Dark DNA

Our records of the human genome may still be missing tens of thousands of 'dark' genes. These hard-to-detect sequences of genetic material can code for tiny proteins, some involved in disease processes like cancer and immunology, a global consortium of researchers has confirmed.

They may explain why past estimates of our genome's size were way larger than what the Human Genome Project discovered 20 years ago.

The new international study, still awaiting peer review, shows our library of human genes very much continues to be a work in progress, as more subtle genetic features are picked up with advances in technology, and as continued exploration uncovers gaps and errors in the record.

These overlooked genes have been hiding away in regions of our DNA thought not to code for proteins. These regions were once dismissed as 'junk DNA' but it turns out small bits of these sequences are still being used as instructions for mini-proteins.

Institute of Systems Biology proteomicist Eric Deutsch and colleagues found a large cache of them by searching genetic data from 95,520 experiments for fragments of protein-coding sequence. These include studies using mass spectrometry to investigate small proteins, as well as catalogues of protein snippets detected by our own immune systems.

Instead of the long, well-known codes that initiate the reading of DNA instructions for protein creation, indicating the starting point of a gene, these 'dark' genes are preceded by shorter versions which have allowed them to be overlooked by scientists.

Despite these missing parts in their start sequences, the non-canonical open reading frame (ncORF) genes are still used as a template to create RNA and some of those are then used to make small proteins with only a handful of amino acids. Previous studies have shown cancer cells contain hundreds of such tiny proteins.

"We believe the identification of these newly-confirmed ncORF proteins is immensely important," the team writes in their paper. "Their proteins… may have direct biomedical relevance, which is manifested in the growing interest in targeting such cryptic peptides with cancer immunotherapy, including cellular therapies and therapeutic vaccines."

Some of the genes that encode these cryptic peptides are transposons that move around our genomes, including sequences inserted into us by viruses.

Others are what the researchers call aberrant. For example, some of the proteins known to exist from mass spectrometry evidence have only ever been located in cancer samples, so their associated genes may not naturally belong in our bodies.

"Thus, it remains possible that certain ncORF peptides reflect aberrant proteins whose existence is deemed out of context with the canonical proteome," Deutsch and team explain.

Out of the 7,264 sets of these non-canonical genes identified, the researchers found at least a quarter of them could create proteins. This amounted to at least 3,000 new peptide-coding genes to add to the Human Genome, and the team suspects there are tens of thousands more, all missed by previous proteomic techniques.

"It's not every day that you get to open a research direction and say, 'We might have a whole new class of drug targets for patients,'" University of Michigan neurooncologist John Prensner told Elizabeth Pennisi at Science.

The tools the team have developed will help other researchers to continue to uncover more of this dark genetic matter.

This research is awaiting peer review on bioRxiv.

https://www.sciencealert.com/dark-genes-hiding-unseen-in-human-dna-have-just-been-revealed

It was barely a generation ago – during the spring of 2003, in fact – when scientists at The Human Genome Project completed their work sequencing the human genome.

But even for the world’s leading geneticists, the ‘Book of Life’ is a heavy read. Researchers are still making sense of it.

It was a landmark moment, of course, not just in science, but in life on Earth – the first time an organism catalogued the very building blocks that it’s made of. It sparked the genetic revolution that we’re currently living through, but it also raised some serious questions.

Questions like, ‘Why is there so much of it?’

One of the strange and startling things about the completed human genome was how little of it seemed to be doing anything. There are around three billion nucleotide pairs in the human genome (the ‘letters’ in our DNA: A, C, G and T).

Less than two per cent of those (around 20,000) represent protein-encoding genes that give the cells in our bodies their marching orders. So, what’s the rest of it doing?

Some called it junk DNA. Genetic gibberish – a pile of leftovers from millions of years of evolution or an impossible word search where very little makes sense.

And it seems that at least some of it is indeed non-functioning. But not all of it.

Scientists are beginning to shed light on this dark matter of the human genome. Far from a junk heap, it performs a crucial regulatory or modifying function for the protein-encoding genes. Some have likened these DNA sequences to volume-control buttons for how our genes are expressed.

For example, enhancer sequences increase the transcription of genes from DNA to RNA. Silencers do the reverse.

Large swathes of the dark genome are also made up of long, repetitive sequences of DNA known as transposons.

These too play a critical role in the way our genes are expressed, and they’re linked to momentous evolutionary steps and our ability to adapt to our environments.

Also known as ‘jumping genes’, transposons can move from one section of a genome to another. This ability can trigger seismic genetic mutations and reversals.

Scientists believe, for example, that transposons are linked to the development of opposable thumbs in humans and the loss of tails in our species and other great apes.

They may also be responsible for tumour development in some circumstances, as well as certain hereditary diseases. Haemophilia and Duchenne muscular dystrophy are two examples thought to arise from repetitive DNA sequences linked to transposons.

That’s just one reason why the dark genome is now a hotbed of medical research. Scientists hope that in the next two decades, our growing understanding of these once-ignored chapters from the ‘Book of Life’ will lead to a new generation of therapies for treating genetic disorders.

