Scientists Discover a Connection Between the Genome’s Dark Matter and Autoimmune Diseases


Babraham and Wellcome Sanger Institutes partnered in a major research project and discovered a connection between the genome’s non-protein coding ‘dark matter’ region and autoimmune or allergic diseases.

A recent article about the project was published by Science Magazine and the journal Nature. The project has identified a new target for treating inflammatory diseases.

The genetic foundation of people being susceptible to diseases such as ulcerative colitis, Crohn’s disease, asthma, and type 1 diabetes is now focused on a region of chromosome 11.

What is a Genome?

The genome resides in each cell containing a nucleus. It includes noncoding DNA and coding regions of genes.

The paradigm goes something like this:

  • Each human genome contains over three billion chemically attached nucleic acids called DNA sequence or base pairs
  • These base pairs are contained in the twenty-three pairs of tiny spaghetti-like structures called chromosomes that are in the nucleus of all cells
  • Each chromosome holds hundreds to many thousands of genes. The gene is a string of DNA. It contains instructions to make proteins
  • The proteins perform functions in our cells
  • The genome is the entire set of DNA and that includes its genes
  • DNA contains a chemical code that guides our development, health, and growth.

What is Gene Expression             

When the instructions in our DNA are converted into a protein, the process is called “gene expression.”

The Human Genome Project (HGP) of 2000

The HGP was an international research project that had a goal of identifying the base pairs that comprise the human DNA. It was intended to also identify and map all the genes of the human genome. It still holds the distinction of being the world’s largest biological project.

During the project, the researchers mapped the unique “human genome” of a number of individuals. They assembled the genomes together in order to complete an entire sequence for each chromosome. It is for that reason that the completed human genome is a mosaic and does not represent any particular individual.

The researchers searched for the genome’s functional protein-coding units (genes) but found only one percent of the three billion DNA base pairs.

The majority of the genome (99%) is called non-coding DNA or the dark matter region. The non-coding DNA does not contain instructions for producing proteins.

But it is now evident to the scientists that some of the non-coding DNA may be critical to cell function, especially with regard to controlling gene activity.

About the Dark Matter

After decades of research, scientists discovered that the majority of genetic variations that affect a person’s susceptibility to complex allergic and immune diseases are situated in areas in the genome that do not encode proteins. This is the dark matter. It does not give scientists a clear target to investigate or to develop treatments.

About Enhancers

One of the researchers, Dr. Roychoudhuri, commented that after decades of research, scientists have been able to identify variations in genomes that cause some people to be more susceptible to a variety of inflammatory diseases.

He adds that on the downside, many immune diseases occur in regions that are non-protein coding. It is therefore very difficult to grasp the implications of a variety of changes.

But advances in sequencing-based methodology show that genetic changes are primarily in regions of DNA called enhancers. These enhancers function as switches to regulate gene expression.

The researchers found an enhancer element called Tregs (cells) that balance immune response during infections. Although Tregs represent only a very small part of the immune system, they are essential and mediate excessive inflammation.

In one of the experiments, the scientists demonstrated that when the enhancer element was deleted, that triggered inflammation in the lining of the colon.

Scientists are still optimistic that this type of study will link them to genetic switches and the genes that the switches control found in non-coding areas.

This has the potential to discover new cell types and the genes associated with disease biology. But mainly it will lead to new targets in therapeutic development.

What are your thoughts about the potential of research into the dark matter to better understand allergic and autoimmune diseases? Share your stories, thoughts, and hopes with the Patient Worthy community!

Rose Duesterwald

Rose Duesterwald

Rose became acquainted with Patient Worthy after her husband was diagnosed with Acute Myeloid Leukemia (AML) six years ago. During this period of partial remission, Rose researched investigational drugs to be prepared in the event of a relapse. Her husband died February 12, 2021 with a rare and unexplained occurrence of liver cancer possibly unrelated to AML.

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