Exploring RNA Interference

Imagine a molecular switch within your cells, one that can selectively turn off the production of specific proteins. This isn't science fiction; it's the power of RNA interference (RNAi), a groundbreaking biological process that has revolutionized our understanding of gene expression and holds immense potential for medicine and beyond.

The discovery of RNAi, like many scientific breakthroughs, was serendipitous. In the 1990s, Andrew Fire and Craig Mello were studying gene expression in the humble roundworm, Caenorhabditis elegans (a tiny worm). While injecting worms with DNA to study a specific gene, they observed an unexpected silencing effect - not just in the injected cells, but throughout the organism. This puzzling phenomenon, initially named "co-suppression," was later recognized as a universal mechanism: RNAi.

Their groundbreaking work, awarded the Nobel Prize in 2006, sparked a scientific revolution. Researchers delved deeper, unveiling the intricate choreography of RNAi. Double-stranded RNA molecules, the key players, bind to a protein complex called RISC (RNA-induced silencing complex). RISC, equipped with an "Argonaut" enzyme, acts as a molecular matchmaker, pairing the incoming RNA with its target messenger RNA (mRNA) - the blueprint for protein production. This recognition triggers the cleavage of the target mRNA, effectively silencing the corresponding gene.

So, how exactly does RNAi silence genes? Imagine a bustling factory where DNA blueprints are used to build protein machines. RNAi acts like a tiny conductor, wielding double-stranded RNA molecules as batons. These batons bind to specific messenger RNA (mRNA) molecules, the blueprints for proteins. Now comes the clever part: with the mRNA "marked," special molecular machines chop it up, effectively preventing protein production. This targeted silencing allows scientists to turn down the volume of specific genes, observing the resulting effects and understanding their roles in health and disease.

The intricate dance of RNAi involves several key players:dsRNA: The conductor, a long molecule with two complementary strands. Dicer: The technician, an enzyme that chops dsRNA into small interfering RNAs (siRNAs), about 20-25 nucleotides long. RNA-induced silencing complex (RISC): The ensemble, containing Argonaute proteins and the siRNA. Target mRNA: The specific "instrument" to be silenced, carrying the genetic instructions for protein synthesis.

The siRNA within RISC identifies and binds to the complementary sequence on the target mRNA. This binding triggers either:Direct cleavage: Argonaute acts like a molecular scissors, severing the mRNA, preventing protein production. Translation inhibition: RISC recruits other proteins that block ribosomes from translating the mRNA into a protein.

From Labs to Life: The Diverse Applications of RNAi

The ability to silence genes with high specificity unlocks various applications across different fields:

Unlocking Gene Function: Researchers use RNAi to study gene function in various organisms, from model systems like fruit flies to complex human cells. Silencing specific genes reveals their roles in development, disease, and other biological processes.

Therapeutic Potential: RNAi holds immense promise for treating various diseases. siRNA-based drugs are being developed to target genes involved in cancer, viral infections, neurodegenerative diseases, and more. Several clinical trials are underway, showcasing the potential for personalized medicine.

Crop Improvement: In agriculture, RNAi offers sustainable solutions for pest control and crop development. Silencing genes in insects can create pest-resistant crops, while altering plant genes can improve yield, nutritional value, and stress tolerance.

Beyond the Obvious: RNAi applications extend beyond these core areas. It's being explored for gene therapy, stem cell research, and functional genomics, pushing the boundaries of scientific exploration.

Despite its exciting potential, RNAi raises ethical concerns. Off-target effects, unintended silencing of non-target genes, and potential environmental risks need careful consideration. Open and responsible research, coupled with public discourse, is crucial to ensure we harness this powerful tool for good.

Resident Upheaval

Using imaging mass cytometry and single-cell RNA sequencing to analyse the cellular composition and topology of the tissue changes with ulcerative colitis – inflammatory macrophages replace resident macrophages

Read the original article here

Image from work by Juan Du, Junlei Zhang, Lin Wang and Xun Wang, and colleagues

Zhejiang University School of Medicine, Hangzhou, China

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Published in Nature Communications, June 2023

It's all in the math: New tool provides roadmap for cell development

Researchers at Columbia University Medical Center have created a new tool to describe the many possible ways in which a cell may develop. Rooted in the mathematical field of topology, the tool provides a roadmap that offers detailed insight into how stem cells give rise to specialized cells.                                

The study was published today in Nature Biotechnology.

Every organism begins with one cell. As that cell divides, its copies branch off to become specialized cells—such as heart, bone, or brain cells—in a process known as differentiation. To understand the internal and external cues that move cells along this path, scientists can sequence their RNA—the molecular messenger that translates DNA into proteins and other products.

Sequencing RNA from a batch of cells is not ideal, however, because the cells are usually in different states of development. To address this problem, scientists have developed single-cell RNA sequencing. "It's like a new microscope, giving us the ability to study many biological phenomena at once," said Raul Rabadan, PhD, associate professor of systems biology and biomedical informatics at Columbia and co-author of the paper. "However, researchers are still left with the problem of understanding the relationships between different cell states, which drive the process of development."

Single-cell topological RNA-seq analysis reveals insights into cellular differentiation and development, Nature Biotechnology (2017). nature.com/articles/doi:10.1038/nbt.3854

Single Cell Survey

For a long time, scientists thought that there were only three types of blood cell in fruit flies, each produced at different points in the journey from larva to adult insect. Then a team of curious researchers decided to take a closer look. First, they purified nearly 20,000 individual cells from the blood of fruit fly larvae that were either healthy, had been parasitised by wasps or damaged with a fine needle. Analysing the patterns of gene activity in each cell using a technique called single cell sequencing revealed 16 distinct clusters, each representing a distinct population of cells (the different coloured clusters in this graphic representation of the data). Fruit flies are a widely used model organism in biomedical research, including studying immune responses to injury and infection, so mapping the true complexity of the fly immune system is an important step forward in understanding these seemingly simple animals.

Written by Kat Arney

Image from work by Sudhir Gopal Tattikota and colleagues

Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA

Image originally published with a Creative Commons Attribution 4.0 International (CC BY 4.0)

Research published in eLife, May 2020

Delivering Livers

If someone’s liver is so damaged that it can no longer operate as it should, a liver transplant might be the only option. But as donor organs are in short supply scientists in the world of regenerative medicine are addressing this problem by developing ways to use stem cells to replace and restore damaged tissue. Pictured is a liver organoid – a 3D organ-like mass of cells in culture – generated by coaxing stem cells to differentiate using precise molecular signalling. These types of organoids provide researchers with a ‘life-like’ experimental environment, allowing them to gain a more in-depth understanding of how the human liver develops. On this occasion, researchers used RNA sequencing to observe genes, signalling molecules and their receptors in order to monitor the molecular conversations that occur between developing liver cells and with their surrounding environment. These miniature organs could soon help with the treatment of liver diseases.

Written by Katie Pantell

Image from Cincinnati Children's Hospital /Max Planck Institute

Department of Evolutionary Genetics, Max Planck Institute; Department of Regenerative Medicine, Yokohama City University Graduate School of Medicine, Japan and Department of Pediatrics, Cincinnati Children’s Hospital Medical Center

Image copyright held by the original authors

Research published in Nature, June 2017

Last week, we completed our third sequencing workshop with Illumina, and we are grateful to Katherine Sullivan, Cameron Robertson, Curtis Provencher, and Michelle Benitez for their patience, expertise, and encouragement. Their sponsorship provided the opportunity for 7 students, plus me, and Alex and Megan at UMaine CORE, to learn how to prepare their samples for sequencing. We are also grateful…