Posts tagged genome
Articles and news from the latest research reports.
Epigenetic processes orchestrate neuronal migration
Neurobiologists at the Friedrich Miescher Institute for Biomedical Research (FMI) are the first to show that directional migration of neurons during brain development is controlled through epigenetic processes. In an elaborate study bridging epigenetics and neurobiology, the scientists found that the migratory pattern is orchestrated through epigenetic regulation of genes within neurons and spatial signals in the environment. Their study has been published in Science.
As the foundation for our mind is laid, 100 billion cells are formed and appropriately connected in the brain. Despite the huge number of cells, no aspect of this process is left entirely to chance. Neurons divide, take on defined identities, migrate to the correct nodes in the network and send out their connecting axons along predefined paths to make contact with specific target neurons. The blueprint for these arrangements is encoded in the genome. However, how coordinated transcription of genes is finely tuned to achieve the precision of these processes is not yet clear.
A study by the research group of Filippo Rijli, group leader at the FMI and Professor of Neurobiology at the University of Basel, shows now for the first time that long-distance neuronal migration in the developing brain is regulated through transcriptional programs that are epigenetically controlled.
In their study published in Science, the neurobiologists have looked at a part of the brain called the brain stem and, in particular, at the neuronal ensembles forming the so-called precerebellar pontine nuclei. These nuclei are particularly important for the relay of information from the sensory and motor cortex to the cerebellum. During development, neurons, which will gather to form the pontine nuclei, migrate a long way from a distant progenitor compartment to their final positions, where they form connections that are vital for coordinated movement. The migratory path of these cells is defined by the relative position of the neuron in the progenitor compartment and is controlled by its specific combinatorial expression of Hox genes. Hox genes encode transcription factors and play an important role in many developmental processes that rely on a body plan and confer cellular identity.
It has been known that neurons in the precerebellar pontine nuclei start to migrate in the wrong direction as soon as their Hox identity has been disrupted. The Rijli team has now shown that epigenetic processes control the maintenance of appropriate Hox expression during migration. The key player in this scenario is a major contributor to mammalian epigenetic control, the histone methyl-transferase Ezh2. Ezh2 methylates histones and silences specific stretches of DNA, thus maintaining certain Hox genes repressed, while allowing expression of others.
Ezh2 also regulates the appropriate response to environmental clues that direct neuronal migration. The cells in the brain stem bathe in a sea of attractants and repellants. They respond to these stimuli depending on their identity and adapt their migratory paths. Rijli and colleagues found that Ezh2 controls transcription of both environmental Netrin, a neuronal attractant molecule and of its repellant receptor Unc5b in migrating neurons, such that the appropriate balance between attraction and repulsion is maintained throughout migration to keep neurons on track.
“Being able to link epigenetic regulation with a complex process such as long-distance directional neuronal migration during brain development is extremely exciting,” comments Rijli. “All the more we were delighted to see that the migratory pattern is not only epigenetically maintained through an intrinsic program established in the progenitor, but is also coordinated with an Ezh2-dependent silencing program that regulates the spatial distribution of extrinsic signals in the migratory environment. The knowledge gained from our studies contributes as well to our understanding of certain neurological syndromes that are caused by faulty neuronal migration and are currently incurable.”
(Source: fmi.ch)
Cheap and easy technique to snip DNA could revolutionize gene therapy
A simple, precise and inexpensive method for cutting DNA to insert genes into human cells could transform genetic medicine, making routine what now are expensive, complicated and rare procedures for replacing defective genes in order to fix genetic disease or even cure AIDS.
Discovered last year by Jennifer Doudna and Martin Jinek of the Howard Hughes Medical Institute and University of California, Berkeley, and Emmanuelle Charpentier of the Laboratory for Molecular Infection Medicine-Sweden, the technique was labeled a “tour de force” in a 2012 review in the journal Nature Biotechnology.
That review was based solely on the team’s June 28, 2012, Science paper, in which the researchers described a new method of precisely targeting and cutting DNA in bacteria.
Two new papers published last week in the journal Science Express (1 , 2) demonstrate that the technique also works in human cells. A paper by Doudna and her team reporting similarly successful results in human cells has been accepted for publication by the new open-access journal eLife.
