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The Human Genome Contains ‘Dark Matter.’ What Is Its Purpose?

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Oct 10, 2022

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There’s information within us that’s, for all intents and purposes, hidden away. Earlier this year, we managed to map the entirety of the human genome. And while we may now know what constitutes our architecture, we don’t know a lot about what its component pieces do. More specifically: over 98% of our genome is “non-coding,” which means that it doesn’t contain the codes required to construct the proteins that make us. This is “dark matter” DNA — and it’s a mystery that science has increasingly been racing to crack.

Deoxyribonucleic acid (DNA) is a complicated molecule, but one that contains all the crucial elements of what makes humans, well, humans. DNA codes RNA (ribonucleic acid) that, in turn, codes for protein. But of these, some — especially long noncoding RNAs (lncRNAs) — don’t do that; it’s unclear what exactly they do at all. This is the big black box in our understanding of our own genome — but where we began by relegating this category of DNA as “junk,” we’re now beginning to find out some of the ways they do influence our bodies.

“So far, the data suggest that there are hundreds of thousands of functional regions in the human genome whose task is to control gene expression: it turns out that much more space in the human genome is devoted to regulating genes than to the genes themselves,” noted an editorial in the journal Nature.

“The human genome was sequenced 20 years ago, but interpreting the meaning of this book of life continues to be challenging… A major reason is that the majority of the human DNA sequence, more than 98 percent, is non-protein-coding, and we do not yet have a genetic code book to unlock the information embedded in these sequences,” said Bing Ren, professor of cellular and molecular medicine at UC San Diego School of Medicine.

With the help of the Encyclopedia of DNA Elements (ENCODE) project, launched in 2003, scientists now estimate that over 10-20% of dark matter in our genome does have a specific function. Determining what they are is a painstaking process: a functional test, where deleting specific genes can reveal their functionality by showing the consequences.

The most recent advance with respect to figuring out how our genome’s dark matter works is with respect to non-small cell lung cancer (NSCLC). Researchers at the University of Bern and the Insel Hospital, University Hospital Bern, found that inhibiting the production of certain lncRNAs inhibited cell division in cancer cells, without affecting non-cancerous cells. The finding shows that although previously overlooked, lncRNAs could play a role in diseases — and understanding genomic dark matter could then subsequently unlock the mechanisms of these diseases themselves, and give us a fighting chance at treating them.

“Like a telescope that can be quite easily repositioned to study a different part of space, our approach should be easily adaptable to reveal new potential treatment types for other cancer types,” said Roberta Esposito, co-first author of the study.


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But lncRNA has other applications, besides serving as a biosignature for cancer. Recent research has found that although they don’t encode proteins, dark matter can significantly influence gene expression and even regulate the expression of more than 60% of human-coding genes. Given this, dark matter could potentially help in regenerative medicine — particularly in stem cell research. Moreover, there’s a family of non-coding RNAs called transcribed ultra-conserved regions (T-UCRs) that have been shown to play a role in the development of malignancy in tumors precisely through the regulatory role they play. Recent advances have shown how it plays a role in pancreatic cancer. In addition, lncRNA has been implicated in breast, thyroid, prostate, renal, ovarian, and other cancers too.

Some non-coding genes are transposable, in that they jump from one region to another to regulate gene expression. But sometimes, these genes have been found to be involved in the neurodegenerative disease ALS — depending on where they jump, and how they control gene expression there.

Within dark matter, the “darkest” of dark matter is a family of transposable elements called LINEs, which research has now found to play a key role in T-cell expression. To recap: T-cells are important immune cells that are key to fighting diseases. Besides, they might also play a role in brain development — a finding that employed the aforementioned functional tests to ascertain what certain non-coding genes actually do. Herein lies the paradox of dark matter in our genome: it’s both vital to life, and could also speed up its end.

So why haven’t we investigated this sooner? “Genes that are studied in the past tend to be the ones that are studied in the future,” goes one hypothesis. In short, here’s what we know: “How lncRNAs influence complex physiological processes and the onset of diseases are questions of great relevance. Our current knowledge indicates that lncRNAs fine-tune cell specification and disease.”

Shining a light into this previously unknown frontier could be the key to unraveling the mysteries of how we tick.

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Written By Rohitha Naraharisetty

Rohitha Naraharisetty is an Associate Editor at The Swaddle. Previously, she was a freelance writer and independent researcher working in the intersection of gender, social movements, and international relations. She can be found on Instagram at @rohitha_97 or on Twitter at @romimacaronii.

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