Our genetic codes control not only which proteins our cells produce, but also to a great extent in what quantity. This ground-breaking discovery, applicable to all biological life, was recently made by systems biologists at Chalmers University of Technology, Sweden, using supercomputers and artificial intelligence. Their research, which could also shed new light on the mysteries of cancer, was recently published in the scientific journal Nature Communications.
DNA molecules contain instructions for cells for producing various proteins. This has been known since the middle of the last century when the double helix was identified as the information carrier of life.
But until now, the factor which determines what quantity of a certain protein will be produced has been unclear. Measurements have shown that a single cell can contain anything from a few molecules of a given protein, up to tens of thousands.
With this new research, our understanding of the mechanisms behind this process, known as gene expression, has taken a big step forward. The group of Chalmers scientists have shown that most of the information for quantity regulation is also embedded in the DNA code itself. They have demonstrated that this information can be read with the help of supercomputers and AI.
You could compare this to an orchestral score. The notes describe which pitches the different instruments should play. But the notes alone do not say much about how the music will sound, he explains.
Information for the tempo and dynamics of the music are also required, for example. But instead of written instructions such asallegroorfortein connection with the notation, the language of genetics spreads this information over large areas of the DNA molecule. Previously, we could read the notes, but not how the music should be played. Now we can do both, states Aleksej Zelezniak.
Another comparison could be that now we have found the grammar rules for the genetic language, where perhaps before we only knew the vocabulary.
What then is this grammar, which determines the quantity of gene expression? According to Aleksej Zelezniak, it takes the form of reoccurring patterns and combinations of the four notes of genetics the molecular building blocks designated A, C, G and T. These patterns and combinations are known as motifs.
The crucial factors are the relationships between these motifs how often they repeat and at exactly which positions in the DNA code they appear.
We discovered that this information is distributed over both the coding and non-coding parts of DNA meaning, it is also present in the areas that used to be referred to as junk DNA.
The researchers tested the method in seven different model organisms from yeast and bacteria to fruit flies, mice, and humans and found that the mechanism is the same. The discovery they have made is universal, valid for all biological life.
According to Aleksej Zelezniak, the discovery would have not been possible without access to state-of-the-art supercomputers and AI. The research group conducted huge computer simulations both at Chalmers University of Technology and other facilities in Sweden.
This tool allows us to look at thousands of positions at the same time, creating a kind of automated examination of DNA. This is essential for being able to identify patterns from such huge amounts of data.
Jan Zrimec, postdoctoral researcher in the Chalmers group and first author of the study, agrees, saying:
With previous technologies, researchers had to tell the system which motifs in the DNA code to search for. But thanks to AI, the system can now learn on its own, identifying different motifs and motif combinations relevant to gene expression.
He adds that the discovery is also due to the fact they were examining a much larger part of DNA in a single sweep than had previously been done.
The new knowledge could also make it possible to better understand how mutations can affect gene expression in the cell and therefore, eventually, how cancers arise and function. The applications which could most rapidly be significant for the wider public are in the pharmaceutical industry.
It is conceivable that this method could help improve the genetic modification of the microorganisms already used today as biological factories leading to faster and cheaper development and production of new drugs, he speculates.
Reference: Zrimec J, Brlin CS, Buric F, et al. Deep learning suggests that gene expression is encoded in all parts of a co-evolving interacting gene regulatory structure. Nat Commun. 2020;11(1):6141. doi:10.1038/s41467-020-19921-4.
This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.
Read more here:
Deep Learning Shows How Genetic Motifs Conduct the Music of Life - Technology Networks
- Main Show Only - Genetic Engineering - Coast to Coast AM - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- RTPB | Genetic Engineering [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Stop Monsanto From Poisoning Hawai'i: Genetic Engineering Chemical Warfare - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Informatics 161 PSA: Human Genetic Engineering - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Don't Trust Whole Foods or Other Health Food Stores For Non- GMO Foods | Genetic Engineering - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Genetic Engineering - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Easier Genetic Engineering! (Brainstorm Ep69) - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- TEDxUCIrvine - Francisco Ayala - Cloning, Genetic Engineering, [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Genetic Engineering in Agriculture - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Infowars Special Report : Genetic Engineering - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Glowing Rats and Extreme Genetic Engineering - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Endangered Cat Born at Audubon - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Danger of Genetic Engineering - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- AQA GCSE core science and B1 - Genetic Engineering - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- genetic engineering rDNA.wmv - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Genetic Engineering for Human Enhancement.mp4 - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Genetic Engineering - Seven Wonders of the Microbe World (6/7) - Video [Last Updated On: September 7th, 2012] [Originally Added On: September 7th, 2012]
- Promising new drug target for inflammatory lung diseases [Last Updated On: September 8th, 2012] [Originally Added On: September 8th, 2012]
- Mandatory GM Labeling Would Require Major Change [Last Updated On: September 10th, 2012] [Originally Added On: September 10th, 2012]
- GEN reports on ocular therapeutics targeting the retina [Last Updated On: September 11th, 2012] [Originally Added On: September 11th, 2012]
- Prop. 37: Another example of the perils of the initiative process [Last Updated On: September 15th, 2012] [Originally Added On: September 15th, 2012]
