Maize Centromere Structure and Evolution: Sequence Analysis of Centromeres 2 and 5 Reveals Dynamic Loci Shaped Primarily by Retrotransposons

Abstract

We describe a comprehensive and general approach for mapping centromeres and present a detailed characterization of two maize centromeres. Centromeres are difficult to map and analyze because they consist primarily of repetitive DNA sequences, which in maize are the tandem satellite repeat CentC and interspersed centromeric retrotransposons of maize (CRM). Centromeres are defined epigenetically by the centromeric histone H3 variant, CENH3. Using novel markers derived from centromere repeats, we have mapped all ten centromeres onto the physical and genetic maps of maize. We were able to completely traverse centromeres 2 and 5, confirm physical maps by fluorescence in situ hybridization (FISH), and delineate their functional regions by chromatin immunoprecipitation (ChIP) with anti-CENH3 antibody followed by pyrosequencing. These two centromeres differ substantially in size, apparent CENH3 density, and arrangement of centromeric repeats; and they are larger than the rice centromeres characterized to date. Furthermore, centromere 5 consists of two distinct CENH3 domains that are separated by several megabases. Succession of centromere repeat classes is evidenced by the fact that elements belonging to the recently active recombinant subgroups of CRM1 colonize the present day centromeres, while elements of the ancestral subgroups are also found in the flanking regions. Using abundant CRM and non-CRM retrotransposons that inserted in and near these two centromeres to create a historical record of centromere location, we show that maize centromeres are fluid genomic regions whose borders are heavily influenced by the interplay of retrotransposons and epigenetic marks. Furthermore, we propose that CRMs may be involved in removal of centromeric DNA (specifically CentC), invasion of centromeres by non-CRM retrotransposons, and local repositioning of the CENH3.

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

“…The CENH3-binding domain of B73 chromosome 3 (Cen3) was mapped between positions 99.78 and 100.76 Mb (chromosome 3 is 232.1 Mb long) ( Fig. 2A; Table 1), which is in agreement with the Cen3 position mapped previously based on a total of 149,756 ChIP-454 sequence reads (Wolfgruber et al 2009). We note that B73 Cen3 may, in fact, be larger than ;1 Mb, since the assembly is not complete for this centromere.…”

“…This replicates prior ChIP experiments on B73 using lower-coverage 454 sequencing (Wolfgruber et al 2009). We obtained a total of 84 million (M) paired sequence reads, including 12.9 M reads (one end or both ends of a paired read, 7.7% of the 168 M total ends) related to CentC or CRM repeats.…”

“…However, the CentC/CRM arrays account for only a portion of the CENH3-binding domains in several other maize centromeres, and in these cases, the CENH3 boundaries can be defined by mapping the sequences associated with CENH3 nucleosomes (Wolfgruber et al 2009). …”

“…Since B73 has been fully sequenced (Schnable et al 2009), the sizes of individual B73 centromeres in the maize and oat backgrounds can be directly compared. Cen2 is the best sequenced B73 centromere because it contains the least amount of CentC repeats (Wolfgruber et al 2009 Fig. 7B; Table 1).…”

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

“…Maize centromeres also contain highly repetitive DNA sequences, including several centromeric retrotransposons (CRM1 and CRM2) and the CentC tandem repeat (Zhong et al, 2002;Wolfgruber et al, 2009). However, functional centromeres can only be clearly differentiated from pericentromeres by binding of centromeric histone H3 (CENH3), a histone H3 variant (Gent et al, 2012).…”