Modelling,Genome Wide Association Studies and Blog links

Loads of Reading!

Modelling Reviews:

http://www.nature.com/nrg/series/modelling/index.html

Genome Wide Association Studies Reviews:
http://www.nature.com/nrg/series/gwas/index.html

Also a good Nature Molecular Systems Biology blog called Seven Stones:http://blogs.nature.com/sevenstones/

Related articles

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R-loops break walls of gene silencing

From :http://www.news.ucdavis.edu/search/news_detail.lasso?id=10165

Researchers at the University of California, Davis, have figured out how the human body keeps essential genes switched “on” and silences the vast stretches of genetic repeats and “junk” DNA.

Frédéric Chédin, associate professor in the Department of Molecular and Cellular Biology, describes the research in a paper published today (March 1) in the journal Molecular Cell. The work could lead to treatments for lupus and other autoimmune diseases, by reversing the gene-silencing process known as cytosine methylation.

“R-loops” are the key, say graduate student Paul Ginno, Chédin and colleagues. The loops emerge in the RNA transcription process in DNA sections that are rich in cytosine and guanine, the C and G in the four-letter DNA code. These C and G stretches serve as “on” switches, or promoters, for about 60 percent of human genes.

Scientists have known since the 1980s that these so-called CG island promoters are not subject to methylation. But, Chédin said, the mechanism has been a long-standing mystery.

The UC Davis researchers built a catalog of almost 8,000 CG islands in the human genome, studied their DNA sequences and found the CG sequences to be skewed toward having one strand of the double helix rich in guanine, and the complementary strand rich in cytosine.

Then, in RNA transcription, the G-rich RNA remains stably bound to a C-rich DNA strand, forcing the G-rich DNA strand into a loop — which then prevents methylation.

DNA methylation is considered part of the new field of epigenetics, which studies inheritable genetic changes that are not directly coded in the DNA sequence. However, the new work shows that, at least at CG islands, the epigenetic state is determined by the DNA sequence.

Scientists know that reduced methylation of DNA plays a key role in triggering autoimmunity in lupus, Chédin said. However, the molecular events behind this DNA under-methylation have been unclear.

“Our work establishes that excessive R-loop formation may drive under-methylation and autoimmunity,” Chédin said.

Co-authors: Paul Lott, graduate student; Holly Christensen, undergraduate; and Ian Korf, associate professor in the Department of Molecular and Cellular Biology and the Genome Center.

The National Institutes of Health and the Foundation for Prader-Willi Research supported the project.

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Researchers ask for new focus on ‘sudden death’ heart disorder

An abrupt, fatal heart attack in a young athlete on the playing field is a tragedy destined to repeat itself over and over until more is understood about hypertrophic cardiomyopathy (HCM), a genetic disorder that is the most common cause of sudden death in young people but which affects people of all ages. So says a task force of cardiologists and cardiac biologists, headed by Thomas L. Force, M.D., James C. Wilson Professor of Medicine at Thomas Jefferson University, in the September 14th online edition of the journal Circulation.

Their special report is the culmination of a 1.5-year effort to sum up the relatively little that is known, and much that remains a mystery, about HCM, and to list what future research priorities should be – all with a goal of developing novel treatments. All 21 researcher-physicians, from institutions around the country, participated in an HCM working group convened by the National Heart, Lung, and Blood Institute. HCM is believed to affect 1 in 500 people, yet without a detailed family and genetic history, many people may not know they are at risk for sudden death, says Dr. Force, who, as a nationally-known cardiology investigator, had led a number of symposiums and study groups to focus on causes and novel therapies for patients with sickened hearts.

“Unbelievably to me, this problem is still not understood or even known to exist by many people, and it remains a very challenging disease to treat,” he says. “The medical management of HCM has changed very little over the past decades.”

