Research shows how ‘junk’ RNA controls our genes

Researchers at Arizona State University have made a significant advance in understanding how genes are controlled in living organisms. The new study, published in the journal Nucleic Acids Researchfocuses on critical parts of RNA in the small transparent worm Caenorhabditis elegans (C. elegans).

The study provides a detailed map of the 3’UTR regions of RNA in C. elegans. 3’UTRs (untranslated regions) are segments of RNA involved in gene regulation.

The new map is a valuable tool for scientists studying how DNA genes are turned on and off after they are transcribed into RNA. Using this data, scientists can make improved predictions about how small RNA (miRNA) molecules interact with genes to control their activity. The researchers also explored crucial regions of 3’UTRs that help process and regulate RNA molecules.

By studying the genetic material in this model organism, researchers are gaining deeper insights into the mysteries of gene behavior, shedding light on fundamental biological processes essential to human health and disease.

“This monumental work represents a culmination of 20 years of hard work. We finally have the complete picture of how genes are formed in higher organisms,” says Marco Mangone, corresponding author of the new study.

“With this complete data, we can now define and study all the regulatory and processing elements within these gene sections. These elements determine the duration of gene expression, their specific locations within cells and the required level of expression.”

Mangone is a researcher at the Virginia G. Piper Biodesign Center for Personalized Diagnostics and a professor in the ASU School of Life Sciences.

Genes are only half the story

Genes are segments of DNA that contain the blueprints for an amazing diversity of life on Earth. However, part of the secret of this versatility lies not in the genes themselves, but in the way their effects are finely tuned. Genes provide instructions for making proteins, which play essential roles in building and repairing cells and tissues, speeding up chemical reactions, and defending the body against pathogens.

To make proteins, genes require an intermediary molecule called RNA. During this process, DNA is first copied into RNA, which acts as a bridge between the DNA template and the resulting proteins. Although our DNA genome is fixed from birth, RNA provides the body with great flexibility by regulating how genes are expressed.

After genetic instructions are transcribed from DNA into messenger RNA (mRNA), specialized segments of mRNA 3’UTRs can regulate how proteins are made.

3’UTRs are sections of RNA located at the end of a messenger RNA molecule. They help govern how and when proteins are made by controlling mRNA stability and efficiency. This regulation allows dynamic responses to environmental changes and enables control over protein production, which is essential to adapt to different physiological needs.

3’UTRs revisited

Initially, non-coding RNAs such as 3’UTRs were considered non-essential genetic fragments because they themselves do not code for proteins. However, recent research reveals that they are essential for modifying gene behavior and influencing mRNA stability, localization, and translation efficiency. Translation refers to the process of converting RNA into proteins composed of amino acid sequences.

3’UTRs are an integral part of a sophisticated and highly adaptable system of checks and balances in protein production. Furthermore, these RNA regulatory elements often contain binding sites for other elements responsible for protein regulation, including microRNAs and RNA-binding proteins.

Despite their importance, scientists previously knew little about them. The new study addresses this gap by mapping the 3’UTR for nearly all genes in C. elegans, providing the most complete map of its kind for any animal.

A window into gene function and disease

C. elegans is a small transparent nematode that is one of the most widely studied model organisms in biological research. Its importance lies in its simplicity, short life cycle and well-designed genetic structure.

The organism shares many essential biological pathways with humans, making it invaluable for studying gene function, development, and disease processes. Its transparent body allows researchers to observe cellular processes in real time, and its genetic makeup enables precise gene manipulation.

These characteristics make C. elegans a powerful tool for uncovering fundamental mechanisms of biology that are often conserved across species, including humans.

The study found that the process of switching between different 3’UTRs is less common in C. elegans than previously thought. This challenges previous beliefs and highlights the complexity of gene regulation. Using the new data, the scientists updated predictions about how microRNAs interact with genes.

The insights gained from the new study have far-reaching implications for human health. Problems with gene control can lead to diseases such as cancer, diabetes and neurological disorders. By providing a detailed map of 3’UTRs and their regulatory elements, the research provides new insights that may lead to better treatments and therapies.

The new data produced in the study will be a key resource for scientists studying genetics and human health. The ASU team plans to continue their research to further explore how these regulatory elements work and their critical impact on gene control.