BioQuakes

AP Biology class blog for discussing current research in Biology

Tag: Gene expression

CRISPR-ing the Code: Deciphering Gene Regulation with Epigenome Editing

Let’s embark on a journey through the labyrinth of our genetic blueprint, scientists wield a powerful new tool, epigenome editing. Imagine having the ability to fine tune the orchestra of our genes, adjusting the volume of each instrument to compose the perfect symphony of life. In a groundbreaking study recently unveiled in Nature Genetics, researchers from the Hackett Group at EMBL Rome have unveiled a modular epigenome editing platform. This revolutionary system offers a glimpse into the intricate dance between our DNA and the proteins that regulate it, shedding light on how subtle molecular tweaks can orchestrate the grand narrative of biological existence. Join us as we delve into the captivating realm of chromatin modifications, CRISPR technology, and the tantalizing secrets they unveil about gene regulation.

CRISPR CAS9 technology

The researchers used CRISPR technology to precisely program nine important chromatin marks in the genome. The CRISPR technology served as the magic wand in the hands of researchers, enabling them to meticulously sculpt the epigenetic landscape of the genome. With CRISPR’s unparalleled precision and accuracy, scientists from the Hackett Group at EMBL Rome were able to program nine crucial chromatin marks at precise locations within the genome. This level of control allowed them to investigate the cause-and-consequence relationships between these chromatin modifications and gene regulation. CRISPR technology facilitates the development of reporter systems, which enable researchers to measure changes in gene expression at the single-cell level. This high-resolution analysis provides deeper insights into the dynamics of gene regulation and allows for the exploration of how different factors, such as chromatin structure and DNA sequence, interact to modulate gene activity. Additionally, CRISPR facilitated the creation of a ‘reporter system’, empowering researchers to measure changes in gene expression at the single-cell level. This enabled them to investigate the causal relationships between chromatin marks and gene regulation, shedding light on how these marks affect transcription, the process of copying genes into mRNA for protein synthesis. By employing a reporter system, they could measure changes in gene expression at the single-cell level and explore how DNA sequence influences the effects of each chromatin mark.

CRISPR Cas9 technology

Surprisingly, they discovered a new role for a chromatin mark called H3K4me3, which was previously thought to be a consequence of transcription. Their findings suggest a complex regulatory network involving multiple factors such as chromatin structure, DNA sequence, and genomic location.The researchers aim to further explore the implications of their findings by targeting genes across different cell types and at scale. This technology not only provides insights into the role of epigenetic changes in gene activity during development and disease but also offers potential applications in precision health by enabling the programming of desired gene expression levels.

The research conducted at he Hackett Group at EMBL Rome connects to a topic we have done in AP Biology. This is Gene Expression and Regulation. gene expression and regulation are fundamental concepts that delve into how genetic information stored in DNA is utilized by cells to produce proteins and carry out various functions. Here’s how the study conducted by scientists from the Hackett Group at EMBL Rome connects to gene expression and regulation in AP Biology. Chromatin Modifications and Transcription. The study investigates how chromatin modifications, such as histone methylation, influence the process of transcription, where genes are copied into mRNA molecules. This aligns with the AP Biology curriculum’s focus on understanding the role of chromatin structure in regulating access to DNA and controlling gene expression. Another way is Regulatory Mechanisms. The study provides insights into the regulatory mechanisms that govern gene expression by examining the causal relationships between chromatin marks and transcriptional activity. Students can learn about the intricate interplay between transcription factors, chromatin modifications, and regulatory DNA sequences in controlling gene expression levels.

Gene Editing Could Cure Sickle Cell Disease

Do you know anybody with sickle cell disease? Sickle cell disease is the most common genetic blood disorder in the world. 70,000 to 100,000 Americans have it. It’s very likely that you know of someone who suffers from the disease or carries the gene.

Sickle cell anemia, a form of sickle cell disease, is caused by a gene mutation that changes the shape of the hemoglobin protein. The shape change causes blood cells which should be round, to be a sickle, curved shape. The deformed cells can clog blood vessels, causing severe pain and other dangerous symptoms. Another form of sickle cell disease is called beta-thalassemia which occurs when the body doesn’t produce enough hemoglobin and red blood cells, leading to low oxygen levels. As a result, children experience growth issues and fatigue.

