Posts Tagged ‘RNA’

A new way to edit RNA

 :: Posted by American Biotechnologist on 10-03-2013

A tiny but unexpected change to a segment of RNA in a single-cell organism looks a lot like a mistake, but is instead a change to the genetic information that is essential to the organism’s survival.

Scientists have discovered this RNA “edit” in Trypanosoma brucei, a parasite that causes sleeping sickness in Africa and Chagas disease in Latin America. Though the organism is a model system for this work, the finding could lead to a new drug target to fight the parasite if higher species don’t share this genetic behavior.

Some of the organism’s genetic activity was already known. In the case of gene products called tRNAs, which help assemble the amino acids that make proteins, T. brucei was known to have only one tRNA with a specific segment of RNA that ensures the tRNA’s proper function. Additionally, examples of RNA editing have been discovered before.

But in this case, the way genetic information necessary for the protein production process was changed – through a swap of three nucleotides for three others that are completely out of place – has never been seen before.

“These are changes for which no chemistry is known and has never been described. We don’t know what enzyme is involved and that is the million-dollar question: What mechanism is doing this? We haven’t a clue,” said Juan Alfonzo, professor of microbiology at The Ohio State University and senior author of the study.

“If the activity is unique to a trypanosome, then you have a good drug target. If it is widespread, then you have to reconsider one more time what coding sequences really mean in the sense that you can indeed change them in a very programmed fashion by activities that don’t exist – that have not been described,” said Alfonzo, also an investigator in Ohio State’s Center for RNA Biology.

The work is the result of Alfonzo’s longtime collaboration with co-lead author Christopher Trotta, senior director of biology at PTC Therapeutics in South Plainfield, N.J.

The study appears online in the journal Molecular Cell and is scheduled for print publication on Oct. 24.

The finding was not only unexpected, but serendipitous. Alfonzo’s lab was analyzing an enzyme affecting T. brucei’s tRNA behavior in response to a request from Trotta, a drug developer who is considered a pioneer of research on tRNAs. To begin the analysis, Alfonzo sought to identify the intron, a specific segment of RNA, that needs to be removed before the tRNA can participate in the selection of the right amino acids during protein production.

This critical function of removing the intron is called splicing – in essence, a pre-requisite chemical reaction affirming that tRNA can deliver the correct instructions for protein production. If a tRNA is not spliced, it will not work in protein production and the cell will die.

The trouble was, Alfonzo couldn’t locate the intron that he knew was there. After multiple attempts, he found that the intron’s sequence in this organism changed after transcription, the point at which a copy of RNA is made from a DNA sequence as the first step of gene expression.

This edit – hard to find because of its odd nature – consisted of a change to three nucleotides, the molecules that form DNA and RNA. Because of its rarity and unusual nature, it is called a noncanonical edit.

“It’s noncanonical because it is not typical. It is completely not typical,” Alfonzo said. “And for the first time, we show the biological significance. We show that if you don’t edit, you don’t splice. This editing is required for splicing, and splicing is required for functionality. Otherwise, cells die.”

Previously known methods of RNA editing include deamination, the removal of sections of molecules from the RNA that change the message from the DNA, and nucleotide insertion, deletion or exchange. The editing described here is a swap of three nucleotides for three others that, according to the rules of biology, do not belong where they end up. This is why it looks like a mistake.

Colleagues have suggested that this edit should have been identified by researchers who do deep sequencing, which involves repeated readings of all nucleotides within an RNA molecule, Alfonzo noted. But he is not surprised that technology didn’t yield these results.

“In massive sequencing, you match RNAs to the sequence in the genome. Any mismatch is called a sequence mistake and is thrown in the trash. So this noncanonical editing may well be in the trash bin of many of these deep sequencing researchers,” he said.

Thanks to Ohio State University for this story.

Editing DNA with programmable RNA scissors

 :: Posted by American Biotechnologist on 06-28-2012

Genetic engineers and genomics researchers should welcome the news from the Lawrence Berkeley National Laboratory (Berkeley Lab) where an international team of scientists has discovered a new and possibly more effective means of editing genomes. This discovery holds potentially big implications for advanced biofuels and therapeutic drugs, as genetically modified microorganisms, such as bacteria and fungi, are expected to play a key role in the green chemistry production of these and other valuable chemical products.

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Rewriting Molecular Biology Textbooks…Again!

 :: Posted by American Biotechnologist on 05-17-2012

Over the past decade, research in the field of epigenetics has revealed that chemically modified bases are abundant components of the human genome and has forced us to abandon the notion we’ve had since high school genetics that DNA consists of only four bases.

Now, researchers at Weill Cornell Medical College have made a discovery that once again forces us to rewrite our textbooks. This time, however, the findings pertain to RNA, which like DNA carries information about our genes and how they are expressed. The researchers have identified a novel base modification in RNA which they say will revolutionize our understanding of gene expression.

Their report, published May 17 in the journal Cell, shows that messenger RNA (mRNA), long thought to be a simple blueprint for protein production, is often chemically modified by addition of a methyl group to one of its bases, adenine. Although mRNA was thought to contain only four nucleobases, their discovery shows that a fifth base, N6-methyladenosine (m6A), pervades the transcriptome. The researchers found that up to 20 percent of human mRNA is routinely methylated. Over 5,000 different mRNA molecules contain m6A, which means that this modification is likely to have widespread effects on how genes are expressed.

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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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Why our brains are more unique in our childhood and old age

 :: Posted by American Biotechnologist on 10-27-2011

Despite vast differences in the genetic code across individuals and ethnicities, the human brain shows a “consistent molecular architecture,” say researchers supported by the National Institutes of Health. The finding is from a pair of studies that have created databases revealing when and where genes turn on and off in multiple brain regions through development.

“Our study shows how 650,000 common genetic variations that make each of us a unique person may influence the ebb and flow of 24,000 genes in the most distinctly human part of our brain as we grow and age,” explained Joel Kleinman, M.D., Ph.D., of the National Institute of Mental Health (NIMH) Clinical Brain Disorders Branch.

Kleinman and NIMH grantee Nenad Sestan, M.D., Ph.D. of Yale University, New Haven, Conn., led the sister studies in the Oct. 27, 2011 issue of the journal Nature.
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