Pregnant protein-coding genes carry RNA babies
Scientists characterize large numbers of independently expressed, non-protein-coding RNA genes in the introns of protein-coding genes
Scientists from the Chinese Academy of Sciences have performed a comprehensive analysis of small, non-protein-coding RNAs in the model nematode, C. elegans. They characterize 100 heretofore-undescribed transcripts, including two novel classes; they provide insights into the genomic structure and transcriptional regulation of non-coding RNAs; and they underscore the importance of non-coding RNAs in nematode development. Their work appears this month in the journal Genome Research.
"The significance of non-protein-coding RNAs as central components of various cellular processes has risen sharply over the recent years," explains Prof. Runsheng Chen, principal investigator on the study. Excluding microRNAs (miRNAs), or small transcripts that have recently received widespread attention and are known to play important roles in transcriptional regulation, small non-coding RNAs (or ncRNAs) in C. elegans have not been extensively investigated – until now.
Using a new, high-throughput procedure to clone small, full-length ncRNAs, Chens laboratory isolated and characterized 161 unique transcripts. A major advantage of the new cloning procedure is that it achieves an extraordinarily high detection rate for ncRNAs by current standards. "Studies published over recent years have only been able to reach a detection rate of about 3%, but our method reached a detection rate of 30% – a 10-fold increase in cloning efficiency," explains Chen. "Its like going from a Model T Ford to a Ferrari in one fell swoop!"
Of the 161 transcripts detected by Chens group, 100 were novel and 61 were previously known or predicted. Among the 100 novel genes, 30 had no known function, whereas 70 belonged to the ubiquitous class of small nucleolar RNAs (snoRNAs). Based on sequence and structural features, Chen and his colleagues were able to classify more than half of the 30 unknown RNAs into two new categories: stem-bulge RNAs (sbRNAs) and small nuclear-like RNAs (snlRNAs). Both classes of transcripts exhibited enhanced expression during the later stages of worm development, indicating a functional role for these transcripts in developmental processes.
"The interesting thing about nematodes is that their genomic organization of both snoRNAs and other ncRNAs is quite different from other animals," says Chen. In contrast to the genomes of other metazoans, where most snoRNAs are found in introns and are under the control of independent promoters, nematode snoRNA loci are both intergenic and intronic (with and without promoters). Interestingly, plant snoRNAs are primarily located in intergenic regions. Other ncRNA genes (i.e., non-snoRNA genes) are mainly located in intergenic regions in both plants and animals. But in nematodes, Chens team found that many of these other ncRNA genes are located in the introns of host protein-coding genes and are under the control of independent promoter elements.
Finally, Chen and his colleagues estimated that 2700 ncRNA genes are present in the C. elegans genome. "One particularly intriguing aspect of the non-coding transcriptome is its potential to fill the regulatory gap created by the surprisingly low number of protein-coding genes in higher organisms," says Chen. "Between one-celled yeast, thousand-celled nematodes, and trillion-celled mammals, there is a difference of a mere 6,000 to 19,000 to 25,000 in protein-coding gene numbers. We think that regulation by non-coding RNA accounts for this discrepancy and helps to explain the additional biological complexity of higher organisms."
Maria Smit | EurekAlert!
The most recent press releases about innovation >>>
Die letzten 5 Focus-News des innovations-reports im Überblick:
An international team of scientists has proposed a new multi-disciplinary approach in which an array of new technologies will allow us to map biodiversity and the risks that wildlife is facing at the scale of whole landscapes. The findings are published in Nature Ecology and Evolution. This international research is led by the Kunming Institute of Zoology from China, University of East Anglia, University of Leicester and the Leibniz Institute for Zoo and Wildlife Research.
Using a combination of satellite and ground data, the team proposes that it is now possible to map biodiversity with an accuracy that has not been previously...
Heatwaves in the Arctic, longer periods of vegetation in Europe, severe floods in West Africa – starting in 2021, scientists want to explore the emissions of the greenhouse gas methane with the German-French satellite MERLIN. This is made possible by a new robust laser system of the Fraunhofer Institute for Laser Technology ILT in Aachen, which achieves unprecedented measurement accuracy.
Methane is primarily the result of the decomposition of organic matter. The gas has a 25 times greater warming potential than carbon dioxide, but is not as...
Hydrogen is regarded as the energy source of the future: It is produced with solar power and can be used to generate heat and electricity in fuel cells. Empa researchers have now succeeded in decoding the movement of hydrogen ions in crystals – a key step towards more efficient energy conversion in the hydrogen industry of tomorrow.
As charge carriers, electrons and ions play the leading role in electrochemical energy storage devices and converters such as batteries and fuel cells. Proton...
Scientists from the Excellence Cluster Universe at the Ludwig-Maximilians-Universität Munich have establised "Cosmowebportal", a unique data centre for cosmological simulations located at the Leibniz Supercomputing Centre (LRZ) of the Bavarian Academy of Sciences. The complete results of a series of large hydrodynamical cosmological simulations are available, with data volumes typically exceeding several hundred terabytes. Scientists worldwide can interactively explore these complex simulations via a web interface and directly access the results.
With current telescopes, scientists can observe our Universe’s galaxies and galaxy clusters and their distribution along an invisible cosmic web. From the...
Temperature measurements possible even on the smallest scale / Molecular ruby for use in material sciences, biology, and medicine
Chemists at Johannes Gutenberg University Mainz (JGU) in cooperation with researchers of the German Federal Institute for Materials Research and Testing (BAM)...