Public release date: 28-Feb-2011
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U. Iowa team investigates function of 'junk DNA' in human genes
Part of the answer to how and why primates differ from other mammals, and humans differ from other primates, may lie in the repetitive stretches of the genome that were once considered "junk."
A new study by researchers at the University of Iowa Carver College of Medicine finds that when a particular type of repetitive DNA segment, known as an Alu element, is inserted into existing genes, they can alter the rate at which proteins are produced -- a mechanism that could contribute to the evolution of different biological characteristics in different species. The study was published in the Feb. 15 issue of the journal Proceedings of the National Academy of Sciences (PNAS).
"Repetitive elements of the genome can provide a playground for the creation of new evolutionary characteristics," said senior study author Yi Xing, Ph.D., assistant professor of internal medicine and biomedical engineering, who holds a joint appointment in the UI Carver College of Medicine and the UI College of Engineering. "By understanding how these elements function, we can learn more about genetic mechanisms that might contribute to uniquely human traits."
Alu elements are a specific class of repetitive DNA that first appeared about 60 to 70 million years ago during primate evolution. They do not exist in genomes of other mammals. Alu elements are the most common form of mobile DNA in the human genome, and are able to transpose, or jump, to different positions in the genome sequence. When they jump into regions of the genome containing existing genes, these elements can become new exons -- pieces of messenger RNAs that carry the genetic information.
Although scientists have known for more than a decade that these Alu elements are an important source of new exons in the human genome, it has been more difficult to determine if these new exons are biologically important.
"It's been hard to say whether these Alu-derived exons actually do anything on a genome-wide level," Xing said. "Our new study says they do - they affect protein production by altering the efficiency with which messenger RNA is translated into protein."
Xing noted that in other circumstances, altering the rate of protein production can cause disease, meaning that a mechanism that can affect protein production can have a real impact on the characteristics of an organism.
"This would not be the only mechanism that might differentiate humans from other primates, but our study suggests that the creation of new exons from Alu elements is an important process that contributes to those differences," Xing said.
The UI team, including co-first authors Shihao Shen, doctoral student in the Department of Biostatistics; and Lan Lin, Ph.D., associate in the Department of Internal Medicine, made use of data from a new technology called high throughput RNA sequencing to analyze more than 120 million RNA sequences from human cerebellum. Using this data, the team was able to quantify how often Alu-derived exons were included in the mature RNA sequences, which provide the final blueprint for protein production, and where they were inserted in the genes.
"What we found is that these exons tend to avoid protein-coding regions of the genes and rather they end up in the non-coding region that precedes the protein-coding region, called the five prime untranslated region or 5' UTR," Xing explained. "This is the part of the gene that usually contains regions that help control the stability of the messenger RNA and the efficiency at which the messenger RNA is translated into protein."
Experiments to probe the function of these newly inserted elements proved that Alu exons in this region are able to alter the efficiency of messenger RNA translation, which means they affect how fast protein is produced from the altered genes.
The study also suggests that the effect of the newly created exons might be amplified because of which genes were "targeted" by the Alu exons. The researchers found that Alu exons are highly enriched in genes that code for zinc-finger transcription factors -- proteins that act as master regulators of gene expression and that previously have been linked to human and primate evolution. Because these transcription factors control the expression of thousands of other genes, any changes to the amount of transcription factor available would likely have a cascade effect on the downstream genes.
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In addition to Xing, Shen and Lin, the team included UI researchers Peng Jiang, Ph.D.; Elizabeth Kenkel; Mallory Stroik; Seiko Sato; and Beverly Davidson, Ph.D., professor of internal medicine, neurology and molecular physiology and biophysics. The team also included James Cai, Ph.D., assistant professor of veterinary medicine at Texas A&M University.
The study was funded in part by grants from the National Institutes of Health and the Roy J. Carver Trust.
STORY SOURCE: University of Iowa Health Care Media Relations, 200 Hawkins Drive, Room W319 GH, Iowa City, Iowa 52242-1009
MEDIA CONTACT: Jennifer Brown, 319-356-7124, jennifer-l-brown@uiowa.edu
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Widespread establishment and regulatory impact of
Alu exons in human genes
Shihao Shena,1, Lan Linb,1, James J. Caic, Peng Jiangb, Elizabeth J. Kenkelb, Mallory R. Stroikb, Seiko Satob, Beverly L. Davidsonb,d,e, and Yi Xingb,f,2
-Author Affiliations
Departments of aBiostatistics,
bInternal Medicine,
dMolecular Physiology and Biophysics,
eNeurology, and
fBiomedical Engineering, University of Iowa, Iowa City, IA 52242; and
cDepartment of Veterinary Integrative Biosciences, Texas A&M University, College Station, TX 77845
Edited* by Wing Hung Wong, Stanford University, Stanford, CA, and approved January 12, 2011 (received for review August 28, 2010)
↵1S. Shen and L.L. contributed equally to this work.
Abstract
The Alu element has been a major source of new exons during primate evolution. Thousands of human genes contain spliced exons derived from Alu elements. However, identifying Alu exons that have acquired genuine biological functions remains a major challenge. We investigated the creation and establishment of Alu exons in human genes, using transcriptome profiles of human tissues generated by high-throughput RNA sequencing (RNA-Seq) combined with extensive RT-PCR analysis. More than 25% of Alu exons analyzed by RNA-Seq have estimated transcript inclusion levels of at least 50% in the human cerebellum, indicating widespread establishment of Alu exons in human genes. Genes encoding zinc finger transcription factors have significantly higher levels of Alu exonization. Importantly, Alu exons with high splicing activities are strongly enriched in the 5′-UTR, and two-thirds (10/15) of 5′-UTR Alu exons tested by luciferase reporter assays significantly alter mRNA translational efficiency. Mutational analysis reveals the specific molecular mechanisms by which newly created 5′-UTR Alu exons modulate translational efficiency, such as the creation or elongation of upstream ORFs that repress the translation of the primary ORFs. This study presents genomic evidence that a major functional consequence of Alu exonization is the lineage-specific evolution of translational regulation. Moreover, the preferential creation and establishment of Alu exons in zinc finger genes suggest that Alu exonization may have globally affected the evolution of primate and human transcriptomes by regulating the protein production of master transcriptional regulators in specific lineages.
transcriptome evolution, transposable element, alternative splicing, deep sequencing, uORF
Footnotes
2To whom correspondence should be addressed. E-mail: yi-xing@uiowa.edu.
Author contributions: S. Shen, L.L., and Y.X. designed research; S. Shen, L.L., P.J., E.J.K., M.R.S., and S. Sato performed research; L.L., J.J.C., and B.L.D. contributed new reagents/analytic tools; S. Shen, L.L., J.J.C., and Y.X. analyzed data; and S. Shen, L.L., and Y.X. wrote the paper.
The authors declare no conflict of interest.
↵*This Direct Submission article had a prearranged editor.
This article contains supporting information online at
www.pnas.org/lookup/suppl/doi:10.1073/pnas.1012834108/-/DCSupplemental.
Freely available online through the PNAS open access option.
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