Scientists areciphering mysterious hidden rules across species

None

NEGATIVE
A new study reveals that in the single-celled fungi yeast, “random DNA” is naturally active, whereas in mammalian cells, this DNA is turned off as its natural state in mammalian cells, despite their having a common ancestor a billion years ago and the same basic molecular machinery.
The new finding revolves around the process by which DNA genetic instructions are converted first into a related material called RNA and then into proteins that make up the body’s structures and signals.
In yeast, mice, and humans, the first step in a gene’s expression, transcription, proceeds as DNA molecular “letters” (nucleobases) are read in one direction.
While 80% of the human genome – the complete set of DNA in our cells – is actively decoded into RNA, less than 2% actually codes for genes that direct the building of proteins.
A longstanding mystery in genomics then is what is all this non-gene-related transcription accomplishing.
Is it just noise, a side effect of evolution, or does it have functions?
A research team at NYU Langone Health sought to answer the question by creating a large, synthetic gene, with its DNA code in reverse order from its natural parent.
Then they put synthetic genes into yeast and mouse stem cells and watched transcription levels in each.
Published in the journal Nature, the new study reveals that in yeast the genetic system is set so that nearly all genes are continually transcribed, while the same “default state” in the mammalian cells is that transcription is turned off.
Methodology and FindingsInterestingly, say the study authors, the reverse order of the code meant that all of the mechanisms that evolved in yeast and mammalian cells to turn transcription on or off were absent because the reversed code was nonsense.
Like a mirror image, however, the reversed code reflected some basic patterns seen in the natural code in terms of how often DNA letters were present, what they fell near, and how often they were repeated.
With the reversed code being 100,000 molecular letters long, the team found that it randomly included many small stretches of previously unknown code that likely started transcription much more often yeast, and stopped it in mammalian cells.
“Understanding default transcription differences across species will help us to better understand what parts of the genetic code have functions, and which are accidents of evolution,” said corresponding author Jef Boeke, PhD, the Sol and Judith Bergstein Director of the Institute for Systems Genetics at NYU Langone Health.
“This in turn promises to guide the engineering of yeast to make new medicines, or create new gene therapies, or even to help us find new genes buried in the vast code.”The work lends weight to the theory that yeast’s very active transcriptional state is set so that foreign DNA, rarely injected into yeast for instance by a virus as it copies itself, is likely to get transcribed into RNA.
If that RNA builds a protein with a helpful function, the code will be preserved by evolution as a new gene.
Unlike a single-celled organism in yeast, which can afford risky new genes that drive faster evolution, mammalian cells, as part of bodies with millions of cooperating cells, are less free to incorporate new DNA every time a cell encounters a virus.
Many regulatory mechanisms protect the delicately balanced code as it is.
Big DNAThe new study had to account for the size of DNA chains, with 3 billion “letters” included in the human genome, and some genes being 2 million letters long.
While famous techniques enable changes to be made letter by letter, some engineering tasks are more efficient if researchers build DNA from scratch, with far-flung changes made in large swaths of pre-assembled code swapped into a cell in place of its natural counterpart.
Because human genes are so complex, Boeke’s lab first developed its “genome writing” approach in yeast, but then recently adapted it to the mammalian genetic code.
The study authors use yeast cells to assemble long DNA sequences in a single step, and then deliver them into mouse embryonic stem cells.
For the current study, the research team addressed the question of how pervasive transcription is across evolution by introducing a synthetic 101 kilobase stretch of engineered DNA – the human gene hypoxanthine phosphoribosyl transferase 1 (HPRT1) in reverse coding order.
They observed widespread activity of the gene in yeast despite the lack in the nonsense code of promoters, DNA snippets that evolved to signal for the start of transcription.
Further, the team identified small sequences in the reversed code, repeated stretches of adenosine and thymine building blocks, known to be recognized by transcription factors, proteins that bind to DNA to initiate transcription.
Just 5 to 15 letters long, such sequences could easily occur randomly and may partly explain the very active yeast default state, the authors said.
To the contrary, the same reversed code, inserted into the genome of a mouse

In spite of the fact that mammals and yeast shared a common ancestor billions of years ago and the same basic molecular machinery, a recent study shows that while “random DNA” is naturally active in yeast, it is inactive in mammalian cells.

The process by which the genetic instructions contained in DNA are translated, first into RNA, a related material, and then into proteins, which comprise the body’s structures and signals, is the focus of the new discovery. Nucleobases, or DNA molecules, are read in one direction during transcription, the initial stage of gene expression in humans, mice, and yeast. Less than 2% of the total DNA in human cells, or the genome, genuinely codes for genes that control the synthesis of proteins, despite the fact that 80% of the DNA is actively translated into RNA.