This article is an answer to the question (asked by Asa Mcintyre, via email) 'If genes only make up around two per cent of our DNA, What makes up the other 98 per cent?'

https://www.sciencefocus.com/the-human-body/dark-dna

One of our strongest defenders in the battle against cancer is a gene called p53, known in the science world as “the guardian of the genome.” It’s the most important of several “tumor suppressors” that keep us safe by controlling cell division, repairing DNA damage and destroying abnormal cells. This gene is so important that in most cancers, it’s the one most likely to be disabled, often due to mutations, or changes, in DNA. Mutations can cause cells to behave abnormally. Sometimes they can even transform p53 from a protective gene into an oncogene, causing it to switch sides in the battle so that it can actually help the cancer grow.

A decade ago, research revealed a previously unknown way that non-mutated p53 protects us from cancer. Led by Andrei Gudkov, PhD, DSci, Senior Vice President of Research Technology and Innovation and the Garman Family Chair in Cell Stress Biology at Roswell Park Comprehensive Cancer Center, a team of scientists first demonstrated that p53 also silences, or suppresses, genetic elements called retrotransposons. About 40% of our DNA is made up of millions of copies of retrotransposons, often referred to as the “dark genome.”

Technically, retrotransposons are viruses that entered human DNA in the far-distant past and underwent several explosive expansions. In normal cells they’re inactive, hidden behind a dense layer of proteins. “They’re asleep in the DNA of our normal cells,” explains Dr. Gudkov.

But they become active in tumor cells, and like all viruses, they’re laser-focused on one thing: making copies of themselves. They insert those copies into places in our DNA where they don’t belong. “This process is very dangerous, because they can disrupt important genes in the new places they enter and cause other forms of DNA damage,” says Dr. Gudkov. “This can change the genetic program of cells and create new kinds of cells that can become cancerous. Cells with activated retrotransposons are like cells that contain a piece of uranium or radium.”

Thanks to that discovery by Dr. Gudkov’s lab — and follow-up work in his and other labs — today p53 is acknowledged as a silencer of the dark genome. While other control mechanisms also help keep the dark genome in check, p53 is especially important to that effort — and things go haywire when it’s unable to do its job. “In the absence of p53, the risk of the retrotransposons awakening increases dramatically,” says Dr. Gudkov.

Although p53 has great potential for preventing cancer, so far it has been impossible to develop drugs that would restore its lost function in tumor cells. But, the discovery that p53 acts as a silencer of retrotransposons provided a new opportunity to solve that puzzle.

Dr. Gudkov and his colleagues came up with the idea of using a drug that could serve as a substitute for the disabled p53 gene and take over its job of silencing the retrotransposons. Retrotransposons replicate themselves using a process called reverse transcription, which relies on an enzyme called reverse transcriptase. It’s the same process used by HIV — the virus that causes AIDS — to replicate itself. Drugs called reverse transcriptase inhibitors, which block the HIV replication process, are essential ingredients in “drug cocktails” that keep the disease under control.

“Some of these drugs appeared to be quite effective ,” explains Dr. Gudkov. “This gave us the idea of repurposing those anti-HIV drugs to use in cancer cells in which retrotransposons are awake and actively expanding, to suppress the process and thereby partially restore p53 function.”

Studies conducted by Dr. Gudkov and his team went on to prove that the strategy works in preclinical models, dramatically extending remission time after chemotherapy. “Based on this result, we initiated a clinical trial at Roswell Park for people with one of the most challenging cancers — small cell lung cancer. We hope we can extend their life by extending the time of remission.”

Currently underway at Roswell Park under the direction of medical oncologist and lung cancer expert Grace Dy, MD, the study will enroll approximately 30 patients, who will receive standard treatment along with an anti-HIV drug to hit cancer with a one-two punch. Researchers at another U.S. cancer center have adopted the same approach in a study for patients with late-stage colorectal cancer, and the encouraging results have demonstrated its potential role in cancer therapy.

“This could provide a fantastic opportunity for improving any given cancer treatment by making it more reliable, with drugs we already have in place and simply need to repurpose from one disease to another,” says Dr. Gudkov.

Dark genome research may point to better screening and treatment options

Additional insight into the dark genome grew from other recent research led by Dr. Gudkov and his colleagues, who showed that humans can develop an immune response against retrotransposons, generating high levels of antibodies against their encoded proteins. This response is especially strong in some patients with lung, pancreatic, ovarian, liver and esophageal cancer, which are among the deadliest cancers. Often called “silent killers,” they usually don’t cause symptoms until the disease has progressed to the late stages, when a cure is far less likely. But antibodies against retrotransposons can be detected in the blood of these patients even in the early stages and could serve as a red flag to indicate the presence of disease when it’s more treatable.

“This discovery sets the stage for the development of improved diagnostics and immunotherapies for these challenging cancers,” says Dr. Gudkov.

What’s ahead? “If we could create immunotherapies directed at the cells linked to retrotransposons, it would mark a significant breakthrough in the prevention and treatment of various types of cancer,” says Dr. Gudkov. “This is a long road, but we’re on the way.”

https://www.roswellpark.org/cancertalk/202409/outsmarting-dark-side-our-dna