chip was performed using tagged tap - abp1 and tap - cbh1 strains with an anti - calmodulin binding protein antibody ( millipore ) and a polyclonal serum against the native sap1 protein9 .
high throughput sequencing was performed on the illumina g2 genome analyzer , and analyzed for polymorphism detection or statistical analysis of enrichment .
2d gel electrophoresis was performed as described11 , see supplementary information for construction of the episomal system .
 centromere - binding protein b ( cenp - b ) is a widely conserved dna binding factor associated with heterochromatin and centromeric satellite repeats1 . in fission yeast , cenp - b homologs 
 have been shown to silence long terminal repeat ( ltr ) retrotransposons by recruiting histone deacetylases2 . 
 however , cenp - b factors also have unexplained roles in dna replication3 , 4 . here 
 , we show that a molecular function of cenp - b is to promote replication fork progression through the ltr . 
 mutants have increased genomic instability caused by replication fork blockage that depends on the dna binding factor switch activating protein 1 ( sap1 ) , which is directly recruited by the ltr . 
 the loss of sap1-dependent barrier activity allows the unhindered progression of the replication fork , but results in rearrangements deleterious to the retrotransposon . 
 we conclude that retrotransposons influence replication polarity through recruitment of sap1 and transposition near replication fork blocks , while cenp - b counteracts this activity and promotes fork stability . our results may account for the role of ltr in fragile sites , and for the association of cenp - b with pericentromeric heterochromatin and tandem satellite repeats . 
Methods summary
Supplementary Material