HCM

HCM is a thickening of a portion of the myocardium (heart muscle) without any obvious cause.A cardiomyopathy is a primary disease that affects the muscle of the heart. With hypertrophic cardiomyopathy (HCM), the sarcomeres (contractile elements) in the heart replicate causing heart muscle cells to increase in size which causes the heart muscle to thicken. In addition, the normal alignment of muscle cells is disrupted, a phenomenon known as myocardial disarray. HCM also causes disruptions of the electrical functions of the heart.[1]

Genetics  of HCM

HCM is most commonly due to a mutation  in one of of 9 sarcomeric genes that results in a mutated protein in the sarcomere, the primary component of the myocyte (the muscle cell of the heart).[1,3]The sarcomere is a network of proteins that make up the molecular motor of the heart and coordinate the contraction and relaxation of the heart muscle.Around two-thirds of all cases of hypertrophic cardiomyopathy are due to mutations in one of three genes, which code for proteins called the beta -myosin heavy chain, the cardiac troponin T, and myosin binding protein-C.[2]

Hypertrophic cardiomyopathy is an autosomal dominant condition. The term autosomal means that the genes which can cause the disease are located on autosomes, and not on sex chromosomes (in humans there are 22 pairs of autosomes and also the X and Y sex chromosomes ).As a result, this condition can affect females and males in equal numbers and the term dominants means that only one copy of the gene needs to be inherited for the disease to develop.[2]

There are also other genes, including genes that are important in maintaining the heart’s energy supply from stored sugar (glycogen),that can cause a condition that mimics HCM, causing a similar-appearing thickening of the heart muscle.[3]

Inheritance of HCM

A person that carries a mutation has a 50% chance of passing the mutation on to his/her children, regardless of whether he/she has an obvious diagnosis.HCM can also arise in people who have no known family history of it. There may be a few reasons for this to happen. The mutation may have arisen spontaneously in that individual during early embryologic development, rather than being inherited from an affected parent. This is referred to as a sporadic or spontaneous mutation and is typically contained in all, or most, of the cells in the body. Therefore,a person with a sporadic mutation has the same 50/50 chance of passing the mutation on to his/her children as a person with an established and recognized family history of HCM. [3]

Task Force Findings

Diagram of the Heart-Blue components indicate de-oxygenated blood pathways and red components indicate oxygenated blood pathways

“The reason it can be deadly is because people with the disease are often unaware that they have it and physical exertion – such as sports – can bring on the sudden, fatal series of events that causes the heart to go into arrest,” Dr. Force says.

HCM patients can also be significantly disabled by heart failure, and atrial and ventricular tachyarrhythmas. A few medical therapies such as implanting a cardiac defibrillator exist for selected, high-risk patients, but most medical therapies have largely focused on alleviating symptoms of the disease, not on altering its natural history, he says.

Because so little is known about HCM, some have lobbied for mass screening of young athletes, but most physicians feel it is impractical and would lead to a lot of false positives. “A cardiac exam in a general practitioner’s office is not very precise, and more detailed examinations such as routine ECGs would likely be prohibitively expensive and might still miss a significant number of children or could needlessly alarm parents and children,” he says. “Some children with HCM have only a minor amount of hypertrophy in their hearts but they are still prone to sudden death, and people can experience sudden death before any symptoms of heart trouble occur. Again family history becomes very important in identifying potentials at risk”

Given these issues, the recommendations of the task force are important in identifying mechanisms and, ultimately, developing novel therapies, Dr. Force says.

Among them are to:

  • Define all genetic causes: HCM is caused by hundreds of different mutations in genes that encode components of the sarcomere, the contractile apparatus of cardiac muscle. But knowledge of the full spectrum of genes and mutations in HCM is needed to explain how the disease develops and, thus, how it can be treated. For example, Dr. Force says some mutations lead to heart failure, while others lead to sudden death with little evidence of heart damage.
  • Study the natural history of the disease: Establish a multi-center prospective observational cohort study of HCM that represents a range of mutations. This will provide insights into the diagnosis and progression of HCM that will refine clinical practice.
  • Support clinical trials: When potential therapeutic strategies are identified in pre-clinical studies and early clinical trials, a randomized, placebo-controlled multi-center clinical trial should test the therapies. A major goal in treatment of HCM is to limit the life-threatening consequences of arrhythmia, the researchers say.
  • Prevent mutant gene expression: Pharmacologic therapies may only alleviate symptoms, so in order to impact patient survival, strategies are needed that significantly reduce or eliminate expression of HCM mutant genes, the task force says.

Sources

http://www.eurekalert.org/pub_releases/2010-09/tju-rna091410.php

http://circ.ahajournals.org/cgi/content/extract/122/11/1130

References

[1] Hypertrophic Cardiomyopathy wiki

[2] http://www.brighthub.com/science/genetics/articles/77009.aspx#ixzz0zY3P4f4B

[3] http://www.brighamandwomens.org/cvcenter/genetics/documents/GeneticsBasics-long.pdf (pdf)

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