Maize Centromeres: Organization and Functional Adaptation in the Genetic Background of Oat

Abstract

Centromeric DNA sequences in multicellular eukaryotes are often highly repetitive and are not unique to a specific centromere or to centromeres at all. Thus, it is a major challenge to study the fine structure of individual plant centromeres. We used a DNA fiber-fluorescence in situ hybridization approach to study individual maize (Zea mays) centromeres using oat (Avena sativa)-maize chromosome addition lines. The maize centromere-specific satellite repeat CentC in the addition lines allowed us to delineate the size and organization of centromeric DNA of individual maize chromosomes. We demonstrate that the cores of maize centromeres contain mainly CentC arrays and clusters of a centromere-specific retrotransposon, CRM. CentC and CRM sequences are highly intermingled. The amount of CentC/CRM sequence varies from ;300 to >2800 kb among different centromeres. The association of CentC and CRM with centromeric histone H3 (CENH3) was visualized by a sequential detection procedure on stretched centromeres. The analysis revealed that CENH3 is always associated with CentC and CRM but that not all CentC or CRM sequences are associated with CENH3. We further demonstrate that in the chromosomal addition lines in which two CenH3 genes were present, one from oat and one from maize, the oat CENH3 was consistently incorporated by the maize centromeres.

Maize centromeres expand and adopt a uniform size in the genetic background of oat

“…The CentC/CRM arrays span several megabases of DNA in some maize centromeres (Jin et al 2004;Ananiev et al 2009). The CENH3-binding domains of these heavily repetitive centromeres generally cannot be delineated by sequencing-based approaches.…”

“…All primer sequences are provided in Supplemental Table S3. ChIP, ChIP-seq, and RNA-seq A CENH3 antibody developed in rice recognizes both maize and oat CENH3 (Jin et al 2004). This antibody was used for all immunoassay and ChIP experiments.…”

“…FISH, GISH, and immunoassays on chromosomes were performed according to published protocols (Jiang et al 1995;Jin et al 2004). In the GISH procedure, oat genomic DNA was used as a probe, and unlabeled maize genomic DNA was used as a blocker.…”

Identification and Preliminary Analysis of Several Centromere‐associated Bacterial Artificial Chromosome Clones from a Diploid Wheat Library

“…In addition, at the interphase cells, the centromeres of diploid species usually clustered at one pole and formed a ring-like allocation in the period before metaphase. Centromeres play critical roles in the faithful segregation of sister chromatids during the period of mitosis and meiosis (Presting et al 1998;Jin et al 2004). Although they have the same function, the DNA sequences of centromeric regions are not conserved among species (Clarke 1990;Houben and Schubert 2003;Ito et al 2004;Jin et al 2004).…”

“…Centromeres play critical roles in the faithful segregation of sister chromatids during the period of mitosis and meiosis (Presting et al 1998;Jin et al 2004). Although they have the same function, the DNA sequences of centromeric regions are not conserved among species (Clarke 1990;Houben and Schubert 2003;Ito et al 2004;Jin et al 2004). Owing to highly heterochromatic structure and complex repeats, it is more difficult to clone, map, sequence, and assemble the centromeres than the low-copy number DNA.…”