BACKGROUND: Polyadenylated, mRNA-like transcripts with no coding potential are 
abundant in eukaryotes, but the functions of these long non-coding RNAs (ncRNAs) 
are enigmatic. In meiosis, Rec12 (Spo11) catalyzes the formation of dsDNA breaks 
(DSBs) that initiate homologous recombination. Most meiotic recombination is 
positioned at hotspots, but knowledge of the mechanisms is nebulous. In the 
fission yeast genome DSBs are located within 194 prominent peaks separated on 
average by 65-kbp intervals of DNA that are largely free of DSBs.
METHODOLOGY/PRINCIPAL FINDINGS: We compared the genome-wide distribution of DSB 
peaks to that of polyadenylated ncRNA molecules of the prl class. DSB peaks map 
to ncRNA loci that may be situated within ORFs, near the boundaries of ORFs and 
intergenic regions, or most often within intergenic regions. Unconditional 
statistical tests revealed that this colocalization is non-random and robust 
(P<or=5.5 x 10(-8)). Furthermore, we tested and rejected the hypothesis that the 
ncRNA loci and DSB peaks localize preferentially, but independently, to a third 
entity on the chromosomes.
CONCLUSIONS/SIGNIFICANCE: Meiotic DSB hotspots are directed to loci that express 
polyadenylated ncRNAs. This reveals an unexpected, possibly unitary mechanism 
for what directs meiotic recombination to hotspots. It also reveals a likely 
biological function for enigmatic ncRNAs. We propose specific mechanisms by 
which ncRNA molecules, or some aspect of RNA metabolism associated with ncRNA 
loci, help to position recombination protein complexes at DSB hotspots within 
chromosomes.