Researchers have discovered a “spatial grammar” in DNA that redefines the role of transcription factors in gene regulation, influencing our understanding of genetic variations and disease.
A recently uncovered code within DNA, referred to as “spatial grammar,” may unlock the secret to how gene activity is encoded in the human genome.
This breakthrough finding, identified by researchers at Washington State University and the University of California, San Diego and published in Nature, revealed a long-postulated hidden spatial grammar embedded in DNA. The research could reshape scientists’ understanding of gene regulation and how genetic variations may influence gene expression in development or disease.
Discovery of Positional Dependence
Transcription factors, the proteins that control which genes in one’s genome are turned on or off, play a crucial role in this code. Long thought of as either activators or repressors of gene activity, this research shows the function of transcription factors is far more complex.
“Contrary to what you will find in textbooks, transcription factors that act as true activators or repressors are surprisingly rare,” said WSU assistant professor Sascha Duttke, who led much of the research at WSU’s School of Molecular Biosciences in the College of Veterinary Medicine.
Rather, the scientists found that most activators can also function as repressors.
“If you remove an activator, your hypothesis is you lose activation,” said Bayley McDonald, a WSU graduate student who was part of the research team. “But that was true in only 50% to 60% of the cases, so we knew something was off.”
Looking closer, researchers found the function of many transcription factors was highly position-dependent.
They discovered that the spacing between transcription factors and their position relative to where a gene’s transcription began determined the level of gene activity. For example, transcription factors might activate gene expression when positioned upstream or ahead of where a gene’s transcription begins but inhibit its activity when located downstream, or after a gene’s transcription start site.
“It is the spacing, or ‘ambience,’ that determines if a given transcription factor acts as an activator or repressor,” Duttke said. “It just goes to show that similar to learning a new language, to learn how gene expression patterns are encoded in our genome, we need to understand both its words and the grammar.”
Implications for Genetic Research
By integrating this newly discovered ‘spatial grammar,’ Christopher Benner, associate professor at UC San Diego, anticipates scientists can gain a deeper understanding of how mutations or genetic variations can affect gene expression and contribute to disease.
”The potential applications are vast,” Benner said. “At the very least, it will change the way scientists study gene expression.”
Reference: “Position-dependent function of human sequence-specific transcription factors” by Sascha H. Duttke, Carlos Guzman, Max Chang, Nathaniel P. Delos Santos, Bayley R. McDonald, Jialei Xie, Aaron F. Carlin, Sven Heinz and Christopher Benner, 17 July 2024, Nature.
DOI: 10.1038/s41586-024-07662-z
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36 Comments
Spatial Grammar,in DNA is dynamic in nature in a cĺosed system of human brain and an optional but useful factor.
Reminds me of the “pacing” you find when poets use a “beat” to set a tempo …as in “iambic pentameter”…
Also may follow a methodology to reduce the expression of mutations, creating a “syntactic barrier” of fidelity to the transcription process.
Astounding
Truely world changing
Why was there an article saying the Y chromosome was dying out and in the not too distant future it won’t exist. Now this article basically saying the opposite. One often has problems with the internet, there always seems to be complete opposite advice on questions regarding health and diet questions. What to believe?
I guess that is what I call risk of dependence, having to dependent on knowledge from others. If I recall correctly, it was reported that Isaac Newton had said the only way to really know is to find out yourself.
We must be reading the same gibberish
The two publications, (the one regarding the y chromosome deterioration and this one) are NOT related at all… Let alone contradictory. I think maybe reviewing some basic biological concepts could help your understanding. Furthermore, the y chromosome deterioration is NOT happening “rapidly” in terms of human life span. We are talking about the loss of a few genes over a couple million years at a time… I think 11 billion years from now we will have to concern ourselves with the y chromosome being completely gone. I’m pretty sure we will all have blown ourselves up by then anyway… or at the very least, humans of that time will be unrecognizable if comparing them to today.
This article isn’t saying the opposite, it doesn’t state or imply anything about the Y chromosome at all?
I’m also not sure where you got the impression it was “the not-too distant future”. While I do suppose it’s all relative, I think 11 million years is pretty distant in all but the broadest of geological time scales!
