JUN 07, 2016 11:46 AM PDT

‘Junk DNA' Exposed - Transient Gene Expression Can Now Be Studied

WRITTEN BY: Carmen Leitch

Long regions of seemingly unimportant strands of DNA were named ‘junk DNA’ and long thought to be unimportant or at least, totally misunderstood. That view is shifting, however, as more and more regulatory signals are found to be in those areas; mutations in them can contribute to human disease.

 Genes that code for protein are transcribed as an mRNA intermediate and then translated to a functional protein. Genes that are regulatory or have other roles are transcribed as a functional, non-coding RNA. Image:Thomas Shafee

Typically, a gene in DNA will encode for a protein. Those genes, the corresponding RNA, and their protein products can be analyzed and manipulated in many ways as part of basic molecular biology. But not all genes are expressed in every place in the body at all time. Controlling that expression is vital to the proper function of cells, which makes the regulatory portions of DNA very important. The DNA that ends up getting expressed in cells as RNA is called the transcriptome.

"Regulatory DNA regions are essential for development in humans, tissue preservation, and the immune response, among others," explained Professor Patrick Cramer, a director at the Max Planck Institute for Biophysical Chemistry. "Furthermore, they play an important role in various diseases. For example, patients suffering from cancer or cardiovascular conditions show many mutations in exactly those DNA regions," he said.

Identifying and studying those governing regions is difficult though, because when DNA that does the regulating is active, it’s made into short-lived RNA transcripts that are used and then quickly degraded. But those fleeting transcripts that are so challenging to study are crucial activators of genes and play a prominent role in gene expression.

Scientists have now developed a way to capture those transcripts so they can be analyzed in depth. Researchers collaborating and working with Dr. Cramer have created a precise way to identify and capture RNA molecules, even those with a brief, transitory existence. The work was published in Science. They’ve called the new technique the TT-Seq (transient transcriptome sequencing) method, and it can gather and sequence all RNA segments that are made in cells over a period of 5 minutes – an insufficient amount of time to degrade even very transient RNA.

 An overview of 4sU-seq and TT-seq protocols

They use a molecule, 4-thiouridine (4sU), that gets incorporated into the RNA as it is made for a kind of tag, and then isolate whatever contains that tagging molecule for sequencing.

"The RNA molecules we caught with the TT-Seq method provide a snapshot of all DNA regions that were active in the cell at a certain time – the genes as well as the regulatory regions between genes that were so hard to find until now," Cramer said. "With TT-Seq we now have a suitable tool to learn more about how genes are controlled in different cell types and how gene regulatory programs work," added co-author Julien Gagneur, Professor of Computational Biology at the Technical University of Munich.

To learn more about the transcriptome, check out the video below.

 


Sources: Science, Technical University of Munich
 

 

About the Author
  • Experienced research scientist and technical expert with authorships on 28 peer-reviewed publications, traveler to over 60 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
AUG 13, 2018
Cell & Molecular Biology
AUG 13, 2018
In a First, Stem Cell Therapy for Parkinson's in Human Patients
A clinical trial that is the first of its kind has been started in Japan....
AUG 20, 2018
Genetics & Genomics
AUG 20, 2018
Using Population Genetics to Predict Disease Risk
Using genetics, this work has created a way to identify people at higher risk for five common diseases - before they show any symptom....
SEP 07, 2018
Videos
SEP 07, 2018
The Therapeutic Potential of Venoms
Over 220,000 species, around 15 percent of the world's described animals, are known to be venomous....
OCT 09, 2018
Drug Discovery
OCT 09, 2018
Pharmacological Manipulation of a Brain-Signaling Mechanism Reverses An Autism-Related Pathway
According to a study published in the Proceedings of the National Academy of Sciences (PNAS), researchers at Florida Atlantic University have discovered a...
OCT 14, 2018
Technology
OCT 14, 2018
4-D Microscope Offers Look Into Early Development
A recent developed microscope has allowed scientists to hold a front-row view on the “drama of mammalian development”. Scientists can now see i...
OCT 20, 2018
Videos
OCT 20, 2018
Understanding how the Immune System is Controlled
Scientists are trying to learn more about a gene, PTPN22, that is especially critical to the immune system....
Loading Comments...