Posts Tagged ‘transcription’

Stopping Junk DNA in its Tracks

 :: Posted by American Biotechnologist on 06-24-2013

Intergenic DNA, or junk DNA as its more colloquially known, was once thought of as “extra” DNA strands that play no role in the transcriptional process. However, in recent years, it has been shown that Junk DNA is actually transcribed into Junk RNA which is not tranlasted into protein (unlike their non-junk counterparts). In fact, researchers have demonstrated that Junk RNA is actually created by upstream transcription which occurs when the transcriptional process moves both upstream and downstream from the DNA promoter region. Since coding RNA is created from the downstream process, upstream transcription results in non-translatable RNA.

In a new study published in Nature this week, researchers at MIT described a mechanism by which cells initiate but then halt the copying of RNA in the non-protein coding direction while allowing the downstream activity to continue unhindered. In this model, the poly-A-tail, along with a factor known as U1 snRNP, work together to halt the upstream copying of RNA and actually chop up “Junk RNA” before it becomes too long.

For further reading see MIT biologists reveal how cells control the direction in which the genome is read

New study suggests researchers may be discarding important RNA information

 :: Posted by American Biotechnologist on 02-02-2012

Traditional RNA isolations kits and techniques usually isolate linear RNA transcripts while discarding circular material that are thought to be unimportant. However, a new study at the Stanford School of Medicine suggests that circular RNA may play a more important role in gene expression than previously thought.

In the classical model of gene expression, the genetic script encoded in our genomes is expressed in each cell in the form of RNA molecules, each consisting of a linear string of chemical “bases”. It may be time to revise this traditional understanding of human gene expression, as new research suggests that circular RNA molecules, rather than the classical linear molecules, are a widespread feature of the gene expression program in every human cell. The results are published in the Feb. 1 issue of the online journal PLoS ONE.

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miRNA controversy: translational inhibition versus mRNA destabilization

 :: Posted by American Biotechnologist on 09-28-2010

The Harvard Medical School Blog, it takes 30, recently wrote a post on the controversy surrounding microRNA’s mechanism of action. In a nutshell, the controversy surrounds whether or not microRNAs act by inhibiting mRNA translation or mRNA stability. The studies involved used what may be considered not so robust methodologies which may have clouded the accuracy of their results.

In any event, the issue is quite interesting for anyone involved in transcriptional/translational research and the post does a good job of sizing up the debate. Below is a short snippit from the post itself:

A recent paper from the Bartel and Weissman groups (Guo et al. Mammalian microRNAs predominantly act to decrease target mRNA levels, Nature 466 835-40, PMID: 20703300) provides an interesting snapshot of the journey of a field from consensus to controversy to (one day?) consensus again.

At issue is the question of how microRNAs — small RNAs that control gene expression — have their effect. Clearly they bind specifically to messenger RNAs that carry a short target sequence; clearly, the overall result is that a reduced amount of protein is expressed from the targeted mRNA. But is the translation of the mRNA blocked, or is the mRNA itself destabilized, or both? The answer could affect everything from the way you measure an miRNA effect to the way you think about choosing targets for therapeutic applications. And the consensus in the field seems to be swinging fairly hard — or has swung, depending on who you talk to — from one extreme (the main effect is on translation) almost all the way to the other (most, but not all, of the effect is due to mRNA destabilization).

For more information see the It takes 30 blog from the Department of Systems Biology @ Harvard Medical School

Visualizing Transcriptional Kinetics in Real Time

 :: Posted by American Biotechnologist on 07-21-2010

Interesting publication today in Nature Methods by Israeli scientists who have generated a system for visualizing mRNA transcription in-vivo in real time.

Essentially the group engineered the cyclin D1 gene to bind GFP protein as soon as it has been transcribed. This enabled them to analyze cyclin D1 mRNA production via GFP signal in real time. The group engineered the cell line with a targeted sequence in its genome that ensures that any sequence sent in goes to the correct place and is not plagued by random genome incorporation that has plagued other studies.

The significance in this study is that it is the first time that scientists have been able to view real time expression of a single gene in a single cell.

One important finding of the study is that it confirms,through imaging techniques, that mRNA production is accomplished through periodic bursts rather than via a smooth, uninterrupted process. In the video below, posted on the scientist you can see the transcribing “mother” transcription site and the emergence of the “daughter” transcribing allele situated right beside it. Notice how after replication the cell contains double the amount of DNA which is visualized as periodic bursts of light.

Gordon Hager, a cell biologist at the National Cancer Institute in Bethesda, Maryland told Nature News that “this represents the continuing evolution of a technology that is going to revolutionize the way people think about biology.”