JUN 02, 2021 9:16 PM PDT

Methylation Affects the 3D Structure of the Genome

WRITTEN BY: Carmen Leitch

Gene activity has to be carefully controlled by cells so that they maintain their identity and continue to carry out their proper functions, and there are many different ways that gene expression can be influenced and altered. Epigenetic features of the genome are just one aspect of gene regulation and they exert their influence without making any changes to the sequence of the DNA.

Image credit: Pixabay

Another aspect of gene regulation is the three-dimensional structure of the genome. When genes are active, the cellular machinery that transcribes genes has to be able to physically contact that portion of the genome so it can be copied into an RNA molecule. Methyl groups, chemical tags that can be added to the genome, are yet another aspect of gene expression. It's been suggested, for example, that the presence of many methyl groups in certain places might suppress gene expression.

A new study has also shown that the relationship between methyl groups and gene activity may be even more complex than we thought; it seems that methylation can change the three-dimensional structure of the genome.

DNA methylation has an intrinsic effect on 3D genome structure. / Credit: IRB Barcelona

Reporting in Nature Communications, researchers used yeast cells to show that methyl groups can increase the stiffness of the DNA molecule, which influences the structure and thus, alters gene expression. This mechanism illustrates how closely epigenetic features are linked to gene regulation.

In this study, the researchers utilized budding yeast, which doesn't have the cellular machinery to add methyl groups to its genome. The scientists expressed mouse versions of enzymes called DNA methyltransferases to see how the yeast genome, which did not naturally carry methyl groups, reacted when methyl groups were added to it. The investigators showed that genes that were active displayed varying levels of methylation at the places where transcription started and ended, like what's seen in mammalian cells.

"The new model organism and the theoretical analysis framework that we have developed and published are really innovative and we hope they will facilitate research projects undertaken by many laboratories around the world studying DNA methylation and its impact on gene expression," noted study leader Dr. Modesto Orozco, head of the Molecular Modelling and Bioinformatics Lab at IRB Barcelona.

Computer modeling and simulations were essential to this study. "Using these techniques, we observed that we could recapitulate the characteristic distribution of DNA methylation seen in mammalian genomes, and we confirmed our earlier in vitro result on the relationship between 3D structure, DNA flexibility, and methylation, showing that this also occurs in vivo," explained study co-director Dr. Isabelle Brun Heath, director of the Experimental Bioinformatics Laboratory.

Sources: AAAS/Eurekalert! via Institute for Research in Biomedicine (IRB Barcelona), Nature Communications

 

About the Author
BS
Experienced research scientist and technical expert with authorships on over 30 peer-reviewed publications, traveler to over 70 countries, published photographer and internationally-exhibited painter, volunteer trained in disaster-response, CPR and DV counseling.
You May Also Like
AUG 11, 2022
Cell & Molecular Biology
A Natural Compound Stimulates Repair in Muscle Tissue
AUG 11, 2022
A Natural Compound Stimulates Repair in Muscle Tissue
When tissues in our bodies experience damage, there are various repair mechanisms that can be employed. When muscles are ...
AUG 12, 2022
Immunology
Study Suggests that Terminally Exhausted T cells can be Rejuvenated
AUG 12, 2022
Study Suggests that Terminally Exhausted T cells can be Rejuvenated
Our immune cells can target cancer, but T cells can become worn out and exhausted  during lengthy battles, and they ...
AUG 11, 2022
Neuroscience
A Pathway That Links a Gut Microbe & Alzheimer's Disease
AUG 11, 2022
A Pathway That Links a Gut Microbe & Alzheimer's Disease
The gut microbiome is closely connected to human health and well being in many ways. While many microbes in the gut perf ...
SEP 05, 2022
Cell & Molecular Biology
Making Genetic Engineering at the Chromosome Level Possible
SEP 05, 2022
Making Genetic Engineering at the Chromosome Level Possible
An image by Wang Qiang shows a mouse that carries two chromosomes fused together, the first engineered karyotype in mice ...
SEP 08, 2022
Genetics & Genomics
Evidence of Trauma in DNA Could Predict Who is Most at Risk
SEP 08, 2022
Evidence of Trauma in DNA Could Predict Who is Most at Risk
A recent study has outlined the findings from a 17-year study of almost 500 people who experienced trauma in childhood. ...
SEP 11, 2022
Drug Discovery & Development
Effects of Ketamine in Mice Depend on Sex of Human Experimenter
SEP 11, 2022
Effects of Ketamine in Mice Depend on Sex of Human Experimenter
Researchers found that mice more consistently experience antidepressant effects from ketamine when administered by men a ...
Loading Comments...