Distribution of retroelements in centromeres and neocentromeres of maize

Fluorescent in situ hybridization was used to examine the distribution of six abundant long terminal repeat (LTR) retroelements, Opie, Huck, Cinful-1, Prem-2/Ji, Grande, and Tekay/Prem-1 on maize pachytene chromosomes. Retroelement staining in euchromatin was remarkably uniform, even when we included the structurally polymorphic abnormal chromosome 10 (Abl0) in our analysis. This uniformity made it possible to use euchromatin as a control for quantitative staining intensity measurements in other regions of the genome. The data show that knobs, known to function as facultative neocentromeres when Abl0 is present, tend to exclude retroelements. A notable exception is Cinful-1, which accumulates in TR-1 knob arrays. Staining for each of the six retroelements was also substantially reduced in centromeric satellite arrays to an average of 30% of the staining in euchromatin. This contrasted with two previously described centromere-specific retrotransposable (CR) elements that were readily detected in centromeres. We suggest that retroelements are relatively rare in centromeres because they interrupt the long satellite arrays thought to be required for efficient centromere function. CR elements may have evolved mutualistic relationships with their plant hosts: they are known to interact with the kinetochore protein CENH3 and appear to accumulate in clusters, leaving long satellite arrays intact.