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Researchers Uncover New Evidence for Origin of RNA Splicing Within Human Genes; Strongest Evidence to Date That the Spliceosome Evolved from a Bacterial Group II Intron

Old-school Hollywood editors cut unwanted frames of film and patched in desired frames to make a movie. The human body does something similar--trillions of times per second--through a biochemical editing process called RNA splicing. Rather than cutting film, it edits the messenger RNA that is the blueprint for producing the many proteins found in cells. In their exploration of the evolutionary origins and history of RNA splicing and the human genome, UC San Diego biochemists Navtej Toor, PhD, and Daniel Haack, PhD, combined two-dimensional (2D) images of individual molecules to reconstruct a three-dimensional (3D) picture of a portion of RNA--what the scientists call group II introns. In so doing, they discovered a large-scale molecular movement associated with RNA catalysis that provides evidence for the origin of RNA splicing and its role in the diversity of life on Earth. Their breakthrough research is outlined in the July 25, 2019 issue of Cell. The article is titled “Cryo-EM Structures of a Group II Intron Reverse Splicing into DNA.” "We are trying to understand how the human genome has evolved starting from primitive ancestors. Every human gene has unwanted frames that are non-coding and must be removed before gene expression. This is the process of RNA splicing," stated Dr. Toor, an Associate Professor in the Department of Chemistry and Biochemistry, adding that 15 percent of human diseases are the result of defects in this process.

New CRISPR Platform (RESCUE) Expands RNA Editing Capabilities; Enables Cytosine to Uridine Changes; Zhang Team Shows That Technique Can Be Used to Convert APOE4 Alzheimer’s Risk Variant to APOE2 Non-Risk Variant

CRISPR-based tools have revolutionized our ability to target disease-linked genetic mutations. CRISPR technology comprises a growing family of tools that can manipulate genes and their expression, including by targeting DNA with the enzymes Cas9 and Cas12, and by targeting RNA with the enzyme Cas13. This collection offers different strategies for tackling mutations. Targeting disease-linked mutations in RNA, which is relatively short-lived, would avoid making permanent changes to the genome. In addition, some cell types, such as neurons, are difficult to edit using CRISPR/Cas9-mediated editing, and new strategies are needed to treat devastating diseases that affect the brain. McGovern Institute Investigator and Broad Institute of MIT and Harvard core member Feng Zhang (photo), PhD, and his team have now developed one such strategy, called RESCUE (RNA Editing for Specific C to U Exchange), which they describe in an article published in the July 26, 2019 issue of Science. The article is titled “A Cytosine Deaminase for Programmable Single-Base RNA Editing.” Dr. Zhang and his team, including first co-authors Omar Abudayyeh, PhD, and Jonathan Gootenberg, PhD, (both now McGovern Fellows), made use of a deactivated Cas13 to guide RESCUE to targeted cytosine bases on RNA transcripts, and used a novel, evolved, programmable enzyme to convert unwanted cytosine into uridine -- thereby directing a change in the RNA instructions. RESCUE builds on REPAIR, a technology developed by Zhang's team that changes adenine bases into inosine in RNA. RESCUE significantly expands the landscape that CRISPR tools can target RNA coding for modifiable positions in proteins, such as phosphorylation sites. Such sites act as on/off switches for protein activity and are notably found in signaling molecules and cancer-linked pathways.

Scientists Find New Cause of Cellular Aging--Cells Stop Making Nucleotides--Findings May Have Major Implications for Cancer and Age-Related Conditions

