Thermal Cycler
Since the 1960s, our understanding of genetics has been shaped by the idea that genes are straightforward and linear. By decoding our chromosomes as continuous sequences of nucleotides much like reading sentences—we've been able to pinpoint genes and decipher how mutations affect health.
This linear perspective on genetics was once thought to be universal, applying equally to all forms of life, from humans to bacteria.
However, groundbreaking research from Columbia University has upended this notion. The study reveals that bacteria are capable of creating transient, free-floating genes that exist outside of the traditional genomic framework. This finding suggests that such extra genomic genetic elements might also be present in humans, challenging long-held assumptions about the organization of genetic material.
Samuel Sternberg, Associate Professor of Biochemistry & Molecular Biology at the Vagelos College of Physicians and Surgeons, who led the research with Stephen Tang, an MD/PhD student, explains, “This discovery challenges the long-held belief that the chromosome contains the entire set of instructions required for protein production within cells.”
He adds, “We now understand that in bacteria, there are crucial instructions beyond those encoded in the genome that are vital for cell survival.”
For eons, bacteria and their viruses have been engaged in a relentless conflict. Viruses attempt to insert their DNA into bacterial genomes, while bacteria develop sophisticated defenses, such as CRISPR, to counteract these attacks. Although many bacterial defense mechanisms remain uncharted, they hold promise for developing new genome editing technologies.
In their research, Sternberg and Tang investigated a particularly unusual bacterial defense system. This system involves a piece of RNA with an unknown function and a reverse transcriptase enzyme, which converts RNA into DNA. According to Tang, “Most known bacterial defense mechanisms involve cutting or degrading incoming viral DNA, so the concept of defending the genome through DNA synthesis was quite puzzling.”
Uncovering an Unexpected Bacterial Defense: Discovery of a Free-Floating, Functional Gene
To understand the workings of this unusual defense mechanism, Tang developed a novel method to detect the DNA generated by the reverse transcriptase. He discovered that the DNA was unusually long and repetitive, containing multiple copies of a short sequence derived from the defense system's RNA molecule.
Tang observed that this segment of RNA forms a loop, and the reverse transcriptase circulates this loop repeatedly, producing repetitive DNA. Sternberg likened this process to a photocopier endlessly reproducing the same page: “It’s like you were intending to photocopy a book, but the copier just started churning out the same page over and over again.”
Initially, the researchers suspected their experiments might be flawed or that the enzyme was producing irrelevant DNA. However, Tang's further investigation revealed that the DNA they had detected was a functional, free-floating, transient gene.
This gene encodes a protein, named Neo by the researchers, which plays a crucial role in the bacterial antiviral defense system. When a virus infects the bacteria, Neo is produced to inhibit the virus's replication and prevent its spread to other cells.
Exploring the Presence of Genes Outside the Human Chromosome
If similar free-floating genes are discovered in the cells of higher organisms, it would represent a breakthrough, according to Sternberg. “There could be genes or DNA sequences that exist outside the conventional 23 human chromosomes. These could be specific to certain environments, developmental stages, or genetic contexts, yet they might encode essential information vital for our normal physiology.”
The research team is now applying Tang’s techniques to investigate the presence of extrachromosomal genes in humans, which may be produced by reverse transcriptases.
The human genome contains thousands of reverse transcriptase genes, many of which have unknown functions. “There is a significant opportunity here to uncover new aspects of biology that could provide valuable insights,” Sternberg adds.
Source of Gene-Editing Innovation
Although CRISPR-based gene therapies are advancing, with one recently approved for treating sickle cell disease, the technology is not without limitations.
Emerging techniques that integrate CRISPR with reverse transcriptase are enhancing genome editing capabilities. “Reverse transcriptase allows for the introduction of new genetic information at CRISPR-cut sites, something that CRISPR alone cannot achieve,” explains Tang. However, the reverse transcriptases commonly used are based on older discoveries.
The reverse transcriptase is responsible for creating Neo exhibits unique properties that may improve genome editing and facilitate the development of novel gene therapies. Additionally, numerous unexplored reverse transcriptases in bacteria hold potential for future breakthroughs.
“We believe that bacteria may possess a wealth of reverse transcriptases with untapped potential, which could serve as the foundation for innovative technologies once we fully understand their mechanisms,” says Sternberg.
Source:https://www.cuimc.columbia.edu/news/should-people-kidney-disease-get-genetic-testing
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