 |
|
UD leads $5.3-million research project on rice epigenetics
September 11, 2007Using a novel "deep sequencing" technology that can in one fell swoop decode 50 million sequences representing well over a billion bases of DNA, a research team led by University of Delaware scientists is working to unmask where, why and how certain genes are switched on or off in rice--a crop vital to the world's food supply.
The goal of the four-year project, which is supported by a $5.3-million grant from the National Science Foundation (NSF), is to advance scientific understanding of the rice epigenome--the series of biochemical modifications of the rice DNA that can toggle a gene on or, conversely, silence it. Ultimately, the research may lead to the development of hardier strains of rice, as well as shed light on similar mechanisms at work in corn and other important cereal grains that are closely related to rice.
Blake Meyers, associate professor of plant and soil sciences at UD, is the principal investigator on the project, which also involves Guo-Liang Wang, a rice biologist from Ohio State University; Steven Jacobsen, an expert in epigenetics, and computer scientist Matteo Pellegrini, both from the University of California at Los Angeles; and Yulin Jia, a plant pathologist at the U.S. Department of Agriculture's Dale Bumpers National Rice Research Center in Stuttgart, Ark.
The effort builds on Meyers' previous awards from the NSF Plant Genome Research Program, as well as ongoing investigations of small RNAs--short lengths of ribonucleic acids that act as gene regulators--performed in collaboration with Pamela Green, the Crawford H. Greenewalt Endowed Chair in Plant Molecular Biology at UD, whose lab is next door to Meyers' in the Delaware Biotechnology Institute. These projects have now propelled the research in a new direction, to new frontiers in the field of epigenetics.
"Epigenetics refers to a heritable change that is not a result of a change in DNA sequence, but rather a chemical modification of nucleotides in the DNA or its associated proteins," Meyers said. "That means that these changes can be reversible, and it's easier to switch them on or off. Small RNAs are one of the key 'control switches,' directing these modifications," Meyers noted.
State-of-the-art sequencing by synthesis (SBS) technology developed by Solexa Inc., in Hayward, Calif., will provide the data essential to the project. This novel "deep sequencing" tool, which can decode tens of millions of sequences during a single run, has become available over the last year. The application of SBS to epigenetics research was demonstrated in the human genome only within the past few months. The UD-led effort will be one of the first large-scale projects to use this approach in crop plants.
"If you think of a gene as part of a set of chromosomes, a gene is just a small fraction of a percent of a complete genome," Meyers said. "If we learn about that gene by random sampling, by using 50 million total sequences, which is what SBS provides, we can characterize that gene at depth," he noted. "Using this method, we can obtain statistically robust data for nearly all genomic regions in a single experiment."
The scientists will use the technology to look for chemical modifications in chromatin, the building-block material of chromosomes, consisting of DNA and the proteins that interact with it. The scientists want to know how the chromatin is configured and what role changes in the material play in plant development.
"Formerly, we had a very narrow picture of a plant's genome; with these new sequencing technologies, we now have the opportunity to acquire a comprehensive picture at fine detail," Meyers said. "It's like looking through a high-powered telescope--but now we have a wide-angle lens on that telescope to take in a view with both breadth and depth."
Besides studying the state of the genome using a variety of different strains of rice plants, the research team will develop new bioinformatics methods to process the vast amounts of data and mine new discoveries.
"The project is part biology and part technology," Meyers said. "Developing the bioinformatics to handle the data is critical. You have to know what to do with it. As our bioinformatics capabilities have grown, so have the resources available to the public through our web sites," he noted. "And these online resources have led to important new collaborations."
The data from the current project will be accessible through web sites at UD and UCLA--[http://mpss.udel.edu/rice] and [http://epigenomics.mcdb.ucla.edu].
The research project also includes an innovative education and outreach component targeting graduate students in plant science. Students will write, submit and exchange research proposals with students from different universities. They will then serve on a panel to critique and rank the proposals, modeled after the National Science Foundation's own proposal review process.
"Since planning experiments and justifying these through writing proposals is such an integral part of what a scientist does, I thought this would be a good experience for our students," Meyers said. "This way, they can also see what their advisers go through," he added, grinning.
Meyers developed the educational project several years ago in the advanced plant genetics course (PL636) he teaches in the UD College of Agriculture and Natural Resources. Since then, several colleagues and their classes at Iowa State and Penn State have participated in the program, exchanging proposals with UD, and UCLA and Ohio State are planning to join the program during the current four-year grant.
"My hope is that this program and its proposal exchange system can be used broadly by plant genetics and genomics courses at universities to build writing, communication and critical thinking skills among graduate students," Meyers said.
