DNA Code Has Grammar
Just like words need grammar,
DNA does too. And it has
sophisticated grammatical rules.
The discovery of a “spatial grammar” in the genome could “rewrite genetics textbooks,” announced an article on SciTech Daily on August 23. The finding “may unlock the secret to how gene activity is encoded in the human genome.” Let’s dive in and take a look at all the excitement.
Scientists discover new code governing gene activity (20 Aug 2024, Washington State Univ). This is the press release from WSU’s Babcock School of Veterinary Medicine. With help from researchers at UC San Diego, associate professor Sascha Duttke found something new about gene regulation. Proteins called activators and repressors have been known for years, but it was not known how “position-dependent” they are. Their activity is “far more complex,” it turns out.
“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….
Looking closer, researchers found the function of many transcription factors was highly position dependent.
Just as sentences can mean different things depending on word order, these proteins can trigger activity or repress it, depending on where they latch onto in the genome. What this means is that transcription factors do not just act on the DNA code; they operate according to another code above the genetic code—a set of grammatical rules that tells them when and how to act.
“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.”
They call this a “newly discovered code” within DNA. This finding has vast implications, the press release continues. “At the very least, it will change the way scientists study gene expression.”
Position-dependent function of human sequence-specific transcription factors (Duttke et al., Nature, 17 July 2024). This is the open-access paper in Nature about UW’s findings. Did they need Darwinian theory to make this discovery? Well, not much. They only mentioned evolution one time in the paper, perhaps to show solidarity with the censors. Their obscure sentence says that “binding sites for YY1, which evolved to function at or just downstream of the TSS” commits the fallacy of ascribing purpose to evolution. Nothing “evolves to” do something, because there is no purpose, foresight or plan in Darwin’s Stuff Happens Law.
Aside from that snafu, the paper mentions multiple times how functional information is encoded in transcription factors:
Patterns of transcriptional activity are encoded in our genome through regulatory elements such as promoters or enhancers that, paradoxically, contain similar assortments of sequence-specific transcription factor (TF) binding sites. Knowledge of how these sequence motifs encode multiple, often overlapping, gene expression programs is central to understanding gene regulation and how mutations in non-coding DNA manifest in disease. Here, by studying gene regulation from the perspective of individual transcription start sites (TSSs), using natural genetic variation, perturbation of endogenous TF protein levels and massively parallel analysis of natural and synthetic regulatory elements, we show that the effect of TF binding on transcription initiation is position dependent.
Knowledge of position dependence can help geneticists understand how information is conveyed from genome to organism. Information is a key word in intelligent design theory.
More broadly, these findings reveal how similar assortments of TF binding sites can generate distinct gene regulatory outcomes depending on their spatial configuration and how DNA sequence polymorphisms may contribute to transcription variation and disease and underscore a critical role for TSS data in decoding the regulatory information of our genome.
Without regulation, the genome is merely a sequence of letters. Grammar gives it meaning and life. And embedded in the genomic code is another code—a regulatory code—that turns mere text into functional activity. Other ID keywords include code and function. The word “function” appears dozens of times in the paper.
These findings highlight the importance of accurate TSS positional information to decode TF function, and provide an explanation as to why it has been so challenging to predict gene expression programs from DNA sequence alone.
This paper uses “information” to speak of the human generated knowledge or know-how about gene regulation. What must the authors think of encoded information in DNA and protein molecules with no visible agent to generate it? Could codes within codes arise by unguided natural processes?
ID advocates will certainly want to explore this paper, but actually, ID scientists were way ahead of their materialist counterparts. Dr Jonathan Wells, for instances, has counted six different codes at work in the cell beyond DNA.
Try writing a code within a code, or a code that regulates another code. It’s hard. If our best intelligences can’t pull off a feat like that, how can anyone claim it arose by chance acting on lifeless matter? Without these codes operating from the start, it’s unlikely life could have even survived.