'Junk' DNA proves functional

November 05, 2008

Helps explain human differences from other species

In a paper published in Genome Research on Nov. 4, scientists at the Genome Institute of Singapore (GIS) report that what was previously believed to be "junk" DNA is one of the important ingredients distinguishing humans from other species.

More than 50 percent of human DNA has been referred to as "junk" because it consists of copies of nearly identical sequences. A major source of these repeats is internal viruses that have inserted themselves throughout the genome at various times during mammalian evolution.

Using the latest sequencing technologies, GIS researchers showed that many transcription factors, the master proteins that control the expression of other genes, bind specific repeat elements. The researchers showed that from 18 to 33% of the binding sites of five key transcription factors with important roles in cancer and stem cell biology are embedded in distinctive repeat families.

Over evolutionary time, these repeats were dispersed within different species, creating new regulatory sites throughout these genomes. Thus, the set of genes controlled by these transcription factors is likely to significantly differ from species to species and may be a major driver for evolution.

This research also shows that these repeats are anything but "junk DNA," since they provide a great source of evolutionary variability and might hold the key to some of the important physical differences that distinguish humans from all other species.

The GIS study also highlighted the functional importance of portions of the genome that are rich in repetitive sequences.

"Because a lot of the biomedical research use model organisms such as mice and primates, it is important to have a detailed understanding of the differences between these model organisms and humans in order to explain our findings," said Guillaume Bourque, Ph.D., GIS Senior Group Leader and lead author of the Genome Research paper.

"Our research findings imply that these surveys must also include repeats, as they are likely to be the source of important differences between model organisms and humans," added Dr. Bourque. "The better our understanding of the particularities of the human genome, the better our understanding will be of diseases and their treatments."

"The findings by Dr. Bourque and his colleagues at the GIS are very exciting and represent what may be one of the major discoveries in the biology of evolution and gene regulation of the decade," said Raymond White, Ph.D., Rudi Schmid Distinguished Professor at the Department of Neurology at the University of California, San Francisco, and chair of the GIS Scientific Advisory Board.

"We have suspected for some time that one of the major ways species differ from one another - for instance, why rats differ from monkeys - is in the regulation of the expression of their genes: where are the genes expressed in the body, when during development, and how much do they respond to environmental stimuli," he added.

"What the researchers have demonstrated is that DNA segments carrying binding sites for regulatory proteins can, at times, be explosively distributed to new sites around the genome, possibly altering the activities of genes near where they locate. The means of distribution seem to be a class of genetic components called 'transposable elements' that are able to jump from one site to another at certain times in the history of the organism. The families of these transposable elements vary from species to species, as do the distributed DNA segments which bind the regulatory proteins."

Dr. White also added, "This hypothesis for formation of new species through episodic distributions of families of gene regulatory DNA sequences is a powerful one that will now guide a wealth of experiments to determine the functional relationships of these regulatory DNA sequences to the genes that are near their landing sites. I anticipate that as our knowledge of these events grows, we will begin to understand much more how and why the rat differs so dramatically from the monkey, even though they share essentially the same complement of genes and proteins."

