The distribution of a germline methylation marker suggests a regional mechanism of LINE-1 silencing by the piRNA-PIWI system

We found significantly higher density of mSNPs flanking piRNA clusters in the human genome for flank sizes of 1-16 Mb. A dose-response relationship between number of piRNA genes and mSNP density was found for up to 16 Mb of flanking sequences. The chromosomal density of hypermethylated LINE-1 elements had a significant positive correlation with the chromosomal density of piRNA genes (r = 0.41, P = 0.05). Genome windows of 1-16 Mb containing piRNA clusters had significantly more hypermethylated LINE-1 elements than windows not containing piRNA clusters. Finally, the minimum distance to the next piRNA cluster was significantly shorter for hypermethylated LINE-1 compared to normally methylated elements (14.4 Mb vs 16.1 Mb).Our observations support our hypothesis that the piRNA-PIWI system preferentially methylates sequences in close proximity to the piRNA clusters and perhaps physically adjacent sequences on other chromosomes. Furthermore they suggest that this proximity effect extends up to 16 Mb. This could be due to an unknown localization signal, transcription of piRNA genes near the nuclear membrane or the presence of an unknown RNA molecule that spreads across the chromosome and targets the methylation directed by the piRNA-PIWI complex. Our data suggest a region specific molecular mechanism which can be sought experimentally.Approximately 70% of CpG dinucleotides are methylated in the human genome [1]. Additionally, non-CpG methylation, primarily of the CWG trinucleotide, has recently been described in the human genome [2]. It accounts for 25% of cytosine methylation in embryonic stem cells, compared to only 0.02% of all cytosine methylation in adult cell lines [2]. DNA methylation has several important functions in mammalian genomes, highlighted by the lethal phenotype of homozygous mutants of DNA methyltransferases [3,4]. These functions include regulation of tissue-specific gene expression [5,6], parent-of-origin expression of imprinted genes [7] and the stab