University of Delaware
The effort builds on Meyers' previous awards from the NSF Plant Genome Research Program, as well as ongoing investigations of small RNAs--short lengths of ribonucleic acids that act as gene regulators--performed in collaboration with Pamela Green, the Crawford H. Greenewalt Endowed Chair in Plant Molecular Biology at UD, whose lab is next door to Meyers' in the Delaware Biotechnology Institute. These projects have now propelled the research in a new direction, to new frontiers in the field of epigenetics.
"Epigenetics refers to a heritable change that is not a result of a change in DNA sequence, but rather a chemical modification of nucleotides in the DNA or its associated proteins," Meyers said. "That means that these changes can be reversible, and it's easier to switch them on or off. Small RNAs are one of the key 'control switches,' directing these modifications," Meyers noted.
State-of-the-art sequencing by synthesis (SBS) technology developed by Solexa Inc., in Hayward, Calif., will provide the data essential to the project. This novel "deep sequencing" tool, which can decode tens of millions of sequences during a single run, has become available over the last year. The application of SBS to epigenetics research was demonstrated in the human genome only within the past few months. The UD-led effort will be one of the first large-scale projects to use this approach in crop plants.
"If you think of a gene as part of a set of chromosomes, a gene is just a small fraction of a percent of a complete genome," Meyers said. "If we learn about that gene by random sampling, by using 50 million total sequences, which is what SBS provides, we can characterize that gene at depth," he noted. "Using this method, we can obtain statistically robust data for nearly all genomic regions in a single experiment."
The scientists will use the technology to look for chemical modifications in chromatin, the building-block material of chromosomes, consisting of DNA and the proteins that interact with it. The scientists want to know how the chromatin is configured and what role changes in the material play in plant development.
"Formerly, we had a very narrow picture of a plant's genome; with these new sequencing technologies, we now have the opportunity to acquire a comprehensive picture at fine detail," Meyers said. "It's like looking through a high-powered telescope--but now we have a wide-angle lens on that telescope to take in a view with both breadth and depth."
Besides studying the state of the genome using a variety of different strains of rice plants, the research team will develop new bioinformatics methods to process the vast amounts of data and mine new discoveries.
"The project is part biology and part technology," Meyers said. "Developing the bioinformatics to handle the data is critical. You have to know what to do with it. As our bioinformatics capabilities have grown, so have the resources available to the public through our web sites," he noted. "And these online resources have led to important new collaborations."
The data from the current project will be accessible through web sites at UD and UCLA--[http://mpss.udel.edu/rice] and [http://epigenomics.mcdb.ucla.edu].
The research project also includes an innovative education and outreach component targeting graduate students in plant science. Students will write, submit and exchange research proposals with students from different universities. They will then serve on a panel to critique and rank the proposals, modeled after the National Science Foundation's own proposal review process.
"Since planning experiments and justifying these through writing proposals is such an integral part of what a scientist does, I thought this would be a good experience for our students," Meyers said. "This way, they can also see what their advisers go through," he added, grinning.
Meyers developed the educational project several years ago in the advanced plant genetics course (PL636) he teaches in the UD College of Agriculture and Natural Resources. Since then, several colleagues and their classes at Iowa State and Penn State have participated in the program, exchanging proposals with UD, and UCLA and Ohio State are planning to join the program during the current four-year grant.
"My hope is that this program and its proposal exchange system can be used broadly by plant genetics and genomics courses at universities to build writing, communication and critical thinking skills among graduate students," Meyers said.
University of Delaware
Epigenetics Current Events and Epigenetics News RSSStudy finds genomic changes in the brains of people who commit suicide
Are genes destiny? Alternatively, are we simply the products of our environment? There is a growing sense that neither of these two possibilities fully captures the essence of the risk for psychiatric disorders.
Our genome changes over lifetime, Johns Hopkins experts say
Researchers at Johns Hopkins have found that epigenetic marks on DNA-chemical marks other than the DNA sequence-do indeed change over a person's lifetime, and that the degree of change is similar among family members.
Child abuse may 'mark' genes in the brains of suicide victims
A team of McGill University scientists has discovered important differences between the brains of suicide victims and so-called normal brains. Although the genetic sequence was identical in the suicide and non-suicide brains, there were differences in their epigenetic marking - a chemical coating influenced by environmental factors.
'Destruct' triggers may be jammed in tumor cells, UF geneticists say
Tumor cells living in the cross hairs of radiation or chemotherapy may be able to escape death because their self-destruct mechanisms are jammed, say University of Florida scientists writing in a recent issue of Developmental Cell.
Epigenetic research uncovers new targets for modification enzymes
Enzymes regulating genetic expression can be just as important as the genome itself, increasing evidence shows. The expanding field of epigenetics focuses on the multiple influences on DNA and surrounding molecules that determine whether genes are turned on or off during development and disease processes.
