Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Protein coding 'junk genes' may be linked to cancer

18.11.2013
By using a new analysis method, researchers at Karolinska Institutet and Science for Life Laboratory (SciLifeLab) in Sweden have found close to one hundred novel human gene regions that code for proteins.

A number of these regions are so-called pseudogenes, which may be linked to cancer. The expectation is now that this recently developed protein analysis method, published in the scientific journal Nature Methods, will open up a whole new field of research.

All information about the human genome is stored in the DNA sequence in the cell nucleus, and was mapped in the early 2000s. Genes are defined sections of DNA encoding different types of proteins.

In recent decades, researchers have been able to define around 21,000 protein coding human genes, using DNA analysis, for example. In the different cell types of the body, different protein producing genes are active or inactive, and many medical conditions also depend on altered activity of specific genes.

In humans, only about 1.5% of the human genome or DNA consists of protein-coding genes. Of the remaining DNA, some sequences are used to regulate the genes' production of proteins, but the bulk of the DNA is considered to lack any purpose and is often referred to as "junk DNA". Within this junk DNA there are so-called called pseudogenes. Pseudogenes have been considered as non-functional genes, which are believed to be gene remnants that lost their function during evolution.

In the current paper in Nature Methods, researchers present a new proteogenomics method, which makes it possible to track down protein coding genes in the remaining 98.5% of the genome, something that until now has been an impossible task to pursue. Among other things, the research shows that some pseudogenes produce proteins indicating that they indeed have a function.

"To be able to do this we had to match experimental data for sequences of peptides with millions of possible locations in the whole genome", says Associate Professor and study leader Janne Lehtiö. "We had to develop both new experimental and bioinformatics methods to allow protein based gene detection, but when we had everything in place it felt like participating in a Jules Verne adventure inside the genome."

The Lehtiö team found evidence for almost one hundred new protein-coding regions in the human genome. Similar findings were made in cells from mice. Many of the new proteins encoded by pseudogenes could also be traced in other cancer cell lines, and the next objective on the researchers' agenda is to investigate if these genes in the "junkyard" of the genome play a role in cancer or other diseases.

"Our study challenges the old theory that pseudogenes don't code for proteins", says Dr Lethiö. "The presented method allows for protein based genome annotation in organism with complex genomes and can lead to discovery of many novel protein coding genes, not only in humans but in any species with a known DNA sequence."

The current study was conducted by researchers from Karolinska Institutet, Stockholm University and Royal Institutet of Technology (KTH) all active at Science for Life Laboratory (SciLifeLab). Principle Investigator, Associate Professor Janne Lehtiö, is active at the Department of Oncology-Pathology at Karolinska Institutet and his laboratory is located at SciLifeLab. GE Healthcare Bio-Sciences in Uppsala provided technical support for the method development. The research was funded by the Swedish Research Council, the Swedish Cancer Society, the Stockholm County Council, Stockholm's Cancer Society, and by the EU FP7 project GlycoHit.

Publication: 'HiRIEF LC-MS enables deep proteome coverage and unbiased proteogenomics' Branca R.M.M, Orre L.M., Johansson H.J., Granholm V., Huss M., Pérez-Bercoff Å., Forshed J., Käll L., Lehtiö J., Nature Methods, advance on line publication 17 November 2013, doi: 10.1038/nmeth.2732.

Contact the Press Office of Karolinska Institutet and download images: ki.se/pressroom

More about SciLifeLab: http://www.scilifelab.se

Karolinska Institutet - a medical university: ki.se/english

The Press Office | EurekAlert!
Further information:
http://www.ki.se

More articles from Life Sciences:

nachricht Seeing on the Quick: New Insights into Active Vision in the Brain
15.08.2018 | Eberhard Karls Universität Tübingen

nachricht New Approach to Treating Chronic Itch
15.08.2018 | Universität Zürich

All articles from Life Sciences >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Unraveling the nature of 'whistlers' from space in the lab

A new study sheds light on how ultralow frequency radio waves and plasmas interact

Scientists at the University of California, Los Angeles present new research on a curious cosmic phenomenon known as "whistlers" -- very low frequency packets...

Im Focus: New interactive machine learning tool makes car designs more aerodynamic

Scientists develop first tool to use machine learning methods to compute flow around interactively designable 3D objects. Tool will be presented at this year’s prestigious SIGGRAPH conference.

When engineers or designers want to test the aerodynamic properties of the newly designed shape of a car, airplane, or other object, they would normally model...

Im Focus: Robots as 'pump attendants': TU Graz develops robot-controlled rapid charging system for e-vehicles

Researchers from TU Graz and their industry partners have unveiled a world first: the prototype of a robot-controlled, high-speed combined charging system (CCS) for electric vehicles that enables series charging of cars in various parking positions.

Global demand for electric vehicles is forecast to rise sharply: by 2025, the number of new vehicle registrations is expected to reach 25 million per year....

Im Focus: The “TRiC” to folding actin

Proteins must be folded correctly to fulfill their molecular functions in cells. Molecular assistants called chaperones help proteins exploit their inbuilt folding potential and reach the correct three-dimensional structure. Researchers at the Max Planck Institute of Biochemistry (MPIB) have demonstrated that actin, the most abundant protein in higher developed cells, does not have the inbuilt potential to fold and instead requires special assistance to fold into its active state. The chaperone TRiC uses a previously undescribed mechanism to perform actin folding. The study was recently published in the journal Cell.

Actin is the most abundant protein in highly developed cells and has diverse functions in processes like cell stabilization, cell division and muscle...

Im Focus: Lining up surprising behaviors of superconductor with one of the world's strongest magnets

Scientists have discovered that the electrical resistance of a copper-oxide compound depends on the magnetic field in a very unusual way -- a finding that could help direct the search for materials that can perfectly conduct electricity at room temperatur

What happens when really powerful magnets--capable of producing magnetic fields nearly two million times stronger than Earth's--are applied to materials that...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

VideoLinks
Industry & Economy
Event News

Within reach of the Universe

08.08.2018 | Event News

A journey through the history of microscopy – new exhibition opens at the MDC

27.07.2018 | Event News

2018 Work Research Conference

25.07.2018 | Event News

 
Latest News

Unraveling the nature of 'whistlers' from space in the lab

15.08.2018 | Physics and Astronomy

Diving robots find Antarctic winter seas exhale surprising amounts of carbon dioxide

15.08.2018 | Earth Sciences

Early opaque universe linked to galaxy scarcity

15.08.2018 | Physics and Astronomy

VideoLinks
Science & Research
Overview of more VideoLinks >>>