Sickle Cell Anaemia red blood cells in blood vessels

CRISPR Therapeutics and Vertex have created a treatment called exa-cel, which uses gene editing to cure the disease for at least a year. In December of 2023, the FDA approved this treatment, making the U.S. the second country to approve a CRISPR therapy, following the U.K in November. A company called bluebird bio created another type of gene therapy called lovo-cel, which was approved by the FDA as well.

In exa-cel, the CRISPR system targets the genes that produce hemoglobin. Sickle celled anemia is caused by mutations in the gene HBB. The mutation distorts the structure of hemoglobin, which is what causes the blood cells to to have a curved shape instead of round. Exa-cel helps Cas9, an enzyme, target a gene called BCL11A. This gene stops the body from making a type of hemoglobin only found in fetuses. With Cas9, exa-cel cuts its DNA, which switches off BCL11A in bone marrow stem cells, where red blood cells are produced. As a result, the cells start making the fetal hemoglobin they were originally unable to produce, leading to the creation of healthy-shaped red blood cells. In this new treatment, doctors take out a person’s bone marrow stem cells, edit them with exa-cel, dispose of the rest of their untreated bone marrow, and then put the edited cells back in.

As learned in AP Biology, deletions in DNA can change the process of gene expression. The first part of gene expression is transcription, which happens in three steps: initiation, elongation, and termination. In initiation, the enzyme RNA polymerase binds to a region on a gene called the promoter. This then signals the DNA strand to unwind which allows the RNA polymerase to read the bases. Then in elongation, the RNA polymerase reads the DNA and makes an mRNA strand with complimentary base pairs. During termination, the RNA polymerase crosses a stop sequence, the mRNA strand is complete, and it detaches from the DNA strand. The mRNA then goes on to translation, which is when it is read to make proteins. When exa-cel deletes the DNA that codes for the BCL11A gene, it is never transcribed or translated, it is never expressed, and therefore the body can produce hemoglobin.

Since these modified cells replenish the body over time, exa-cel is seen as a “curative” treatment that is expected to last for the recipient’s lifetime. However, Vertex and CRISPR Therapeutics have only monitored most of their trial participants for less than two years. While nobody is certain that the treatment is permanent and without side effects, this type of gene editing is very significant to the scientific world, and could help thousands of people!

Exa-cel has be tested in about 100 individuals diagnosed with either sickle cell anemia or beta-thalassemia. However, in 2019, the FDA granted the companies a “fast-track” approval, enabling them to test the therapy in smaller groups than what is typically required.

In these ongoing trials, 29 of the 30 participants with sickle cell anemia didn’t experience any pain for one year following their exa-cel transfusions out of the 18 months under observation. Additionally, after receiving exa-cel, 39 out of 42 patients with beta-thalassemia didn’t require blood or bone marrow transplants (standard treatments for the disease) for one year. Vertex and CRISPR Therapeutics plan to track all participants for up to 15 years.

While some could arise earlier, so far the only negative side effects of the treatment are fever and nausea. Additionally, the FDA is worried that the Cas9 enzyme might stay active and cut the genome in places other than BCL11A, leading to what’s called off-target mutations. However, the companies looked into the places where the enzyme would most likely cut in the genome and luckily didn’t find any signs of this happening in the trial participants.
Similar to many gene editing treatments, exa-cel and lovo-cell are estimated to be very expensive. Vertex, CRISPR Therapeutics, and Bluebird Bio have not disclosed the price, but projections indicate they could reach up to $2 million per patient. It is also unclear whether or not the treatment would be covered by insurance, specifically government programs like Medicaid. This is of particular concern given that sickle cell disease predominantly affects people of African descent. African Americans are more reliant on public insurance like Medicaid compared to other groups in the United States.
These treatments are a huge breakthrough in science and could help thousands of people. Unfortunately, they are inaccessible to most people. What do you think these companies can do to make them more accessible? I invite any and all comments to share!

Can We Alter Mammals Social Behavior Using CRISPR Gene Editing Mechanisms?

