When people picture DNA, they often imagine a set of genes that shape our physical traits, influence behavior, and help keep our cells and organs functioning.
But genes make up only a small slice of our genetic code. Just around 2% of DNA comprises our 20,000-odd genes. The opposite 98% has long been labelled the non-coding genome, or so-called ‘junk’ DNA. This larger portion includes most of the control switches that determine when genes activate and the way strongly they act.
Astrocytes and hidden DNA switches within the brain
Researchers from UNSW Sydney have now pinpointed DNA switches that help regulate astrocytes. Astrocytes are brain cells that support neurons, and so they are known to be involved in Alzheimer’s disease.
In research published on December 18 in Nature Neuroscience, a team from UNSW’s School of Biotechnology & Biomolecular Sciences reported that they tested nearly 1000 possible switches in lab-grown human astrocytes. These switches are strings of DNA called enhancers. Enhancers can sit removed from the genes they influence, sometimes separated by a whole lot of hundreds of DNA letters, which makes them difficult to research.
Testing nearly 1000 enhancers directly
To tackle that problem, the researchers combined CRISPRi with single-cell RNA sequencing. CRISPRi is a technique that may switch off small stretches of DNA without cutting it. Single-cell RNA sequencing measures gene activity in individual cells. Together, the tools let the team examine the consequences of nearly 1000 enhancers in a single large-scale test.
“We used CRISPRi to show off potential enhancers within the astrocytes to see whether it modified gene expression,” says lead creator Dr. Nicole Green.
“And if it did, then we knew we might found a functional enhancer and will then determine which gene — or genes — it controls. That is what happened for about 150 of the potential enhancers we tested. And strikingly, a big fraction of those functional enhancers controlled genes implicated in Alzheimer’s disease.”
Cutting the list from 1000 candidates to about 150 confirmed switches greatly reduces the search area within the non-coding genome for genetic clues linked to Alzheimer’s disease.
“These findings suggest that similar studies in other brain cell types are needed to focus on the functional enhancers within the vast space of non-coding DNA”
Why “in-between” DNA matters for a lot of diseases
Professor Irina Voineagu, who oversaw the study, says the outcomes also provide a useful reference for interpreting other genetic research. The team’s findings create a list of DNA regions that will help explain results from studies in search of disease-related genetic changes.
“When researchers search for genetic changes that designate diseases like hypertension, diabetes and in addition psychiatric and neurodegenerative disorders like Alzheimer’s disease — we regularly find yourself with changes not inside genes a lot, but in-between,” she says.
Her team directly tested those “in-between” stretches in human astrocytes and showed which enhancers truly control key brain genes.
“We’re not talking about therapies yet. But you’ll be able to’t develop them unless you first understand the wiring diagram. That is what this provides us — a deeper view into the circuitry of gene control in astrocytes.”
From gene switches to AI prediction models
Running nearly a thousand enhancer tests within the lab took painstaking effort. The researchers say that is the primary time a CRISPRi enhancer screen of this size has been carried out in brain cells. Now that the groundwork has been done, the dataset may also be used to coach computer models to predict which suspected enhancers are real gene switches, potentially saving years of lab work.
“This dataset will help computational biologists test how good their prediction models are at predicting enhancer function,” says Prof. Voineagu.
She adds that Google’s DeepMind team is already using the dataset to benchmark their recent deep learning model called AlphaGenome.
Potential tools for gene therapy and precision medicine
Because many enhancers are energetic only in specific cell types, targeting them could offer a option to fine-tune gene expression in astrocytes without changing neurons or other brain cells.
“While this just isn’t near getting used within the clinic yet — and far work stays before these findings could lead on to treatments — there may be a transparent precedent,” Prof. Voineagu says.
“The primary gene editing drug approved for a blood disease — sickle cell anemia — targets a cell-type specific enhancer.”
Dr. Green says enhancer research could grow to be a vital a part of precision medicine.
“That is something we wish to have a look at more deeply: checking out which enhancers we are able to use to show genes on or off in a single brain cell type, and in a really controlled way,” she says.