Scientists Clarify a Mechanism of Epigenetic Inheritance
Although letters representing the three billion pairs of molecules that form the "rungs" of the helical DNA "ladder" are routinely called the human "genetic code," the DNA they comprise transmits traits across generations in a variety of ways, not all of which depend on the sequence of letters in the code.
Computation to unravel how genes are regulated and shed light on how cells become different
A closer alliance between computational and experimental researchers is needed to make progress towards one of biology's most challenging goals, understanding how epigenetic marks contribute to regulation of gene expression.
USC researchers explore genetic causes for male infertility
Researchers at the University of Southern California (USC) suggest epigenetics, or the way DNA is processed and expressed, may be the underlying cause for male infertility. The study will be published in the Dec. 12 issue of Public Library of Science One.
Duke scientists map imprinted genes in human genome
Scientists at Duke University have created the first map of imprinted genes throughout the human genome, and they say a modern-day Rosetta stone - a form of artificial intelligence called machine learning - was the key to their success.
New molecules discovered that block cancer cells from modifying cell DNA
Researchers have discovered new small molecules that may prevent prostate cancer cells from turning off normal genes in a process that transforms normal cells into cancer cells.
More Epigenetics Current Events and Epigenetics News Articles
 | Epigenetics The regulation of gene expression in many biological processes involves epigenetic mechanisms. In this new volume, 24 chapters written by experts in the field discuss epigenetic effects from many perspectives. There are chapters on the basic molecular mechanisms underpinning epigenetic regulation, discussion of cellular processes that rely on this kind of regulation, and surveys of organisms in... |
 | The Genie in Your Genes: Epigenetic Medicine and the New Biology of Intention by Dawson Church Dawson Church applies the insights of the new field of Epigenetics (epi=above, i.e. control above the level of the gene) to healing. Citing hundreds of scientific studies, he shows how beliefs and emotions can trigger the expression of DNA strands. He focuses on a class of genes called Immediate Early Genes or IEGs. These genes turn on within a few seconds of a stimulus. They can be triggered by... |
 | Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life (Life and Mind: Philosophical Issues in Biology and Psychology) by Eva Jablonka, Marion J. Lamb Ideas about heredity and evolution are undergoing a revolutionary change. New findings in molecular biology challenge the gene-centered version of Darwinian theory according to which adaptation occurs only through natural selection of chance DNA variations. In Evolution in Four Dimensions, Eva Jablonka and Marion Lamb argue that there is more to heredity than genes. They trace four "dimensions"... |
 | Cancer Epigenetics During the past few decades, it has become increasingly apparent that heredity is not the sole determining factor in disease development, such as cancer. This landmark work covers a wide array of aspects in the relatively new area of epigenetics, ranging from its role in the basic mechanisms of tumorigenesis, to the newest epigenetic drugs being developed and used for cancer therapy. Cancer... |
 | Epigenetics by Jorg Tost |
 | Mental Retardation and Developmental Delay: Genetic and Epigenetic Factors (Oxford Monographs on Medical Genetics) by Moyra Smith Recent advances in neuroscience and genetics have greatly expanded our understanding of the brain and of the etiological factors involved in developmental delay and mental retardation. At the same time, the human genome project has yielded a wealth of information on DNA sequencing, regulation of gene expression, epigenetics, and functional aspects of the genome, which newly propels investigation... |
 | Epigenetics in Biology and Medicine Epigenetic changes are essential to normal development, but these changes can also cause problems including the disabling of genes that suppress tumors. At present, more than a dozen drugs that target epigenetic changes are in clinical trials. Epigenetics in Biology and Medicine offers a comprehensive overview of epigenetics, both in normal functions and disease states. This book presents... |
 | Epigenetics and Chromatin (Progress in Molecular and Subcellular Biology) Epigenetics refers to heritable patterns of gene expression which do not depend on alterations of genomic DNA sequence. This book provides a state-of-the-art account of a few selected hot spots by scientists at the edge in this extremely active field. It puts special emphasis on two main streams of research. One is the role of post-translational modifications of proteins, mostly histones, on... |
 | Epigenetic Inheritance and Evolution: The Lamarckian Dimension by Eva Jablonka, Marion Lamb Does the inheritance of acquired characteristics play a significant role in evolution? In this book, Eva Jablonka and Marion J. Lamb attempt to answer that question with an original, provocative exploration of the nature and origin of hereditary variations. Starting with a historical account of Lamarck's ideas and the reasons they have fallen in disrepute, the authors go on to challenge the... |
 | Epigenetic Principles of Evolution by Nelson R. Cabej Epigenetic Principles of Evolution is a postgenetic treatment of the problem of metazoan evolution. It presents a radically novel epigenetic theory of evolution describing epigenetic mechanisms of evolutionary changes as they arise in the process of individual development. In seven chapters of Part 1 (Epigenetic Basis of Metazoan Heredity, pp. 21-216) the author introduces the reader to... |
| © 2008 BrightSurf.com |