At Georgia State University a team of researchers led by professor H. Elliott Albers and Professor Kim Huhman put gene editing mechanisms to the test to determine if it was possible to alter hamsters behaviors. The hamsters that were utilized in this experiment were Syrian hamsters. These hamsters have been extremelGolden hamster front 1y important in many scientific experiments that look into social behaviors, aggression and communication. Furthermore, hamsters are widely used in scientific research due to the fact that their social skills resemble most similarly to humans.

 

In this experiment, professor H. Elliott Albers and Professor Kim Huhman utilized CRISPR-Cas9 technology to deactivate neurochemical signaling pathways that play a major part in controlling mammalian social behaviors. The regulators of the social phenomena that controls pair bonding, cooperation, social communication, dominance and aggression are the hormone vasopressin and the receptor it acts on, Avpr1a. VasopressinSek

After the gene editing and the observation of the hamsters were complete, the researchers were shocked by their unexpected results. As stated by Professor H. Elliott Albers,  he “anticipated that if we eliminated vasopressin activity, we would reduce both aggression and social communication. But the opposite happened.”

Instead of reducing the hamsters’ aggression and social communication, the absence of the receptor that activates the vasopressin led the hamsters to demonstrate increased levels of social communication behaviors than when observed prior to the gene editing. Furthermore, it was observed that the differences in opposite sex aggression were removed. Both the male and female hamsters showed aggression towards other same-sex hamsters.  

This shocking finding led the researchers to a different conclusion than foreseen. Because it is known that vasopressin correlates with the increase of social behaviors, it can be concluded that the Avpr1a receptor is inhibitory

Moreover, confirming this study done at Georgia State University, another study published in the Proceedings of the National Academy of Sciences, finds that that eliminating the Avpr1a receptor in hamsters windes up deactivating the vasopressin’s action on the receptor, therefore changing the social behavior of the hamsters drastically in ways one would not expect.

Overall, Professor H. Elliott Albers contends that this study is of extreme value as it helps researchers understand the“neurocircuitry involved in human social behavior and our model has translational relevance for human health. Understanding the role of vasopressin in behavior is necessary to help identify potential new and more effective treatment strategies for a diverse group of neuropsychiatric disorders ranging from autism to depression.”

Connection to AP Biology 😀

This study is connected to our AP biology class as we have learned about regulation of gene expression. Without the presence of the Avpr1a receptor, the vasopressin has no way to be mediated, thus enhancing its social behavioral effects. And with the presence of the Avpr1a receptor, the vasopressin is still active, however, muted. 

Maternal Stress During Pregnancy

According to researchers at the University of Cincinnati, maternal stress during pregnancy has a harmful effect on the neurodevelopment of babies. A methyl group gets added to DNA, which is called DNA methylation. This likely plays a role in it. The findings could provide new insight into how the fetal environment potentially influences neurodevelopment, metabolism, and immunologic functions. 

DNA methylation

More than 5,500 people took part in this study, which broke down into 12 different groups. The research examines financial stress, conflict with a partner, conflict with a family member or friend, abuse, and death of a friend or relative. Plus, there is a cumulative score that combines all these categories. 

Two young people demonstrating combat

They found that mothers experienced a great amount of stress during pregnancy. There was an association with DNA methylation in the umbilical cord blood, which is an epigenetic modification in the baby’s development. They found five specific locations of DNA methylation with three different maternal stressors. The three different maternal stressors were conflict with a friend or family, abuse, and death of a close friend or relative.  

Epigenetics modifications

In AP Biology, we have learned that DNA methylation causes nucleosomes to pack tightly together, which prevents transcription factors from binding to the DNA. Gene expression is the process of turning on a gene to produce protein and RNA. 

The researchers plan to further investigate and do some functional analyses to see how the genes work and how the DNA methylation affects their expression. 

 

CRISPR corrects genetic diseases in mice!

Researchers at Duke University have shown that a single systemic treatment using CRISPR genome editing can safely correct Duchenne muscular dystrophy (DMD) in mice for over a year. In 2016 the first successful use for CRISPR to treat an animal model of a genetic disease was published by, Charles Gersbach, the Professor of Biomedical Engineering at Duke. The strategy used by Gersbach can potentially be used for human therapy.

