Scientists decipher the mysterious DNA rules hidden across species

A new study reveals that in unicellular fungi yeast is “random”. DNA“Naturally active, whereas in mammalian cells, this DNA is switched off as its natural state in mammalian cells, despite having a common ancestor a billion years ago and the same basic molecular machinery.

The new discovery revolves around the process by which the genetic instructions of DNA are first converted into a related substance called… RNA And then to the proteins that make up the body's structures and signals. In yeast, mice and humans, the first step in gene expression, transcription, takes place in which the molecular “letters” of DNA (nucleobases) are read in one direction. While 80% of the human genome—the entire collection of DNA in our cells—is actively decoded into RNA, less than 2% of it actually codes for the genes that direct the construction of proteins.

A long-standing mystery in genomics is what all this non-gene-related transcription accomplishes. Is it just noise, a side effect of evolution, or does it have functions?

A research team at NYU Langone Health sought to answer this question by creating a large synthetic gene, with its DNA code in reverse order from its natural parent. They then inserted synthetic genes into yeast and mouse stem cells, and monitored transcript levels in each. Published in the magazine nature, The new study reveals that in yeast the genetic system is tuned so that almost all genes are continuously transcribed, whereas in mammalian cells the same “default state” is to turn off transcription.

Methodology and results

Interestingly, the study authors say, the reverse order of the code meant that all the mechanisms that evolved in yeast and mammalian cells to turn transcription on or off were absent because the reverse code was nonsense. However, like a mirror image, the reversed code reflects some of the basic patterns that appear in the natural code in terms of how often DNA letters are present, what they are close to, and how often they are repeated. Because the reverse code is 100,000 molecular letters long, the team found that it randomly included many small stretches of previously unknown code that likely started transcription more frequently in yeast, and stopped it in mammalian cells.

“Understanding the differences of virtual versions across Classify “Genetics will help us better understand which parts of the genetic code have functions, and what evolutionary accidents are,” said corresponding author Jeff Buckey, Ph.D., director of the Genetics Institute at NYU Langone Health. “This, in turn, promises to guide yeast engineering to make new drugs, create new gene therapies, or even to help us find new genes buried in the massive code.”

This work lends weight to the theory that the very active transcriptional state of yeast is so fine-tuned that foreign DNA is rarely injected into yeast for example by virus Because it copies itself, it is more likely to be transcribed into RNA. If this RNA builds a protein with a useful function, the code will be preserved through evolution as a new gene. Unlike the single-celled organism in yeast, which can afford risky new genes that drive evolution faster, mammalian cells, as part of bodies containing millions of cooperating cells, are less free to incorporate new DNA every time the cell encounters a virus. . Several regulatory mechanisms protect the carefully balanced code as it is.

Big DNA

The new study had to take into account the size of the DNA strands, as there are 3 billion “letters” in the human genome, and some genes are 2 million letters long. While popular techniques enable changes to be made letter by letter, some engineering tasks are more efficient if researchers build DNA from scratch, making far-reaching changes to large swaths of pre-compiled code and replacing it in a cell rather than its natural counterpart. Because human genes are so complex, Bucky's lab first developed the “genome typing” approach in yeast, but has recently modified it to match the mammalian genetic code. The study authors use yeast cells to assemble long sequences of DNA in a single step, then deliver them into mouse embryonic stem cells.

For the current study, the research team addressed the question of the extent of transcriptional spread across evolution by introducing a synthetic 101-kilobase stretch of engineered DNA—the human hypoxanthine phosphoribosyltransferase 1 (HPRT1) gene in reverse coding order. They observed widespread activity of the gene in yeast, despite the lack of nonsense code for promoters, which are snippets of DNA that have evolved to signal the start of transcription.

Furthermore, the team identified small sequences in the reverse code, repetitive stretches of adenosine and thymine building blocks, that are known to be recognized by transcription factors, which are proteins that bind to DNA to initiate transcription. Such sequences, which are only 5 to 15 letters long, can easily occur randomly, and may partly explain the highly active default state of yeast, the authors said.

On the contrary, the same symbol is reversed, inserted into the genome of mouse embryonic stem cells, it did not cause extensive transcription. In this scenario, transcription was repressed even though advanced CpG dinucleotides, known to stop (silence) genes, were not effective in the reverse code. The team believes that other essential elements in the mammalian genome may restrict transcription much more than in yeast, perhaps by directly recruiting a protein complex (the multi-CD complex) known for gene silencing.

“The closer we get to introducing the 'genome value' of nonsense DNA into living cells, the better they can compare it to the actual, evolving genome,” said first author Brendan Camillato, a graduate student in Buckey's lab. “This may lead us to new frontiers of engineered cell therapies, as the ability to insert ever-longer synthetic DNA allows for a better understanding of what the inserted genomes will tolerate, and potentially the inclusion of one or more larger, fully engineered genes.”

Reference: “Inverted synthetic sequences reveal putative genomic states” by Brendan R. Camellato, Ran Brosh, and Hannah J. Ash, and Matthew T. Morano, and Jeff D. Bucky, March 6, 2024, nature.
doi: 10.1038/s41586-024-07128-2