S. pombe NUMTs are not enriched into gene promoters. (A) Insertion sites of S. pombe NUMTs (pale gray), genomic LTRs (white; based on Bowen et al. 2003) and de novo Tf1 (dark gray; based on Behrens et al. 2000 and Singleton and Levin 2002) were classified into three categories of intergenic regions based on transcription direction of the genes flanking the insertion site: tandem, divergent, or convergent. Expected distribution for S. pombe (black) was calculated from http://www.sanger.ac.uk/Projects/S_pombe/genome_stats.shtml and is expressed as percentage of total noncoding DNA. (B) (■) Distribution of the distance from each independent NUMT insertion site to the nearest ORF. All NUMTs from intergenic regions between tandem gene pairs were located 5′ of the nearest gene. (◆) Distribution of the 26 intergenic de novo Tf1 insertions sites described in Behrens et al. (2000). (●) Expected distribution of insertion sites for S. pombe genome was obtained by calculating the size of promoters and 3′ regions from a total of 92 intergenic regions in either divergent or convergent pairs of genes from all three chromosomes. The insertion sites were binned in regions of 200 bp in windows spreading from –2000 to ATG and from STOP to +2000. (C) Transcriptional activity of SPAC1F12.02C and SPBC3B9.17 promoters was performed as described in Methods. The effect of NUMT(s) in these promoters was assessed by measurement of beta-galactosidase activity driven by mutated promoters lacking the NUMT(s). (Gray boxes) NUMT positions. Error bars indicate standard deviations.