 

Since 2009, Gersbach has been working on finding a genetic treatment for DMD and his lab was one of the firsts to focus on CRISPR, which is a defense system that slices apart the DNA of invading viruses.The goal was to cut out the dystrophy exons around the mutation and then let the body naturally repair the DNA and stitch it back together to create a shortened dystrophy gene. After eight weeks it was observed in the mice used for the experiment that functional dystrophin was restored and muscle strength increased but the long term effects of the treatment had not been explored.

GRNA-Cas9

The new goal of Gersbachs study was to figure out these long term effects. To determine this, doctor Christopher Nelson gave both adult and newborn mice with the dystrophy gene a dose of CRISPR. The mice were monitored over the year to see what kind of genetic alterations were made as well as any immune responses. There were no results of toxicity in any of the mice. Although this is a positive result Gersbach and Nelson know that a mouse immune system can function differently than a human immune system which brings further questions of reliability of CRISPR in humans to the table.

 

In my AP biology class we recently learned about gene expression. CRISPR systems have been engineered to control gene expression in bacteria. CRISPR is used to target precise parts of DNA which could help to correct abnormalities that cause diseases.

Bacteria Not So “Bad”, After All?

Photo Link: Wild Garden of Gut Bacteria, By: Nicola Fawcett

Most of us are used to the common notion that bacteria may not be the most beneficial factor in maintaining your health.  Thats why the results of a recent research study conducted by scientists at Babraham Institute in collaboration with colleagues in Brazil and Italy, yielding evidence that in fact good bacteria in the gut can control gene expression in our cells, is game-changing!

The research team, led by Patrick Varga-Weisz, made this discovery by studying the gut bacterias found within various mice. Their attention was quickly drawn to the mice that had lost most of their gut bacteria. It became apparent that in the mice with a very low amount of the bacteria within their gut, contained increased amounts of the “HDAC2 protein”.  When investigating deeper into HDAC2, it was found that increased amounts of this particular protein are associated with increased risk of colorectal cancer.

This new research also resulted in the finding that the amount of chemical markers on our genes, are increased by short fatty acids. These specific chemical gene markers, known as “crotonylations”, were only recently discovered and are newly classified as genome “epigenetic markers”. The researchers then found that by shutting down the HDAC2 protein, short chain fatty acids increase the number of crotonylations.

Ingestion of fruits and vegetables into ones healthy diet are vital – ultimately determining how chemicals produced by gut bacteria, affect genes in the cells of the gut lining. In other words, the short fatty acids, which come from those dietary elements, have the ability to move from bacteria into our own cells, and from there cause changes in gene activity and cell behavior.

In the end, the scientists were strongly convinced that the ability to turn off and on genes, is determined by changes in crotonylation. This inferred that the existence of crotonylation in the genome of cells is vital to protect the body from cancer. Therefore, the pretense of good bacteria is very important for the prevention of disease and illness in the body!

As someone with a strong passion for the science, and also very influenced and intrigued by medicine, I very much enjoyed this study. As the boundary to curing cancer is still a hurtle doctors and scientists try to transcend everyday, studies like these, are both hopeful and fascinating, to me. Also, as someone curious about how the human diet ultimately affects the functions and inner workings of the body, this research again was very engaging and interesting!

Primary Source Article: How good bacteria controls your genes

Secondary Source: Wikipedia – Gut Flora (Gut Bacterias)

 

The Difference between You and a Chimpanzee!

The largest difference between you and a chimpanzee or a monkey can be found in the brain. Despite the fact that all regions of the human brain have very similar molecular signatures to your primate relatives, a new study has found that these regions contain distinct human patterns of gene activity that mark the brain’s evolution. This new study may contribute to our cognitive abilities.

Although human brains are three times larger and have many more cells and therefore more processing power than a chimpanzee, researchers, Zhu and Sousa, have found similarities between humans and our primate relatives in gene expressions in 16 regions of the brain.  A gene similarity was even found in the prefrontal cortex, a place where higher order learning takes place that most distinguishes humans from other apes. However researchers have also found that the striatum had the most human-specific gene expression, a region most commonly associated with movement.

