ScienceDaily (June 12, 2009) — What was once thought of as DNA with zero value in plants--dubbed "junk" DNA--may turn out to be key in helping scientists improve the control of gene expression in transgenic crops.
That's according to Agricultural Research Service (ARS) plant pathologist Bret Cooper at the agency's Soybean Genomics and Improvement Laboratory in Beltsville, Md., and collaborators at Johns Hopkins University in Baltimore, Md.
When ARS plant pathologist Bret Cooper and his collaborators investigated "junk" DNA in the model plant Arabidopsis thaliana, they may have found what could be the key to improving control of gene expression in transgenic crops. (Credit: Photo by Peggy Greb)
For more than 30 years, scientists have been perplexed by the workings of intergenic DNA, which is located between genes. Scientists have since found that, among other functions, some intergenic DNA plays a physical role in protecting and linking chromosomes. But after subtracting intergenic DNA, there was still leftover or "junk" DNA which seemed to have no purpose.
Cooper and collaborators investigated "junk" DNA in the model plant Arabidopsis thaliana, using a computer program to find short segments of DNA that appeared as molecular patterns. When comparing these patterns to genes, Cooper's team found that 50 percent of the genes had the exact same sequences as the molecular patterns. This discovery showed a sequence pattern link between "junk" and coding DNA. These linked patterns are called pyknons, which Cooper and his team believe might be evidence of something important that drives genome expansion in plants.
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Article citation: Jian Feng, Mol. BioSyst., 2009, DOI: 10.1039/b903031j
Coding DNA repeated throughout intergenic regions of the Arabidopsis thaliana genome: evolutionary footprints of RNA silencing
Jian Feng, Daniel Q. Naiman and Bret Cooper
Pyknons are non-random sequence patterns significantly repeated throughout non-coding genomic DNA that also appear at least once among coding genes. They are interesting because they portend an unforeseen connection between coding and non-coding DNA. Pyknons have only been discovered in the human genome, so it is unknown whether pyknons have wider biological relevance or are simply a phenomenon of the human genome. To address this, DNA sequence patterns from the Arabidopsis thaliana genome were detected using a probability-based method. 24654 statistically significant sequence patterns, 16 to 24 nucleotides long, repeating 10 or more times in non-coding DNA also appeared in 46% of A. thaliana protein-coding genes. A. thaliana pyknons exhibit features similar to human pyknons, including being distinct sequence patterns, having multiple instances in genes and having remarkable similarity to small RNA sequences with roles in gene silencing. Chromosomal position mapping revealed that genomic pyknon density has concordance with siRNA and transposable element positioning density. Because the A. thaliana and human genomes have approximately the same number of genes but drastically different amounts of non-coding DNA, these data reveal that pyknons represent a biologically important link between coding and non-coding DNA. Because of the association of pyknons with siRNAs and localization to silenced regions of heterochromatin, we postulate that RNA-mediated gene silencing leads to the accumulation of gene sequences in non-coding DNA regions.
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