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. 24 
654 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.