“The ability to modify specific elements of an organism’s genes has been essential to advance our understanding of biology, including human health,” said Doudna, a professor of molecular and cell biology and of chemistry and a Howard Hughes Medical Institute Investigator at UC Berkeley. “However, the techniques for making these modifications in animals and humans have been a huge bottleneck in both research and the development of human therapeutics.
“This is going to remove a major bottleneck in the field, because it means that essentially anybody can use this kind of genome editing or reprogramming to introduce genetic changes into mammalian or, quite likely, other eukaryotic systems.”
“I think this is going to be a real hit,” said George Church, professor of genetics at Harvard Medical School and principal author of one of the Science Express papers. “There are going to be a lot of people practicing this method because it is easier and about 100 times more compact than other techniques.”
“Based on the feedback we’ve received, it’s possible that this technique will completely revolutionize genome engineering in animals and plants,” said Doudna, who also holds an appointment at Lawrence Berkeley National Laboratory. “It’s easy to program and could potentially be as powerful as the Polymerase Chain Reaction (PCR).”
The latter technique made it easy to generate millions of copies of small pieces of DNA and permanently altered biological research and medical genetics.
Editing the genome with high precision
Researchers at MIT, the Broad Institute and Rockefeller University have developed a new technique for precisely altering the genomes of living cells by adding or deleting genes. The researchers say the technology could offer an easy-to-use, less-expensive way to engineer organisms that produce biofuels; to design animal models to study human disease; and to develop new therapies, among other potential applications.
To create their new genome-editing technique, the researchers modified a set of bacterial proteins that normally defend against viral invaders. Using this system, scientists can alter several genome sites simultaneously and can achieve much greater control over where new genes are inserted, says Feng Zhang, an assistant professor of brain and cognitive sciences at MIT and leader of the research team.
“Anything that requires engineering of an organism to put in new genes or to modify what’s in the genome will be able to benefit from this,” says Zhang, who is a core member of the Broad Institute and MIT’s McGovern Institute for Brain Research.
Zhang and his colleagues describe the new technique in the Jan. 3 online edition of Science. Lead authors of the paper are graduate students Le Cong and Ann Ran.
Early efforts
The first genetically altered mice were created in the 1980s by adding small pieces of DNA to mouse embryonic cells. This method is now widely used to create transgenic mice for the study of human disease, but, because it inserts DNA randomly in the genome, researchers can’t target the newly delivered genes to replace existing ones.
In recent years, scientists have sought more precise ways to edit the genome. One such method, known as homologous recombination, involves delivering a piece of DNA that includes the gene of interest flanked by sequences that match the genome region where the gene is to be inserted. However, this technique’s success rate is very low because the natural recombination process is rare in normal cells.
More recently, biologists discovered that they could improve the efficiency of this process by adding enzymes called nucleases, which can cut DNA. Zinc fingers are commonly used to deliver the nuclease to a specific location, but zinc finger arrays can’t target every possible sequence of DNA, limiting their usefulness. Furthermore, assembling the proteins is a labor-intensive and expensive process.
Complexes known as transcription activator-like effector nucleases (TALENs) can also cut the genome in specific locations, but these complexes can also be expensive and difficult to assemble.
Precise targeting
The new system is much more user-friendly, Zhang says. Making use of naturally occurring bacterial protein-RNA systems that recognize and snip viral DNA, the researchers can create DNA-editing complexes that include a nuclease called Cas9 bound to short RNA sequences. These sequences are designed to target specific locations in the genome; when they encounter a match, Cas9 cuts the DNA.
This approach can be used either to disrupt the function of a gene or to replace it with a new one. To replace the gene, the researchers must also add a DNA template for the new gene, which would be copied into the genome after the DNA is cut.
Each of the RNA segments can target a different sequence. “That’s the beauty of this — you can easily program a nuclease to target one or more positions in the genome,” Zhang says.
The method is also very precise — if there is a single base-pair difference between the RNA targeting sequence and the genome sequence, Cas9 is not activated. This is not the case for zinc fingers or TALEN. The new system also appears to be more efficient than TALEN, and much less expensive.
The new system “is a significant advancement in the field of genome editing and, in its first iteration, already appears comparable in efficiency to what zinc finger nucleases and TALENs have to offer,” says Aron Geurts, an associate professor of physiology at the Medical College of Wisconsin. “Deciphering the ever-increasing data emerging on genetic variation as it relates to human health and disease will require this type of scalable and precise genome editing in model systems.”