The purpose of all this transcription unrelated to genes has been a longstanding puzzle in genomics. Or does it serve a purpose? Is it merely noise or a byproduct of evolution?

In order to provide an answer, a research team at NYU Langone Health constructed a sizable synthetic gene with the DNA coding of its natural parent reversed. After that, they inserted artificial genes into mouse and yeast stem cells and measured the transcription levels in each. The new research, which was published in the journal Nature, shows that transcription is turned off in mammalian cells, whereas the genetic system in yeast is configured to produce almost all genes continuously.

Results and Methodology.

It’s interesting to note that, according to the study’s authors, the reversed code was meaningless, so all of the mechanisms that evolved in mammalian and yeast cells to turn transcription on or off were missing. In terms of how frequently DNA letters were present, what they fell near, and how often they were repeated, the reversed code, like a mirror image, reflected some fundamental patterns found in the natural code. The researchers discovered that, despite the reversed code having 100,000 molecular letters, it arbitrarily contained numerous brief segments of previously unidentified code that, in yeast cells, most likely initiated transcription and, in mammalian cells, ended it.

The corresponding author, Jef Boeke, PhD, the Sol and Judith Bergstein Director of the Institute for Systems Genetics at NYU Langone Health, said, “Understanding default transcription differences across species will help us to better understand what parts of the genetic code have functions, and which are accidents of evolution.”. This in turn holds the potential to direct the engineering of yeast to produce novel gene therapies, new medications, or even to assist in the discovery of novel genes hidden within the massive code. “.

The research supports the idea that yeast’s extremely active transcriptional state is designed to increase the likelihood that foreign DNA, which is sporadically injected into yeast—for example, by a virus replicating itself—will be transcribed into RNA. Evolution will preserve the code as a new gene if that RNA produces a protein with a useful function. Mammalian cells are part of bodies with millions of cooperating cells, so they are less free to incorporate new DNA every time a cell encounters a virus than a single-celled organism in yeast, which can afford risky new genes that drive faster evolution. The carefully calibrated code as it stands is protected by numerous regulatory mechanisms.

large DNA.

The human genome consists of 3 billion “letters,” and some genes are 2 million letters long. The size of DNA chains had to be taken into consideration in this new study. Even though modifications can be made letter by letter using well-known techniques, some engineering tasks are more effectively completed by researchers building DNA from scratch and making extensive modifications to large swaths of pre-assembled code that are then substituted into a cell for their natural counterpart. Boeke’s lab developed its “genome writing” method in yeast initially due to the complexity of human genes; however, it was recently adapted to the genetic code of mammals. The researchers deliver lengthy DNA sequences into mouse embryonic stem cells after assembling them in a single step using yeast cells.

In order to answer the question of how widespread transcription is throughout evolution, the research team in this study inserted a synthetic 101 kilobase stretch of engineered DNA, which encodes the human gene hypoxanthine phosphoribosyl transferase 1 (HPRT1) in reverse coding order. The absence of the nonsense code of promoters—DNA fragments that have evolved to signal the initiation of transcription—was not enough to explain the extensive expression of the gene in yeast.

The group also discovered brief segments in the flipped code, which are repetitive adenosine and thymine stretches that are recognized by transcription factors—proteins that attach to DNA and start transcription. Such sequences, which are only 5 to 15 letters long, could appear at random and, according to the authors, could help to explain why yeast defaults to a highly active state.

On the other hand, widespread transcription was not triggered by the same reversed code that was introduced into the genome of mouse embryonic stem cells. In this case, evolved CpG dinucleotides, which are known to actively silence genes, were not functional in the reversed code, but transcription was nevertheless suppressed. The team speculates that additional fundamental components in the mammalian genome may significantly more tightly regulate transcription than in yeast, possibly by directly enlisting the help of a protein complex called the polycomb complex, which is known to mute genes.

First author Brendan Camellato, a graduate student in Boeke’s lab, stated that “the closer we get to introducing a ‘genome’s worth’ of nonsense DNA into living cells, the better they can compare it to the actual, evolved genome.”. Because we can insert longer and longer synthetic DNAs, we can learn more about the types of insertions that genomes can withstand and potentially incorporate one or more larger, complete engineered genes. This could open up new avenues for the development of engineered cell therapies. “.

The article “Synthetic reversed sequences reveal default genomic states” was written by Hannah J., Ran Brosh, and Brendan R. Camellato. ASH, Matthew T. Nature, Maurano and Jef D. Boeke, March 6, 2024.

s41586-024-07128-2 (DOI: 10.1038).

Leave a Reply

scroll to top