A surprising difference was found in the cerebellum, one of the evolutionarily most ancient regions of the brain, and therefore most likely to share similarities across species. Researches found the gene ZP2, a gene active in only the human cerebellum, which is surprising considering the same gene has been linked to sperm selection by human ova. Zhu, a postdoctoral researcher, says that they, “have no idea what it is doing there.”

Researchers Zhu and Sousa have focused on one gene, TH, which is involved in the production of dopamine. TH is a neurotransmitter crucial to higher-order function and depleted in people living with Parkinson’s disease. They found that TH was highly expressed in human neocortex and striatum but absent from the neocortex of chimpanzees.

This research could be important in finding the cure to certain diseases like Parkinson’s disease. Also would be helpful in understanding how the human mind processes higher-order actions.

How A Chemical From the Cypress Tree Could Advance Epigenetics Against Cancer

by Czechmate on Wikimedia Commons

Found in the essential oil extracted from the bark of a cypress tree, a chemical named hinokitiol shows potential to impact epigenetic tags on DNA and stop the activity of genes that assist the growth of tumors.

In order to develop an of understanding cancer, researches have had to comprehend the DNA methylation, an epigenetic function which controls gene expression. In regular DNA methylation, genes that work to fight against tumors are turned on, reducing the risk of cancer. However, if DNA methylation is negatively altered, then those cancer-fighting genes will be silenced, helping to progress cancer development. Scientists have tried to combat irregular DNA methylation and over-silencing of genes by creating epigenetic anti-cancer medications that reverse non-beneficial methylation effects. Like in most cases of medication usage, the users face unappealing side effects. Hinokitiol is attractive to scientists because it is a natural compound with many health benefits and way less side effects than modified drugs that can possibly cause mutagenesis and cytotoxicity.

 

Researchers from the Korea University College of Medicine tested the productivity of the hinokitiol chemical in a study by giving doses of it to colon cancer cells. It was found that this chemical helped to inhibit the colon cancer cells efficiency without affecting the colon cells without cancer. The scientists also found through careful inspection that the presence of hinokitiol decreases the expression of proteins DNMT1 and UHRF1; both of which are proteins that encourage carcinogenesis. In summary, the doses of hinokitiol appear to have allowed normal cells to remain healthy, while reducing the ability for the colon cancer cells to thrive and ceasing the production of proteins that promote cancer maturation.

Researchers are continuing their search for natural compounds, as opposed to artificial medications, that can prevent the flourishing of cancer in our bodies through playing a positive role in gene expression and DNA methylation.

http://www.whatisepigenetics.com/cypress-trees-epigenetically-protect-cancer/

 

 

https://commons.wikimedia.org/wiki/File:Raindrops_on_leyland_cypress.jpg

The Gene Switch

Researchers at the Stowers Institute for Medical Research have created a high-resolution mechanism to “precisely and reliably map individual transcription factor binding sites in the genome.” This new technique, published in Nature Biology today, has proven to be more efficient and successful than those previously studied.

All of the cells in an organism carry DNA; however different cells in the body express different portions of it to function properly. For instance, nerve cells express genes that facilitate them carrying messages to other nerve cells. This process is known as gene expression and is responsible for making our bodies function the way we do. Despite our limited knowledge on gene expression, researchers are aware that it is is controlled by proteins called transcription factors that bind to specific sites around a gene and,  in the right order, allow the gene’s sequence to be read.

Transcription factor binding sites in DNA are extremely difficult to locate but, thanks to new technology, it is becoming easier to track their location. “The transcription factor binding sites that are likely functional leave behind clear footprints, indicating that transcription factors consistently land on very specific sequences. In contrast, questionable binding sites that were previously detected as bound showed a more scattered unspecific pattern that was no longer considered bound.”