New research from the USC Viterbi School of Engineering could be key to our understanding of how the aging process works. The findings potentially pave the way for better cancer treatments and revolutionary new drugs that could vastly improve human health in the twilight years. The work, from Assistant Professor of Chemical Engineering and Materials Science Nick Graham, PhD, and his team in collaboration with Scott Fraser, PhD, Provost Professor of Biological Sciences and Biomedical Engineering, and Pin Wang, PhD, Zohrab A. Kaprielian Fellow in Engineering, was published online on May 28, 2019 in the Journal of Biological Chemistry. The article is titled “Inhibition of Nucleotide Synthesis Promotes Replicative Senescence of Human Mammary Epithelial Cells.” "To drink from the fountain of youth, you have to figure out where the fountain of youth is, and understand what the fountain of youth is doing," Dr. Graham said. "We're doing the opposite; we're trying to study the reasons cells age, so that we might be able to design treatments for better aging." To achieve this, lead author Alireza Delfarah, a graduate student in the Graham lab, focused on senescence, a natural process in which cells permanently stop creating new cells. This process is one of the key causes of age-related decline, manifesting in diseases such as arthritis, osteoporosis, and heart disease. "Senescent cells are effectively the opposite of stem cells, which have an unlimited potential for self-renewal or division," Delfarah said. "Senescent cells can never divide again. It's an irreversible state of cell cycle arrest." The research team discovered that the aging, senescent cells stopped producing nucleotides, which are the building blocks of DNA.

Newly Identified Pluripotent Liver Cell May Ultimately Provide Alternative to Liver Transplants; Single-Cell RNA Sequencing Key to This Major Discovery

Researchers at King's College London have used single cell RNA sequencing to identify a type of cell that may be able to regenerate liver tissue, treating liver failure without the need for transplants. In a paper published online on July 26, 2019 in Nature Communications, the scientists describe identying a new type of cell called a hepatobiliary hybrid progenitor (HHyP), that forms during our early development in the womb. The open-access article is titled “Single Cell Analysis of Human Foetal Liver Captures the Transcriptional Profile of Hepatobiliary Hybrid Progenitors.” Surprisingly, HHyP also persist in small quantities in adults and these cells can grow into the two main cell types of the adult liver (hepatocytes and cholangiocytes) giving HHyPs stem cell like properties. The team examined HHyPs and found that they resemble mouse stem cells which have been found to rapidly repair mice liver following major injury, such as occurs in cirrhosis. Senior author Dr. Tamir Rashid (photo) from the Centre for Stem Cells & Regenerative Medicine at King's College London said: "For the first time, we have found that cells with true stem-cell-like properties may well exist in the human liver. This in turn could provide a wide range of regenerative medicine applications for treating liver disease, including the possibility of bypassing the need for liver transplants." Liver disease is the fifth biggest killer in the UK and the third most common cause of premature death, and the number of cases is continuing to rise. It can be caused by lifestyle issues such as obesity, viruses, alcohol misuse, or by non-lifestyle issues such as autoimmune and genetic-mediated disease.

Unexpected Developmental Hierarchy Revealed in New Study of Highly Unusual Disease (Langerhans Cell Histiocytosis)--Epigenomics and Single-Cell Sequencing Were Key

Langerhans cell histiocytosis (LCH) is a very unusual disease: Often classified as a cancer because of uncontrolled cell growth in different parts of the body, it also has features of an autoimmune disease, as LCH lesions attract immune cells and show characteristic tissue inflammation. LCH is clinically variable and often difficult to diagnose. Skin involvement in babies with LCH can look like a nappy rash, whereas bone involvement can be mistaken as sarcoma in an X-ray picture. In its most aggressive form, LCH can present as leukemia-like disease and lead to organ failure. These diverse manifestations and the enormous clinical heterogeneity of LCH continue to puzzle medical doctors and scientists around the world. Studying LCH lesions under the microscope, Caroline Hutter, MD, PhD-- a pediatric oncologist at St. Anna Children's Hospital Research Center (CCHR) in Vienna, Austria, principal investigator at CCRI and co-lead investigator of this study -- observed striking heterogeneity among LCH cells. To investigate this diversity in full molecular detail, she assembled an interdisciplinary team including experimental and computational researchers from CCRI and CeMM (Research Center in Molecular Medicine—Vienna Austria), as well as medical doctors from St. Anna Children's Hospital and Vienna General Hospital. Her aim was to answer two fundamental questions: What are the mechanisms behind LCH, and how can we improve treatment of children affected by this disease? Utilizing state-of-the-art technology in the laboratory of co-lead investigator Christoph Bock (CeMM), PhD, LCH lesions were analyzed for their molecular composition at single-cell resolution.

