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Archive - Aug 26, 2013

Breakthrough in TALE-Based DNA Editing Technology

Scientists at The Scripps Research Institute (TSRI) have found a way to apply a powerful new DNA-editing technology more broadly than ever before. “This is one of the hottest tools in biology, and we’ve now found a way to target it to any DNA sequence,” said Dr. Carlos F. Barbas III, the Janet and Keith Kellogg II Chair in Molecular Biology and Professor in the Department of Chemistry at TSRI. The breakthrough concerns a set of designer DNA-binding proteins called TALEs, which biologists increasingly use to turn on, turn off, delete, insert, or even rewrite specific genes within cells—for scientific experiments and also for potential biotech and medical applications, including treatments for genetic diseases. TALE-based methods had been considered useful against only a fraction of the possible DNA sequences found in animals and plants, but the new finding removes that limitation. Dr. Barbas and his team reported their finding on August 26, 2013 in an advance online edition of the journal Nucleic Acids Research. Molecular biologists have long dreamt of being able to manipulate DNA in living cells with ease and precision, and by now that dream is nearly a reality. TALE-based designer proteins, introduced just a few years ago, are arguably the most user-friendly and precise DNA-directed tools that have yet been invented. Designer TALEs (transcription-activator-like effectors) are based on natural TALE proteins that are produced by some plant-infecting bacteria. These natural TALEs help bacteria subvert their plant hosts by binding to specific sites on plant DNA and boosting the activity of certain genes—thereby enhancing the growth and survival of the invading bacteria. Scientists have found that they can easily engineer the DNA-grabbing segment of TALE proteins to bind precisely to a DNA sequence of interest.

Researchers Discover That Cohesin Stabilizes DNA

Dr. Jan-Michael Peters and his team at the Research Institute of Molecular Pathology (IMP) in Vienna, Austria, have found that the structure of chromosomes is supported by a kind of molecular skeleton, made of cohesin. This discovery was reported online on August 25, 2013 in Nature. Every single cell in the human body contains an entire copy of the genetic blueprint, the DNA. Its total length is about 3.5 meters and all of it has to fit into the cell’s nucleus, just one-hundredth of a millimeter in diameter. Blown up in proportion, this would equal the task of squeezing a 150-km-long string into a soccer ball. Just how the cell manages to wrap up its DNA so tightly is still poorly understood. One way of compacting DNA is achieved by coiling it tightly around histone proteins. This mechanism has been studied in detail and is the focus of an entire discipline, epigenetics. However, simple organisms such as bacteria have to manage their DNA packaging without histones, and even in human cells, histones probably cannot do the job on their own. In its Nature article, Dr. Peters’ IMP research team in Vienna presents evidence for an additional mechanism involved in structuring DNA. IMP Managing Director Dr. Peters and his research group discovered that a protein complex named cohesin has a stabilizing effect on DNA. In evolutionary terms, cohesin is very old and its structure has hardly changed over billions of years. It was present long before histones and might therefore provide an ancient mechanism in shaping DNA. Cell biologists are already familiar with cohesin and its role in cell division. The protein complex is essential for the correct distribution of chromosomes to daughter cells.

RNA Double Helix Structure Identified Using Synchrotron Light

When Francis Crick and James Watson discovered the double-helical structure of deoxyribonucleic acid (DNA) in 1953, their findings began a genetic revolution to map, study, and sequence the building blocks of living organisms. DNA encodes the genetic material passed on from generation to generation. For the information encoded in the DNA to be made into the proteins and enzymes necessary for life, ribonucleic acid (RNA), single-stranded genetic material found in the ribosomes of cells, serves as intermediary. Although usually single-stranded, some RNA sequences have the ability to form a double helix, much like DNA. In 1961, Alexander Rich along with David Davies, Watson, and Crick, hypothesized that the RNA known as poly (rA) could form a parallel-stranded double helix. Some fifty years later now, scientists from McGill University have successfully crystallized a short RNA sequence, poly (rA)11, and used data collected at the Canadian Light Source (CLS) and the Cornell High Energy Synchrotron to confirm the hypothesis of a poly (rA) double helix. The detailed 3D structure of poly (rA)11 was published by the laboratory of McGill Biochemistry professor Dr. Kalle Gehring, in collaboration with Dr. George Sheldrick, University of Göttingen, and Dr. Christopher Wilds, Concordia University. Dr. Wilds and Dr. Gehring are members of the Quebec structural biology association GRASP. The paper was published online on June 27, 2013 in the journal Angewandte Chemie International Edition. “After 50 years of study, the identification of a novel nucleic acid structure is very rare. So when we came across the unusual crystals of poly (rA), we jumped on it,” said Dr. Gehring, who also directs the McGill Bionanomachines training program. Dr.

Antisense Oligo Corrects Transcriptional Abnormalities in Huntington Disease Mice

Findings from postmortem studies of the brains of Huntington's disease (HD) patients suggest that transcriptional dysregulation may be an early step in the pathogenesis of HD before symptoms appear. Other studies report transcriptional alterations in the brains of some mouse models of HD. A new study has found transcriptional changes in mouse striatum which correlate with progressive motor and psychiatric deficits and, most importantly, reports for the first time, that an antisense oligonucleotide (ASO) may be used therapeutically to both correct striatal transcriptional abnormalities and improve motor and behavioral problems. The article is published in the latest issue of the Journal of Huntington's Disease (Volume 2, Number 2, 2013). "Down-regulation of the expression of key molecules at the mRNA level could well be one of the underlying mechanisms leading to neuronal dysfunction in HD," says Lisa M. Stanek, Ph.D., of Genzyme Corporation's Rare Disease Unit, Framingham, Massachusetts. "The data presented here provide strong evidence that transcriptional correction has great potential as a novel therapeutic biomarker for HD." HD is an inherited progressive neurological disorder for which there is presently no cure. It is caused by a dominant mutation in the HD gene leading to expression of mutant huntingtin (HTT) protein (image shows structure of HTT protein). Expression of mutant HTT causes subtle changes in cellular functions, which ultimately results in jerking, uncontrollable movements, progressive psychiatric difficulties, and loss of mental abilities. The current study focuses on what is happening early in the disease process before symptoms or even neuropathological changes are apparent. The authors believe that mutant HTT may be disrupting normal transcriptional processes in susceptible neurons.