These techniques are implemented through a method called chromatin immunoprecipitation or ChIP, a tool that determines the relativity of the proteins to their positions on the DNA, cuts the DNA into reasonable sizes, and then isolates the sections that are bound by the proteins. While the research is largely preliminary, scientist Zeitlinger attests to the significance of this creation; ”If we do this kind of analysis for lots of transcription factors, we will gather information needed to better understand gene expression.”

chIP

chIP mechanism

The Harm Stress Causes

http://upload.wikimedia.org/wikipedia/commons/c/c6/DNA_double_helix_45.PNG

https://www.sciencenews.org/article/chronic-stress-can-wreak-havoc-body

Recently scientists have begun to discover why stress can have a negative effect on the human body. Although stress is needed when dealing with situations which require hormones to trigger a fight or flight, consistent stress can lead to a multitude of health problems. Chronic stress can lead to mental instability, and an increased risk in heart attacks, strokes, infection, etc. The decrease in health is due to inflammation and warped genetic material caused by epigenetics (chemical interactions that activate and deactivate regions of a genome to carry out specific functions). Recently scientists have discovered that  changes in epigenetics can affect activity levels in genes which directly change responsibilities of certain cells including immune cells. The stress causes a genetic response that deactivates certain areas of a genome which stops an immune cell from working properly, which of course leads to an increase in diseases that cannot be properly taken care of. Hopefully, as we continue to understand epigenetics, we will be able to take appropriate steps that will both further our understanding of the human genome, as well as help increase the longevity and immune system of individuals.

Save the Devils

When most people hear the name Tasmanian Devil, they think of the small and ferocious little animal from the Looney Tunes named Taz. Just like in the show, Tasmanian Devils (carniverous marsupials)  are tough, rugged and very aggressive animals. Unfortunately, over the past two decades, a rare case of contagious facial cancer, with a 100% mortality rate, has decimated the population. Scientists have estimated that this specific cancer has wiped out about 85% of the entire population, almost to the point of extinction. The cancer is typically spread when the Devils bite each other in the face during battle, killing it in a matter of months. Scientists are working tirelessly to find out how this cancer is slipping by the immune system and hope to find a cure.

Until recently, scientists believed that the cancer was able to develop, without

being detected by the immune system, because Tasmanian Devils lack genetic diversity. However, a study led by the University of Cambridge claims it is much more complex. On the surface of most cells are histocompatability complex (MCH) molecules, which determine whether other cells are good or bad. If the cell happens to be a threat, then the cell triggers an immune response. According to the research, these DFTD cancer cells lack theses complexes and can therefor avoid detection.

Researchers also found that the DFTD cells have just lost the expression of MCH molecules and that its genetic code is still in tact (it can be turned on). By introducing specific signaling molecules, scientists believe they can force the DFTD cells to express these molecules, leading to the detection of the cancer. Not only will this research help save the Devils, but it will also give scientists a head start on contagious cancers in other species when the time comes.

Breakthrough in Epigenetics!

 

This file (Arabidopsis thaliana flower) is in public domain, not copyrighted, no rights reserved, free for any use

 

For several dozen years scientists have searched for a way to understand the role of a single RNA strand in gene expression.  Scientists have been without a method to pinpoint 1 type of RNA strand and isolate its effect thus discovering its influence and its corresponding proteins role in influencing the way our bodies work.

However a breakthrough was made this march regarding such obstacles.  A team of scientists from Michigan Technological University discovered a way to turn off small RNA strands in order to figure out what they are up to.  They did this by inserting their own custom DNA strand that codes for something called a small tandem target mimic or “STTM” into a plant known as “Arabidopsis“.  Inside the plant, these DNA strands gave rise to STTM’s that blocked the ability of a target RNA to express itself.  The particular target for the STTM was a type of RNA strand suspected to be involved with facilitating vertical growth of the plant.  The STTM’s stopped the RNA from being able to cut itself into smaller bits, and prompted the target RNA’s to destroy all of its own smaller RNA’s that would normally slice the target RNA.  This effectively lead to the disappearance of the target RNA’s protein products thus resulting in no expression of the gene the target RNA from transcribed from.

The result was outstanding.  “The control Arabidopsis plants grew upward on a central stem with regularly shaped leaves and stems. The mutant plants were smaller, tangled, and amorphous.”

The above process is said to be “a highly effective and versatile tool” for studying the functions of small RNA.  One researcher on the team who discovered this method stated that she intends to use this discovery to study type 2 diabetes.

 

Reference

http://www.sciencedaily.com/releases/2012/03/120301143756.htm

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