Agency for Science, Technology and Research (A*STAR), Singapore

---

---

	The Myth of Junk DNA by Jonathan Wells Ph.D. (Author) According to the modern version of Darwin’s theory, DNA contains a program for embryo development that is passed down from generation to generation; the program is implemented by proteins encoded by the DNA, and accidental DNA mutations introduce changes in those proteins that natural selection then shapes into new species, organs and body plans. When scientists discovered forty years ago that about 98% of our DNA does not encode proteins, the non-protein-coding portion was labeled “junk” and attributed to molecular accidents that have accumulated in the course of evolution. Recent books by Richard Dawkins, Francis Collins and others have used this “junk DNA” as evidence for Darwinian evolution and evidence against intelligent design (since an intelligent designer would...
	Mobile DNA: Finding Treasure in Junk (FT Press Science) by Haig H. Kazazian (Author) This book thoroughly reviews our current scientific understanding of the significant role that mobile genetic elements play in the evolution and function of genomes and organisms–from plants and animals to humans. Highly-regarded geneticist Haig Kazazian offers an accessible intellectual history of the field’s research strategies and concerns, explaining how advances opened up new questions, and how new tools and capabilities have encouraged progress in the field.   Kazazian introduces the key strategies and approaches taken in leading laboratories (including his own) to gain greater insight into the large proportion of our genome that derives from mobile genetic elements, including viruses, plasmids, and transposons. He also presents intriguing insights into long-term research...
	Junk DNA: A Collection of Sonnets by Teresa Middleton (Author) Here is the genius of these poems, for they bring together everything under the sun--people, known and unknown; days recorded and days buried; natural phenomena of all sorts and human behaviors of all manner. Poets like to say that nothing is foreign to their enterprise. This books limns that creed while it pursues everything from Blaise Pascal to Princess Di, from owls to the RMS Carpathia. One feels that there is no stopping this imagination as it inhabits such a remarkable range of sympathies. --Baron Wormser
	Trace Your Roots with DNA: Use Your DNA to Complete Your Family Tree by Megan Smolenyak (Author), Ann Turner (Author) Written by two of the country's top genealogists, this authoritative book is the first to explain how new and groundbreaking genetic testing can help you research your ancestry According to American Demographics, 113 million Americans have begun to trace their roots, making genealogy the second most popular hobby in the country (after gardening). Enthusiasts clamor for new information from dozens of subscription-based websites, email newsletters, and magazines devoted to the subject. For these eager roots-seekers looking to take their searches to the next level, DNA testing is the answer. After a brief introduction to genealogy and genetics fundamentals, the authors explain the types of available testing, what kind of information the tests can provide, how to interpret the...
	The Cosmic Serpent: DNA and the Origins of Knowledge by Jeremy Narby (Author) This adventure in science and imagination, which the Medical Tribune said might herald "a Copernican revolution for the life sciences," leads the reader through unexplored jungles and uncharted aspects of mind to the heart of knowledge. In a first-person narrative of scientific discovery that opens new perspectives on biology, anthropology, and the limits of rationalism, The Cosmic Serpent reveals how startlingly different the world around us appears when we open our minds to it.
	Gene activity makes the difference in development of human qualities: 'junk DNA' helps to distinguish people from other primates.: An article from: Science News by Rachel Ehrenberg (Author) This digital document is an article from Science News, published by Science Service, Inc. on September 27, 2008. The length of the article is 457 words. The page length shown above is based on a typical 300-word page. The article is delivered in HTML format and is available immediately after purchase. You can view it with any web browser. Citation Details Title: Gene activity makes the difference in development of human qualities: 'junk DNA' helps to distinguish people from other primates. Author: Rachel Ehrenberg Publication: Science News (Magazine/Journal) Date: September 27, 2008 Publisher: Science Service, Inc. Volume: 174 Issue: 7 Page: 13(1) Distributed by Gale, a part of Cengage...
	Turns out that 'junk DNA' wasn't just talking trash.(FROM THE EDITOR)(Editorial): An article from: Science News by Tom Siegfried (Author)
	DNA: A Graphic Guide to the Molecule that Shook the World by Israel Rosenfield (Author), Edward Ziff (Author), Borin van Van Loon (Author) With humor, depth, and philosophical and historical insight, DNA reaches out to a wide range of readers with its graphic portrayal of a complicated science. Suitable for use in and out of the classroom, this volume covers DNA's many marvels, from its original discovery in 1869 to early-twentieth-century debates on the mechanisms of inheritance and the deeper nature of life's evolution and variety. Even readers who lack a background in science and philosophy will learn a tremendous amount from this engaging narrative. The book elucidates DNA's relationship to health and the cause and cure of disease. It also covers the creation of new life forms, nanomachines, and perspectives on crime detection, and considers the philosophical sources of classical Darwinian theory and recent, radical...
	The Making of the Fittest: DNA and the Ultimate Forensic Record of Evolution by Sean B. Carroll (Author) DNA evidence not only solves crimes—in Sean Carroll's hands it will now end the Evolution Wars.DNA is the genetic material that defines us as individuals. Over the last two decades, it has emerged as a powerful tool for solving crimes and determining guilt and innocence. But, very recently, an important new aspect of DNA has been revealed—it contains a detailed record of evolution. That is, DNA is a living chronicle of how the marvelous creatures that inhabit our planet have adapted to its many environments, from the freezing waters of the Antarctic to the lush canopy of the rain forest. In the pages of this highly readable narrative, Sean Carroll guides the general reader on a tour of the massive DNA record of three billion years of evolution to see how the fittest are...
	DNA and Tradition: The Genetic Link to the Ancient Hebrews by Yaakov Kleiman (Author) Did the Twelve Tribes of Israel really exist? Are the scattered groups of modern Jews really the direct descendants of the ancient Hebrews of the Bible? This extraordinary book chronicles the latest discoveries in the cutting-edge field of Molecular Population Genetics that add empirical evidence and scientific confirmation to Biblical tradition. The areas that are analyzed include: The Discovery of the "Cohen Gene", DNA Tests of Tradition, Confirming the Origin of World Jewry, Discovering the Genetic Matriarchs, Abraham’s Chromosome Signature