrogels, with variable stiffness, are widely used in tissue engineering to investigate substrate stiffness effects on cell properties. Transcriptome analysis is a critical method for understanding cell physiology. However, significant RNA degradation was observed during the process of isolating and purifying RNA from cells encapsulated in the PEG hydrogel, ther...