CRISPR Activation Screen Identifies Genes That Protect Cells from Zika Virus Infection and Also Prevent Death of Zika-Infected Cells

The Zika virus (image) has affected over 60 million people, mostly in South America. It has potentially devastating consequences for pregnant women and their unborn children, many of whom are born with severe microcephaly and other developmental and neurological abnormalities. There is currently no vaccine or specific treatment for the virus. A new Tel Aviv University (TAU) study uses a genetic screen to identify genes that protect cells from Zika viral infection. The research, led by Dr. Ella H. Sklan of TAU's Sackler School of Medicine, was published online on May 29, 2019 in the Journal of Virology. It may one day lead to the development of a treatment for the Zika virus and other infections. The article is titled “A CRISPR Activation Screen Identifies Genes Protecting from Zika Virus Infection.” The study was based on a modification of the CRISPR-Cas9 gene-editing technique. CRISPR-Cas9 is a naturally occurring bacterial genome editing system that has been adapted to gene editing in mammalian cells. The system is based on the bacterial enzyme Cas9, which can locate and modify specific locations along the human genome. A modification of this system, known as CRISPR activation, is accomplished by genetically changing Cas9 in a way that enables the expression of specific genes in their original DNA locations. "CRISPR activation can be used to identify genes protecting against viral infection," Dr. Sklan says. "We used this adapted system to activate every gene in the genome in cultured cells. We then infected the cells with the Zika virus. While most cells die following the infection, some survived due to the over-expression of some protective genes. We then used next-generation sequencing and bioinformatic analysis to identify a number of genes that enabled survival, focusing on one of these genes called IFI6.

How Pufferfish Developed Its Unusual Spines

Pufferfish are known for their strange and extreme skin ornaments, but how they came to possess the spiky skin structures known as spines has largely remained a mystery. Now, researchers have identified the genes responsible for the evolution and development of pufferfish spines in a study published online on July 25, 2019 in iScience. The open-access article is titled “Evolution and Developmental Diversity of Skin Spines in Pufferfishes.” It turns out that the process is pretty similar to how other vertebrates get their hair or feathers--and might have allowed the pufferfish to fill unique ecological niches. "Pufferfish are some of the strangest fish in the ocean, particularly because they have a reduced skeleton, beak-like dentition and they form spines instead of scales--not everywhere, but just in certain patches around the body," says corresponding author Gareth Fraser (@garethjfraser), PhD, an Assistant Professor at the University of Florida. Dr. Fraser and his team followed the development of pufferfish spines in embryos. While the scientists had initially hypothesized that the spines formed from scales--that the pufferfish lost its scale component but retained the spine--they found that the spines are developmentally unique from scales. They also found that the development of pufferfish spines relies on the same network of genes that are commonly expressed within feathers and hairs of other vertebrate animals. "It just blows me away that regardless of how evolutionarily-different skin structures in animals are, they still use the same collection of genes during development," Dr. Fraser says.

