 |
|
Study finds value in 'junk' DNA
October 17, 2008Significant number of exons created from junk DNA seem to play a role in gene regulation
For about 15 years, scientists have known that certain "junk" DNA -- repetitive DNA segments previously thought to have no function -- could evolve into exons, which are the building blocks for protein-coding genes in higher organisms like animals and plants. Now, a University of Iowa study has found evidence that a significant number of exons created from junk DNA seem to play a role in gene regulation.
The findings, which increase understanding of how humans differ from other animals, including non-human primates, appear Oct. 17 in the open-access journal PLoS Genetics.
Nearly half of human DNA consists of repetitive DNA, including transposons, which can "transpose" or move around to different positions within the genome. A type of transposon called retrotransposons are transcribed into RNA and then reintegrated into the genomic DNA. The most common form of retrotransposons in the human genome are Alu elements, which have more than one million copies and occupy approximately 10 percent of the human genome.
"Alu elements are a major source of new exons. Because Alu is a primate-specific retrotransposon, creation of new exons from Alu may contribute to unique traits of primates, so we want to better understand this process," said the study's senior author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the University of Iowa Carver College of Medicine and the UI College of Engineering.
To study the impact of Alu-derived exons on human gene expression, the researchers used a high-density exon microarray. The technology has nearly six million probes for monitoring the expression patterns of all human exons. Using data generated by these microarrays, the scientists analyzed 330 Alu-derived exons in 11 human tissues. The team then identified a number of exons with interesting expression and functional characteristics.
"Hundreds of exons in the human genome were created from Alu elements. The whole-genome exon microarray allowed us to quickly identify exons that most likely contribute to the regulation of gene expression and function," said Lan Lin, Ph.D., University of Iowa postdoctoral fellow in internal medicine and the lead author of this study.
Analysis of one human gene, SEPN1, which is known to be involved in a type of muscular dystrophy, along with comparative data from chimpanzee and macaque tissues, suggested that the presence of a muscle-specific Alu-derived exon resulted from a human-specific change that occurred after humans and chimpanzees diverged evolutionarily.
"In this case, this exon is only expressed at a high level in the human muscle but not in any other human or non-human primate tissue, so this implies that the exon plays a functional role in muscle, and this role is human-specific," said Xing, who is also affiliated with University of Iowa Center for Bioinformatics and Computational Biology.
University of Iowa
Nearly half of human DNA consists of repetitive DNA, including transposons, which can "transpose" or move around to different positions within the genome. A type of transposon called retrotransposons are transcribed into RNA and then reintegrated into the genomic DNA. The most common form of retrotransposons in the human genome are Alu elements, which have more than one million copies and occupy approximately 10 percent of the human genome.
"Alu elements are a major source of new exons. Because Alu is a primate-specific retrotransposon, creation of new exons from Alu may contribute to unique traits of primates, so we want to better understand this process," said the study's senior author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the University of Iowa Carver College of Medicine and the UI College of Engineering.
To study the impact of Alu-derived exons on human gene expression, the researchers used a high-density exon microarray. The technology has nearly six million probes for monitoring the expression patterns of all human exons. Using data generated by these microarrays, the scientists analyzed 330 Alu-derived exons in 11 human tissues. The team then identified a number of exons with interesting expression and functional characteristics.
"Hundreds of exons in the human genome were created from Alu elements. The whole-genome exon microarray allowed us to quickly identify exons that most likely contribute to the regulation of gene expression and function," said Lan Lin, Ph.D., University of Iowa postdoctoral fellow in internal medicine and the lead author of this study.
Analysis of one human gene, SEPN1, which is known to be involved in a type of muscular dystrophy, along with comparative data from chimpanzee and macaque tissues, suggested that the presence of a muscle-specific Alu-derived exon resulted from a human-specific change that occurred after humans and chimpanzees diverged evolutionarily.
"In this case, this exon is only expressed at a high level in the human muscle but not in any other human or non-human primate tissue, so this implies that the exon plays a functional role in muscle, and this role is human-specific," said Xing, who is also affiliated with University of Iowa Center for Bioinformatics and Computational Biology.
University of Iowa
Junk Dna Current Events and Junk Dna News RSSResearchers solve piece of large-scale gene silencing mystery
A team led by Craig Pikaard, Ph.D., Washington University in St. Louis professor of biology in Arts & Sciences, has made a breakthrough in understanding the phenomenon of nucleolar dominance, the silencing of an entire parental set of ribosomal RNA genes in a hybrid plant or animal.
New gene silencing pathway found in plants
Biologists at Washington University in St. Louis have made major headway in explaining a mechanism by which plant cells silence potentially harmful genes.
'Junk' DNA proves functional
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.
An ancient protein balances gene activity and silences foreign DNA in bacteria
Compared to humans, bacteria have a much tidier genome. The tiny microorganisms pack their genes closely together, and don't carry around a lot of extraneous DNA, so-called junk DNA that fills in the gaps between genes.
Scientists discover small RNAs that regulate gene expression and protect the genome
RNA is best known as a working copy of the DNA sequence of genes. In this role, it's a carrier of the genes' instructions to the cell, which manufactures proteins according to information in the RNA molecule.
Evolving complexity out of 'junk DNA'
The study, published today in Proceedings of the National Academy of Sciences, USA, claims to have solved this scientific riddle by analysing the genomics of primitive living fishes such as sharks and lampreys and their spineless relatives, such as the sea squirts.
Dartmouth researchers find the root of the evolutionary emergence of vertebrates
Dartmouth College researchers and colleagues from the University of Bristol in the U.K. have traced the beginnings of complex life, i.e. vertebrates, to microRNA. The researchers argue that the evolution of microRNAs, which regulate gene expression, are behind the origin of early vertebrates.
RNA-associated introns guide nerve-cell channel production
Researchers at the University of Pennsylvania School of Medicine have discovered that introns, or junk DNA to some, associated with RNA are an important molecular guide to making nerve-cell electrical channels.
Study reveals how stem cells decide to become either skeletal or smooth muscle
Researchers have discovered a key protein that controls how stem cells "choose" to become either skeletal muscle cells that move limbs, or smooth muscle cells that support blood vessels.
Charting ever-changing genomes
Instead of immutable proprietary software, any species' genetic information resembles open source code that is constantly tweaked and optimized to meet the users' specific needs.
More Junk Dna Current Events and Junk Dna News Articles
| 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 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 DetailsTitle: Gene activity makes the difference... | |
 | Junk DNA by Tania Glyde |
| Isaac Asimov's Science Fiction Magazine: Bruce Sterling Rudy Rucker Junk DNA Vol by Bruce; Rucker, Rudy; Rosenblum, Mary; Reed, Robert; Popkes, Steve Sterling |
| © 2009 BrightSurf.com |