- Genetic test predicts risk for Autism [Last Updated On: September 19th, 2012] [Originally Added On: September 19th, 2012]
- Immediate withdrawal of unsafe GE corn vital - Greens [Last Updated On: September 20th, 2012] [Originally Added On: September 20th, 2012]
- Immediate withdrawal of unsafe GE corn vital [Last Updated On: September 20th, 2012] [Originally Added On: September 20th, 2012]
- NZ out of step on GE [Last Updated On: September 21st, 2012] [Originally Added On: September 21st, 2012]
- Ballot Watch: Labeling genetically engineered foods [Last Updated On: September 30th, 2012] [Originally Added On: September 30th, 2012]
- Just another GE mirage [Last Updated On: October 2nd, 2012] [Originally Added On: October 2nd, 2012]
- The GM Barnyard [Last Updated On: October 3rd, 2012] [Originally Added On: October 3rd, 2012]
- Free Engine [Last Updated On: October 3rd, 2012] [Originally Added On: October 3rd, 2012]
- Cellectis Publishes Results Paving the Way for New Therapeutic Approaches against Cancer and Genetic Diseases [Last Updated On: October 3rd, 2012] [Originally Added On: October 3rd, 2012]
- Does moral decision-making in video games mirror the real world? [Last Updated On: October 3rd, 2012] [Originally Added On: October 3rd, 2012]
- Animals engineered with pinpoint accuracy [Last Updated On: October 3rd, 2012] [Originally Added On: October 3rd, 2012]
- Valley farmers fear 'modified' wording in Prop. 37 [Last Updated On: October 4th, 2012] [Originally Added On: October 4th, 2012]
- No on Proposition 37 [Last Updated On: October 4th, 2012] [Originally Added On: October 4th, 2012]
- The Dangers of Genetic Engineering [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Are inhaled medications effective and safe in critically ill patients on mechanical ventilation? [Last Updated On: October 5th, 2012] [Originally Added On: October 5th, 2012]
- Calif. initiative will test appetite for GMO food [Last Updated On: October 7th, 2012] [Originally Added On: October 7th, 2012]
- Calif. initiative will test appetite for GMO food - Sat, 06 Oct 2012 PST [Last Updated On: October 7th, 2012] [Originally Added On: October 7th, 2012]
- California to vote on 'genetically modified' labels [Last Updated On: October 7th, 2012] [Originally Added On: October 7th, 2012]
- California initiative will test appetite for genetically modified foods [Last Updated On: October 7th, 2012] [Originally Added On: October 7th, 2012]
- Do we have an appetite for genetically modified food? [Last Updated On: October 7th, 2012] [Originally Added On: October 7th, 2012]
- Genetic labelling mooted in California [Last Updated On: October 7th, 2012] [Originally Added On: October 7th, 2012]
- California initiative to test appetite for 'genetically engineered' food [Last Updated On: October 7th, 2012] [Originally Added On: October 7th, 2012]
- New tool for making genetic engineering of microbial circuits reliably predictable [Last Updated On: October 10th, 2012] [Originally Added On: October 10th, 2012]
- Researchers develop new tool for making genetic engineering of microbial circuits reliably predictable [Last Updated On: October 10th, 2012] [Originally Added On: October 10th, 2012]
- A Welcome Predictability [Last Updated On: October 10th, 2012] [Originally Added On: October 10th, 2012]
- Engineered flies spill secret of seizures [Last Updated On: October 12th, 2012] [Originally Added On: October 12th, 2012]
- Genetic 'remix' key to evolution of bee behavior, researchers find [Last Updated On: October 15th, 2012] [Originally Added On: October 15th, 2012]
- Can vaccines be delivered via the lungs instead of by injection? [Last Updated On: October 15th, 2012] [Originally Added On: October 15th, 2012]
- Food labeling regulations [Last Updated On: October 16th, 2012] [Originally Added On: October 16th, 2012]
- Research and Markets: Therapeutic Antibody Engineering: Current and Future Advances Driving the Strongest Growth Area ... [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- Is there a difference between GE & GMO? [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- Port Townsend Food Coop: A Sad Story of GMO Crop Cross Pollination - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- PUT IT IN YOUR MOUTH! Yes to Prop 37 — it's your right to know what's in your food! - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- editta braun company: planet LUVOS (clip, 4:30) - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- Mimic: The Director's Cut (Blu-ray Trailer) - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- South Park Season 1 Episode 7 - An Elephant Makes Love to a Pig - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- Yes on Prop 37: Animated Video - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- The Day of the Triffids Part 1 Full Movie - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- YES on prop 37 "flashmob" march - Santa Cruz, CA Sept. 2012 - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- World's Weirdest Places Discussed - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- THE CLUB OF ROME - DEPOPULATION AGENDA 21 - THE UNHIVED MIND - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- 27-Medical BiotechnologySG Part II.Gene Therapy, Tissue Engineering and Nanotechnology.mov - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- 26-Medical BiotechnologySG Part Ic. Animal and Human Cloning and Genetic Engineering.mov - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- How to Clone Animals - Video [Last Updated On: November 2nd, 2012] [Originally Added On: November 2nd, 2012]
- Fringe Opening sequence (Season 3 - The Day We Died) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Fringe Opening sequence (Season 3 - Olivia) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Fringe Opening sequence (Season 3 - Entrada) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Fringe Opening sequence (Season 4) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Fringe Opening sequence (Season 3) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Fringe Opening sequence (Season 2) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Fringe Opening sequence (1985) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Dendritic Cells: Biology And Clinical Applications - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Port Townsend Food Coop: "I want my food untainted by GMOs" - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Catholic Priest vs. Biologist - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Watch Real Life Superhero Muscles Like Marvel's The Avengers - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Fringe Opening sequence (Season 1) - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Fringe Opening sequence (The Final Season: "Fight For The Future") - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- Port Townsend Food Coop: I Want To Know If GMOs Are In My Food - Video [Last Updated On: November 4th, 2012] [Originally Added On: November 4th, 2012]
- ProCognia jumps on expanded biosimilar collaboration [Last Updated On: November 7th, 2012] [Originally Added On: November 7th, 2012]