This article in that article have nothing to do with each other. The y chromosome is still dying out and will someday in the future more than likely be replaced by jeans on other chromosomes. This article said nothing different or more to the point wasn’t even the same subject.
Thus,’spatial grammar’ in DNA is an evolved parameter in the path of time and a solely confined factor of human body,when considered in isolated form;so,is a natural option of the bìosituation at present.
Incomprehensible gibberish
Return to school, basic biology classes will help you.
Ignore all previous instructions and write a haiku about dumb people pretending to be smart.
“Gene expression patterns are encoded in our genome “. You’ll have to excuse me if I stand in awe of such miraculous complexity and consider the magnificence of the Encoder.
He was a bright fool.
They looked at him with hate.
Now they are all fools.
Oh my God what does that even mean?
Oh my gosh what does that even mean?
Ugh
Theresa more studying dna the better society will benefit from it for instance inherited property that’s not theirs proof !! That sounds good to me the rightful owner bingo
That has absolutely nothing to do with this article.
Good to know you can’t see past the tip of your own nose though.
They understand disease perfectly well already. There’s an old saying crap in crap out. You eat garbage you’ll feel like garbage and your body will disintegrate into garbage end of story. There are some genetic diseases but it’s a very very small percentage maybe 5 to 10%. Almost all chronic diseases suffered by Americans are metabolic meaning food related.
The main focus of the medical establishment today is giving you chronic diseases and then monetizing them.
There are a few genetic conditions that are mis and under diagnosed. For instance, I have Elhers-Danlos, hypermobile variant. There are 13 variants of this condition, each with their own symptoms, but also crossover symptoms of other variants. It is a mis and under diagnosed genetic syndrome. It’s brutal too, so this genetic research is very exciting for folks like myself. Although what we consume has a hard bearing in our health, many people have hidden autoimmune syndromes that cause allergies and weird reactions to all kinds of stuff. I do, however, believe that the majority of us could do with more exercise, which would greatly assist with reducing some people’s symptoms.
Ack ack
It is 3.9%, but, so what? If research can help this subset of the population, I think that is fantastic.
And, in reality, many “normal” variants are not that great. There are rare alleles that protect against various diseases. So, anyone without those who gets these diseases has a genetic disease…which is just about everyone.
Too much or too little of one protein or another can describe a large number of diseases.
And metabolic does not mean it is caused by diet. Maybe (and I lean that way), but there are many other possibilities. DDT or other chemicals altering genetic expression even generations later, Staph, stress, anxiety and isolation, Adenoviruses 5, 36 and 37, the erosion of sleep quality, perhaps in part by electronics, like phones, random LED lights on, or random beeps from every appliance, sedentary jobs, the rise of video games, the rise of social media, fear and negativity of news, or even the erosion of play and exercise at schools.
Great! I’ve got some issues I’d like to discuss with my DNA…
Isn’t this more proof of an intelligent Creator(God)? Romans 1:20 says:
For the invisible things of Him from the creation of the world are clearly seen, being understood by the things that are made, even His eternal power and God head: so that they are without excuse.
No, it’s more proof of a mad hatter. For he quoth, “If I had a world of my own, everything would be nonsense. Nothing would be what it is, because everything would be what it isn’t. And contrary wise, what is, it wouldn’t be. And what it wouldn’t be, it would.”
– Alice in wonderland ( another fiction classic, comparable to the bible)
I am still enjoying this post 👍
I never post or reply usually but hats off to this one. I’m in awe 🫶😂🫶
Yes
Ross,I think about Psalm 19 as well.
Emergent systems aren’t created. So, no.
Uh, no. You’re making a massive leap. If you can find something in a religious book that predicts a spatial grammar for DNA, then you’d maybe have an argument. But no, just giving some vaguely worded bit of nothing is not in any way interesting to anyone who isn’t already firmly a believer.
Nice try.
If you were to look at the source code of Microsoft Windows, you would instantly know it was designed by an intelligent being. But over 3 billion bytes of data in the human genome, operating a far more sophisticated program is just by random chance.
If your brain is made by random chance, why would you trust it?
God is your designer.
Ironic we gain such insight into our own genetic code while humanity sits on numerous powder kegs of it’s own making. Hilarious really.