DNA sequence composition of maize centromeres

Abstract

Centromeres are complex nucleic acid and protein structures essential for the faithful segregation of chromosomes during eukaryotic cell divisions. Despite this extremely conserved function, the DNA sequences of centromeres are exceptionally variable. Zea mays (maize) is an important crop; however, the DNA sequences of maize centromeres are still largely a mystery. Two repeated sequence elements appear to localize to the centromeres of maize according to fluorescence in situ hybridization (FISH) experiments, polymerase chain reaction products from immunoprecipitated centromeric chromatin, and limited sequence annotations of centromeric FISH probes. These centromeric elements are a tandemly repeated sequence (CentC) and the centromeric retrotransposon of maize (CRM). The Maize Genome Sequencing Consortium has recently published gigabases of new maize DNA sequences, revealing nearly the entire genome of this plant for the first time. Using newly available genomic resources this dissertation examines three hypotheses regarding the centromeres of maize: 1) CentC and CRM are the only repeated elements enriched in the DNA sequences of maize centromeres; 2) the DNA sequence composition of maize centromeres differs between chromosomes (e.g., relative amounts of CentC/CRM vary); and 3) CentC is highly variable, duplicated locally, and duplicated in genomic regions strongly associated with a conserved centromeric histone protein, CENH3. Analysis reveals evidence supporting all three hypotheses.