New plant study reveals a 'deeply hidden' layer of the transcriptomeDecember 28, 2007La Jolla, CA - Cells keep a close watch over the transcriptome - the totality of all parts of the genome that are expressed in any given cell at any given time. Researchers at the Salk Institute for Biological Studies and the University of Missouri-Kansas City teamed up to peel back another layer of transcriptional regulation and gain new insight into how genomes work. Converting the "genetic blueprint" into molecular building blocks requires two basic processes: transcription, which copies the information from DNA into RNA transcripts and takes place in the cell's nucleus, and translation, where the RNA serves as a template to manufacture proteins outside the nucleus. But before transcripts can guide protein synthesis or take on regulatory functions, they have to undergo a strict mRNA surveillance system that degrades defective, obsolete, and surplus transcripts. In their study, published in the Dec. 28 issue of Cell, the scientists zoomed in on a specific subclass of transcripts that are under the control of the exosome, a molecular machine in charge of controlled RNA degradation.
"We found evidence for widespread exosome-mediated RNA quality control in plants and a 'deeply hidden' layer of the transcriptome that is tightly regulated by exosome activity," says Joseph R. Ecker, Ph.D., professor in the Plant Biology Laboratory and director of the Salk Institute Genomic Analysis Laboratory. Since the exosome is in the business of chewing things up, the scientists inactivated the multi-unit complex to bring its otherwise invisible substrates to the fore. Then they combed the transcriptional landscape for hitherto unseen peaks of transcripts that now were untouched by the degrading force of the exosome complex and came up with a genome-wide atlas of Arabidopsis exosome targets. "Our careful design and rigorous validation of the system for conditionally and quickly inactivating the exosome turned out to be really crucial for homing in on its RNA targets," explains Dmitry A. Belostotsky of the University of Missouri-Kansas City. "On the other hand, genome-wide analyses of permanent genetic mutations often produce a complex mixture of direct and indirect effects, making it very hard to untangle. Thus, we think our strategy has a broadly-applicable value." "From a genomics perspective it really allowed us to visualize what information from the genome is actually expressed," adds co-first author Brian D. Gregory, Ph.D., a postdoctoral researcher in Ecker's lab. "When you knock down exosome activity, you see changes in the transcriptome that are not visible under any other circumstance." Since the common notion is that the exosome plays a central role in bulk RNA turnover, the researchers say, they expected to find the levels of all transcripts increasing when they inactivated the exosome complex. "But not everything is going up, instead the exosome mechanism seems to be very tightly regulated," says Ecker. "We didn't see regions that are known to be silenced to go up, instead we found a very specific group of transcripts that are regulated in this way." Among them are regular protein-coding RNAs, RNA processing intermediates and hundreds of non-coding RNAs, the vast majority of which hadn't been described before. "These strange transcripts are associated with small RNA-producing loci as well as with repetitive sequence elements," says Gregory. "They are under very tight regulation by the exosome, but we still don't know exactly what this means." "It is likely that these RNAs that are usually 'deeply hidden' become important for genome function or stability under some circumstances", adds co-first author Julia Chekanova, an assistant at the University of Missouri-Kansas City. "We need to do more work to figure out what these circumstances are." Salk Institute Science News and Science Current Events Tag Cloud This tag cloud is a visual representation of term frequencies of random science news topics with common terms grouped together and emphasized by their display size. Salmonella Multiple Sclerosis Retinopathy Pheromones MRSA Cyanobacteria Tumor Suppressor Hurricane Aggression Sexual Selection Colon Polyps Brain Cells Organic Matter Climate Model Blood Thinner Prenatal alcohol exposure Kidney Disease Wheat Climate Schizophrenia Copd Particle Accelerator Blood-brain Barrier Carbon Emissions Radiofrequency Ablation
See More: Science News Tags | |||||||||||||||||||||
|
Related Transcriptome Current Events and Transcriptome News Articles Will IVF work for a particular patient? The answer may be found in her blood For the first time, researchers have been able to identify genetic predictors of the potential success or failure of IVF treatment in blood. Penn Scientists Use RNA to Reprogram One Cell Type into Another For the past decade, researchers have tried to tweak cells at the gene and nucleus level to reprogram their identity. Now, working on the idea that the signature of a cell is defined by molecules called messenger RNAs, which contain the chemical blueprint for how to make a protein, researchers at the University of Pennsylvania School of Medicine, School of Arts and Sciences and School of Engineering have found another way to change one cell type into another. GEN highlights increasing use of digital gene expression profiling A novel technique for carrying out gene-expression profiling is set to challenge the market dominance of the current, widely used methodology, reports Genetic Engineering & Biotechnology News (GEN). Rot's unique wood degrading machinery to be harnessed for better biofuels production An international team led by scientists from the U.S. Department of Energy (DOE) Joint Genome Institute (JGI) and the U.S. Department of Agriculture Forest Service, Forest Products Laboratory (FPL) have translated the genetic code that explains the complex biochemical machinery making brown-rot fungi uniquely destructive to wood. Cancer signatures uncovered A new systematic analysis of the relationship between the neoplastic and developmental transcriptome provides an outline of trends in cancer gene expression. Deep sequencing study reveals new insights into human transcriptome In a collaborative project scientists from the Max-Planck-Institute for Molecular Genetics in Berlin (MPI MolGen), Germany and Genomatix with a business in Munich, Germany and Ann Arbor, MI, USA, applied next generation sequencing and analysis methods to generate an unprecedented view at the human transcriptome. Salivary diagnostics, the 'magic mirror' to your health ... at your personal computer Accuracy, convenience, and non-invasiveness are the most critical characteristics for any diagnostic tool. A new concept, Salivaomics Knowledge Base (SKB), an in silico (i.e., performed on computer or via computer simulation) saliva diagnostic atlas, is launching today during the 37th Annual Meeting of the American Association for Dental Research in Dallas, Texas. Scientists use saliva's 'diagnostic alphabets' to diagnose disease Today, during the 85th General Session of the International Association for Dental Research, scientists are reporting that the use of saliva for clinical detection of major human diseases is only a few years away. Learning the language of DNA An international consortium of scientists, including a team from The University of Queensland's Institute for Molecular Bioscience (IMB), is a step closer to the next generation of treatments to combat disease, after publishing a comprehensive analysis of the human and mouse transcriptomes. Study reveals new genes for excessive alcohol drinking Researchers supported by the National Institute on Alcohol Abuse and Alcoholism (NIAAA), part of the National Institutes of Health (NIH), have identified new genes that may contribute to excessive alcohol consumption. More Transcriptome Current Events and Transcriptome News Articles |
|||||||||||||||||||||
|
|||||||||||||||||||||
|
|||||||||||||||||||||