The research team has deposited the necessary genetic components with a nonprofit called Addgene, making the components widely available to other researchers who want to use the system. The researchers have also created a website with tips and tools for using this new technique.
Engineering new therapies
Among other possible applications, this system could be used to design new therapies for diseases such as Huntington’s disease, which appears to be caused by a single abnormal gene. Clinical trials that use zinc finger nucleases to disable genes are now under way, and the new technology could offer a more efficient alternative.
The system might also be useful for treating HIV by removing patients’ lymphocytes and mutating the CCR5 receptor, through which the virus enters cells. After being put back in the patient, such cells would resist infection.
This approach could also make it easier to study human disease by inducing specific mutations in human stem cells. “Using this genome editing system, you can very systematically put in individual mutations and differentiate the stem cells into neurons or cardiomyocytes and see how the mutations alter the biology of the cells,” Zhang says.
In the Science study, the researchers tested the system in cells grown in the lab, but they plan to apply the new technology to study brain function and diseases.
The evolution of human intellect: Human-specific regulation of neuronal genes
A new study published November 20 in the open-access journal PLOS Biology has identified hundreds of small regions of the genome that appear to be uniquely regulated in human neurons. These regulatory differences distinguish us from other primates, including monkeys and apes, and as neurons are at the core of our unique cognitive abilities, these features may ultimately hold the key to our intellectual prowess (and also to our potential vulnerability to a wide range of ‘human-specific’ diseases from autism to Alzheimer’s).
Exploring which features in the genome separate human neurons from their non-human counterparts has been a challenging task until recently; primate genomes comprise billions of base pairs (the basic building blocks of DNA), and comparisons between the human and chimpanzee genomes alone reveal close to 40 million differences. Most of these are thought to merely reflect random ‘genetic drift’ during the course of evolution, so the challenge was to identify the small set of changes that have functionally important consequences, as these might help to explain the genomic basis of the emergence of human-specific neuronal function.
The key to the present study, led by Dr Schahram Akbarian of the University of Massachusetts and the Mount Sinai School of Medicine, was not to focus on the “letters” of the DNA code, but rather on what might be called its “font” or “typeface”—the DNA strands of the genome are wrapped in protein to make a chromatin fiber, and the way in which they are wrapped, the “chromatin state”, in turn reflects the regulatory state of that region of the genome (e.g. whether a given gene is turned on or off). This is the field that biologists call “epigenetics”—the study of the “epigenome”.
Dr Akbarian and colleagues set out to isolate small snippets of chromatin fibers from the frontal cortex, a brain region involved in complex cognitive operations. They were then able to analyze these snippets for the chemical signals (histone methylation) that define the regulatory state (on/off) of the chromatin. The results of their analysis identified hundreds of regions throughout the genome which showed a markedly different chromatin structure in neurons from human children and adults, compared to chimpanzees and macaques.
This treasure trove of short genomic regions is now providing researchers with interesting new leads involving the evolution of the human brain. Although some of the regions have remained unchanged during primate evolution, some more tantalizing ones have recently changed, having a DNA sequence that is unique to humans and our close extinct relatives, the Neanderthals and the Denisovans.
The study also uncovered examples where several of these regulatory DNA regions appear to physically interact with each other inside the cell nucleus, despite being separated by hundreds of thousands of base pairs on the linear genome. This phenomenon of “chromatin looping” is implicated in controlling the expression of neighboring genes, including several with a critical role for human brain development. The study, from laboratories based in the United States, Switzerland and Russia, draws further attention to the role of epigenetics and the epigenome in our biology and our evolution. As Dr Akbarian notes, “Much about human biology and disease cannot be deduced by simply sequencing the genome. Mapping the epigenome of neurons and other cells will help us to better understand the inner workings of our brain, and where we are coming from.”
(Source: medicalxpress.com)
Most experimental cancer drugs never make it to market because they don’t help enough people in early clinical trials. But even in “failed” drug trials, researchers may find that a few patients see their tumors shrink dramatically. Since it’s not clear why some respond but most don’t, researchers typically shake their heads and move on. But researchers today report that by sequencing the entire genome of one outlier patient’s tumor, they learned why her cancer disappeared when she took an experimental drug that didn’t help others. That drug now has a new lease on life for this cancer, and such testing may help revive other cancer drugs that showed promise in lab studies but initially failed in clinical testing.