Vitamin D Supplementation May Slow Diabetes Progression, New Study Suggests

Vitamin D supplementation may slow the progression of type 2 diabetes in newly diagnosed patients and those with prediabetes, according to a study published online on July 1, 2019 in the European Journal of Endocrinology. The open-access article is titled “Effects of 6-Month Vitamin D Supplementation on Insulin Sensitivity and Secretion: A Randomized, Placebo-Controlled Trial.” The study findings suggest that high-dose supplementation of vitamin D can improve glucose metabolism to help prevent the development and progression of diabetes. Type 2 diabetes is an increasingly prevalent disease that places a huge burden on patients and society and can lead to serious health problems including nerve damage, blindness, and kidney failure. People at high risk of developing type 2 diabetes (prediabetics) can be identified by several risk factors, including obesity or a family history of the disease. Although low vitamin D levels have previously been associated with an increased risk of developing type 2 diabetes, some studies have reported no improvement in metabolic function. However, these studies often had a low number of participants or included individuals with normal vitamin D levels at the start who were metabolically healthy, or who had long-standing type 2 diabetes. Whether vitamin D supplementation has any beneficial effect in patients with prediabetes or with newly diagnosed diabetes, especially in those who have low vitamin D levels, has remained uncertain. In this study, Dr. Claudia Gagnon, and colleagues from Université Laval in Quebec, examined the effect of vitamin D supplementation on glucose metabolism in patients newly diagnosed with type 2 diabetes or identified as at high risk of developing the condition.

Chemists Find Simplest Organic Molecules Can Self-Assemble to Give Cell-Like Structures Under Early Earth Conditions

Before life began on Earth, the environment likely contained a massive number of chemicals that reacted with each other more or less randomly, and it is unclear how things as complex as cells could have emerged from such chemical chaos. Now, a team led by Tony Z. Jia, PhD, of the Earth-Life Science Institute (ELSI) at the Tokyo Institute of Technology and Kuhan Chandru, PhD, of the National University of Malaysia, has shown that simple α-hydroxy acids, like glycolic and lactic acid (which is used in common store-bought facial peels), spontaneously polymerize and self-assemble into polyester microdroplets when dried at moderate temperatures followed by rehydration, as might have happened along primitive beaches and river banks or in drying puddles. These form a new type of cell-like compartment which can trap and concentrate biomolecules like nucleic acids and proteins. These droplets, unlike most modern cells, are able to easily merge and reform and thus could have hosted versatile early genetic and metabolic systems potentially critical for the origins of life. The new work was published online on July 22, 2019 in PNAS in an article titled “Membraneless Polyester Microdroplets As Primordial Compartments at the Origins of Life.” Scientists from around the world are actively working to understand how life began. All modern Earth life, from bacteria to humans, is made up of cells. Cells are comprised of lipids, proteins, and nucleic acids, with the lipid forming the cell membrane, an enclosure that keeps the other components together and interfaces with the environment, exchanging food and waste. How molecular assemblages as complex as cells originally formed remains a mystery.

Molecular Sensor Scouts DNA Damage and Supervises Repair; Xeroderma Pigmentosa Connection

In the time it takes you to read this sentence, every cell in your body suffers some form of DNA damage. Without vigilant repair, cancer would run rampant, and now scientists at the University of Pittsburgh have gotten a glimpse of how one protein in particular keeps DNA damage in check. According to a study published online on July 22, 2019 in Nature Structural & Molecular Biology, a protein called UV-DDB--which stands for ultraviolet-damaged DNA-binding--is useful beyond safeguarding against the sun. This new evidence points to UV-DDB being a scout for general DNA damage and an overseer of the molecular repair crew that fixes it. The article is titled “Damage Sensor Role of UV-DDB During Base Excision Repair.” "If you're going to fix a pothole, you have to find it first. That's what UV-DDB does. It identifies DNA damage so that another crew can come in and patch and seal it," said study senior author Bennett Van Houten, PhD, Professor of Pharmacology and Chemical Biology at the Pitt School of Medicine and UPMC Hillman Cancer Center. Surveying 3 billion base pairs, packed into a nucleus just a few microns wide, is a tall order, Dr. Van Houten said. Not only is it a lot of material to search through, but it's wound up so tightly that many molecules can't access it. Keeping with the pothole analogy, one possible search strategy is to walk along the road, waiting to step in a hole. Another option is to fly around in a helicopter, but because molecules can't "see," this approach would require frequently landing to look for rough patches. To get around these shortcomings, UV-DDB combines both search strategies. "UV-DDB is like a helicopter that can land and then roll for a couple blocks," Dr. Van Houten said.

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