Characterizing the Interplay between Maize Retrotransposons and the Epigenome

University Of Hawaii, Honolulu

Investigators

Abstract

Centromeres are DNA segments that ensure the faithful segregation of chromosomes to daughter cells during division. The structure of centromeres is not well understood, although coordinated changes in the DNA and associated factors are necessary for centromere function. Furthermore, centromere structure and function can change over time raising questions about how the genome responds and adapt at the chromosome level. Centromeres are difficult to study because they are composed of retrotranspons and other mobile elements that consist of highly repetitive sequences. The ability to assemble spans of short repeated sequences is notoriously difficult, so the centromere regions of chromosomes have remained nearly obscure to researchers. This project will sequence and analyze the centromere regions of all ten maize chromosomes using new sequencing technologies and software tools that permit assembly and analysis of the repetitive sequences and will permit study of the associated factors unique to centromeres. The results of this project will add value to the already sequenced maize genome and will result in an improved reference genome fully available to the plant research community. By discovering the structure and function of centromeres, the potential to construct artificial chromosomes will be expanded and agronomic traits associated with centromeres may be identified. As part of the project, undergraduate students will be trained in modern plant engineering methods and synthetic biology. The team of undergraduate students will participate in an international student research competition, thus promoting student and public understanding of plant centromeres and synthetic biology. Little is known about the role of DNA in centromere function and evolution. In a first step, the nature and arrangement of centromere-specific repeats at all ten maize centromeres of the inbred B73 reference genome will be determined using PacBio technology. The impact of these repeats on the deposition of centromere-specific proteins will be determined using a number of different experimental approaches, including comparative genomics and epigenomics, as well as biochemical and genetic assays. Neocentromere formation is an epigenetic change that involves movement of CENH3, the centromere specific histone H3, to a new genomic region. Rapid invasion of neocentromeres by centromeric retrotransposons (CR) provides an unprecedented opportunity to study the interplay of epigenetic and genetic changes. A large number of epigenetic marks have been, or are being, mapped in the standard maize genomes. Histone H2A.Z nucleosomes, which may represent persistent marks of transcribed regions, will be mapped and integrated with all available epigenetic signatures to determine the reciprocal effects of genetic (double-stranded DNA breaks and retrotransposons insertion) and epigenetic (histone variants, histone modifications, gene expression, DNA methylation). At least one additional epigenetic marker that specifically binds centromeric repeats will be characterized in detail. All data produced in the course of this research will be deposited at MaizeGDB (maizegdb.org) and GenBank (http://www.ncbi.nlm.nih.gov/genbank/).