Search results for "Rna degradation"
showing 7 items of 7 documents
RNA uridylation and decay in plants
2018
RNA uridylation consists of the untemplated addition of uridines at the 3′ extremity of an RNA molecule. RNA uridylation is catalysed by terminal uridylyltransferases (TUTases), which form a subgroup of the terminal nucleotidyltransferase family, to which poly(A) polymerases also belong. The key role of RNA uridylation is to regulate RNA degradation in a variety of eukaryotes, including fission yeast, plants and animals. In plants, RNA uridylation has been mostly studied in two model species, the green algae Chlamydomonas reinhardtii and the flowering plant Arabidopsis thaliana . Plant TUTases target a variety of RNA substrates, differing in size and function. These RNA substrates include …
Optimized RNA extraction and northern hybridization in streptomycetes.
2010
Abstract Northern blot hybridization is a useful tool for analyzing transcript patterns. To get a picture of what really occurs in vivo, it is necessary to use a protocol allowing full protection of the RNA integrity and recovery and unbiased transfer of the entire transcripts population. Many protocols suffer from severe limitations including only partial protection of the RNA integrity and/or loss of small sized molecules. Moreover, some of them do not allow an efficient and even transfer in the entire sizes range. These difficulties become more prominent in streptomycetes, where an initial quick lysis step is difficult to obtain. We present here an optimized northern hybridization protoc…
How to preserve and handle fish liver samples to conserve RNA integrity
2019
As transcriptomic studies are becoming more and more common, it is important to ensure that the RNA used in the analyses is of good quality. The RNA integrity may be compromised by storage temperature or freeze-thaw cycles, but these have not been well studied in poikilothermic fishes. This work studied the effects of tissue storage time and temperature, and freeze-thaw cycles of tissue and extracted RNA on RNA integrity in brown trout (Salmo trutta L.) liver. The storage time and temperature had an effect on RNA integrity, but RNA suitable for quantitative reverse transcription PCR (RT-qPCR) (RIN > 7) was still obtained from samples preserved at − 20 °C for 6 months. Freeze-thaw cycles of …
RNaseE-mediated mRNA degradation as determinant of polarity in phage f1.
2008
RNA processing and degradation are important steps in the regulation of gene expression. The genes present on the DNA of filamentous phage f1 are expressed at very different levels. A group of genes which are expressed at a very low level (genes III, VI, I and IV is located in the region IF of the phage DNA. The current model proposes that expression of the genes III. VI and I (which form an operon) is regulated by readthrough transcription at a weak terminator located at the end of gene III, while that of gene IV by a terminator located at the end of it. In contrast with this, we found that very long transcripts complementary to the entire f1 DNA are synthesized in the infected cells and t…
RNA quality control: RppH activity allows selective removal of nonsense messages in E. coli.
2009
Polar effect, the reduced expression level of sequences downstream to mutations reducing translation efficiency, is usually due to transcription termination or inefficient translation reinitiation. Untranslated mRNAs are known to be quickly degraded, probably because of their increased accessibility to degradative enzymes due to the absence of translating ribosomes. In III-VI-I operon of phage f1, a strong polar effect is observed in a gIII 5’ proximal nonsense mutant, resulting in a very fast, RNaseE mediated, degradation of any full-length mRNA. RNaseE is a key component of the E. coli degradosome, the major RNA processing/degrading machinery. Its endonucleolytic activity is strongly enha…
mRNAStab—a web application for mRNA stability analysis
2013
Abstract Eukaryotic gene expression is regulated both at the transcription and the mRNA degradation levels. The implementation of functional genomics methods that allow the simultaneous measurement of transcription (TR) and degradation (DR) rates for thousands of mRNAs is a huge improvement in this field. One of the best established methods for mRNA stability determination is genomic run-on (GRO). It allows the measurement of DR, TR and mRNA levels during cell dynamic responses. Here, we offer a software package that provides improved algorithms for determination of mRNA stability during dynamic GRO experiments. Availability and implementation: The program mRNAStab is freely accessible at h…
Coordinated remodeling of cellular metabolism during iron deficiency through targeted mRNA degradation.
2004
AbstractIron (Fe) is an essential micronutrient for virtually all organisms and serves as a cofactor for a wide variety of vital cellular processes. Although Fe deficiency is the primary nutritional disorder in the world, cellular responses to Fe deprivation are poorly understood. We have discovered a posttranscriptional regulatory process controlled by Fe deficiency, which coordinately drives widespread metabolic reprogramming. We demonstrate that, in response to Fe deficiency, the Saccharomyces cerevisiae Cth2 protein specifically downregulates mRNAs encoding proteins that participate in many Fe-dependent processes. mRNA turnover requires the binding of Cth2, an RNA binding protein conser…