Navigation Links
New plant study reveals a 'deeply hidden' layer of the transcriptome
Date:12/27/2007

La 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 cells 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 Eckers 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 didnt 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 hadnt 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 dont 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.


'/>"/>

Contact: Gina Kirchweger
kirchweger@salk.edu
858-453-4100 x1340
Salk Institute  
Source:Eurekalert

Related biology news :

1. Circadian clock controls plant growth hormone
2. Layered approach may yield stronger, more successful bone implants
3. Clearance of hepatitis C viral infection after liver transplantation
4. Device helps patients survive, regain function til transplant
5. How the plant immune system can drive the formation of new species
6. The American Society of Plant Biologists announces 2007 awards
7. UCR plant cell biologist to study how plant stem cells maintain and change their identity
8. A study proposes a new universal rule to explain the equilibrium of plant populations
9. A study proposes a new universal rule to explain the equilibrium of plant populations
10. Study shows vitamin C is essential for plant growth
11. Clever plants chat over their own network
Post Your Comments:
*Name:
*Comment:
*Email:
Related Image:
New plant study reveals a 'deeply hidden' layer of the transcriptome
(Date:2/8/2017)... 7, 2017 The biometrics market has ... confluence of organizations, desires to better authenticate or ... (password and challenge questions), biometrics is quickly working ... The market is driven by use cases, though ... and enterprise uses cases, with consumer-facing use cases ...
(Date:2/7/2017)... New York , February 7, 2017 ... as ID Global Solutions Corporation [OTC: IDGS], ("Ipsidy" or ... management and electronic transaction processing services, is pleased to ... of the Company. Effective January 31, 2017, ... the Board of Directors, CEO and President.  An experienced ...
(Date:2/2/2017)... , Feb. 2, 2017   TapImmune, Inc. ... immuno-oncology company specializing in the development of innovative ... treatment of cancer and metastatic disease, announced today ... GMP manufacturing of a second clinical lot of ... folate receptor alpha. The manufactured vaccine product will ...
Breaking Biology News(10 mins):
(Date:3/1/2017)... WA (PRWEB) , ... March 01, 2017 , ... ... research into the physiology of aging into clinical applications, announces the formation of ... proprietary oral-transmucosal dosage form of resveratrol, the drug which has been discussed in ...
(Date:2/28/2017)... Linda, Ca (PRWEB) , ... February 28, 2017 , ... ... molecular interactions. SPR is an optical phenomenon that is sensitive to changes in the ... resonance condition is affected by changes in refractive index occurring up to 300 nm ...
(Date:2/28/2017)... , Feb. 28, 2017  Phosphorus, a ... today the formation of the Phosphorus Scientific Advisory ... experts chosen to advise the company on the ... multi-site research initiatives. Please visit http://phosphorus.com/about-us/ ... initiatives. "We,ve gathered some of the ...
(Date:2/28/2017)... -- Xencor, Inc. (NASDAQ: XNCR), a clinical-stage biopharmaceutical company developing ... diseases, asthma and allergic diseases and cancer, today ... full year ended December 31, 2016 and provided ... clinical highlights. "During 2016, we made ... starting five clinical trials across our XmAb portfolio.  ...
Breaking Biology Technology: