The term “unknown DNA” often evokes images of mysterious elements hidden within our genetic code. In a scientific context, “unknown DNA” refers to segments of our genetic material whose origins or functions have not yet been fully deciphered. Unraveling these genetic puzzles is a focus of modern genomics. These investigations are transforming what was once a mystery into a deeper understanding of the complex story written in our DNA.
The Vast Territory of Non-Coding DNA
For many years, scientists observed that only about 1-2% of the human genome contains instructions for building proteins. This led to the term “junk DNA” to describe the other 98%. This label suggested most of our DNA was evolutionary debris with no purpose, a reflection of the research focus on protein-coding genes at the time.
This view has been overturned in recent decades. The term “junk DNA” is now considered a misnomer, replaced by the more accurate term “non-coding DNA.” Research has revealed these once-mysterious regions contain functional elements. Much of this non-coding DNA is integral to cellular life, containing instructions that regulate how and when genes are used.
A primary function of non-coding DNA is gene regulation. If protein-coding genes are computer hardware, non-coding DNA is the software that tells the hardware what to do. It contains sequences called enhancers and silencers, which act as switches to turn genes on or off. This control is important for everything from embryonic development to the daily functioning of tissues.
Beyond regulation, non-coding DNA also plays a structural role. Stretches of repetitive non-coding DNA form telomeres, which are protective caps at the ends of our chromosomes that prevent them from degrading. Other regions are important for maintaining the architecture of the chromosomes, ensuring they are packed correctly within the cell’s nucleus.
Some non-coding DNA is also transcribed into functional RNA molecules. While not translated into proteins, these molecules perform a variety of tasks. These tasks range from helping to assemble proteins to blocking certain gene activities.
Genetic Echoes from Ancient Relatives
A source of once-unknown DNA comes from our extended family tree. Genetic analysis revealed that the ancestors of modern humans interbred with archaic groups like Neanderthals and Denisovans. These encounters occurred as modern humans migrated out of Africa and into Eurasia. This intermingling left a legacy in our genomes, which was once only visible as unusual genetic variations.
People of European or Asian descent carry about 1-2% Neanderthal DNA. The percentage of Denisovan DNA is highest in Melanesian populations, who have between 4-6% from this group. These sequences were identified by comparing modern human genomes to DNA from ancient bones and teeth. This archaic DNA is largely absent in individuals of African ancestry, whose ancestors did not encounter these Eurasian hominins.
The discovery of “ghost DNA” adds more complexity. This term refers to genetic evidence of archaic populations whose existence is inferred from the DNA of modern people, as no fossil remains have been found. For instance, analyses of West African populations have identified DNA from an unknown archaic hominin. This group may have contributed between 2% and 19% of their genetic ancestry.
Similarly, another ghost population appears to have interbred with the ancestors of modern humans in Asia and Oceania. These discoveries highlight that our understanding of human history is incomplete. Our DNA holds clues to relatives we have yet to formally identify.
Viral Fossils Within Our Genome
Another source of unknown genetic material is ancient viral infections. Our genome contains remnants of viruses that infected our ancestors millions of years ago, known as Human Endogenous Retroviruses (HERVs). They make up 8% of our DNA—far more than the percentage that codes for proteins. These sequences became permanent when they infected germline cells (eggs and sperm), allowing them to be passed down through generations.
These HERVs are genomic fossils. Most have been inactivated by mutations over evolutionary time, rendering them unable to produce new viruses. They are the relics of an evolutionary battle between our ancestors and viral pathogens. For a long time, the function of this viral DNA was unknown.
Scientific investigation has revealed that some of these viral fossils have been repurposed, or “co-opted,” for beneficial functions. An example is the role of a viral gene in the development of the placenta. Proteins called syncytins, derived from ancient retroviruses, are important for forming the syncytiotrophoblast. This is a layer of the placenta that facilitates nutrient exchange between mother and fetus.
The original function of these proteins was to fuse the virus to a host cell. Our bodies now use this same property to fuse placental cells together. This process is important for a healthy pregnancy.
Methods for Mapping the Genetic Unknown
Mapping the genome’s unknown regions requires several scientific methods. The foundation is genome sequencing, the process of reading the entire sequence of DNA bases. Advances in sequencing have made it possible to map the genomes of humans and our ancient relatives from fossilized remains. This allows for direct comparisons to identify unique versus inherited sequences.
To understand the function of non-coding DNA, scientists use comparative genomics. This approach compares the human genome with those of other species, from chimpanzees to mice. When a non-coding sequence is highly conserved—unchanged across millions of years of evolution—it implies the sequence has a biological role. This method helps researchers pinpoint functional elements for further study.
Bioinformatics tools are used to analyze the data from sequencing and comparative studies. Algorithms identify patterns, such as regulatory elements or the genetic signatures of “ghost populations.” For instance, computational methods can identify regions in the genomes of modern West Africans that differ greatly from other human DNA. This difference is best explained by interbreeding with an undiscovered archaic hominin group.
These combined techniques are systematically turning the unknown portions of our DNA into a source of information about our evolution, biology, and history.