Monitoring the interplay between transposable element families and DNA methylation in maize


Autoři: Jaclyn M. Noshay aff001;  Sarah N. Anderson aff001;  Peng Zhou aff001;  Lexiang Ji aff002;  William Ricci aff003;  Zefu Lu aff004;  Michelle C. Stitzer aff005;  Peter A. Crisp aff001;  Candice N. Hirsch aff006;  Xiaoyu Zhang aff003;  Robert J. Schmitz aff004;  Nathan M. Springer aff001
Působiště autorů: Department of Plant and Microbial Biology, University of Minnesota, St. Paul MN, United States of America aff001;  Institute of Bioinformatics, University of Georgia, Athens GA, United States of America aff002;  Department of Plant Biology, University of Georgia, Athens GA, United States of America aff003;  Department of Genetics, University of Georgia, Athens GA, United States of America aff004;  Department of Plant Sciences, University of California Davis, Davis CA, United States of America aff005;  Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul MN, United States of America aff006
Vyšlo v časopise: Monitoring the interplay between transposable element families and DNA methylation in maize. PLoS Genet 15(9): e32767. doi:10.1371/journal.pgen.1008291
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pgen.1008291

Souhrn

DNA methylation and epigenetic silencing play important roles in the regulation of transposable elements (TEs) in many eukaryotic genomes. A majority of the maize genome is derived from TEs that can be classified into different orders and families based on their mechanism of transposition and sequence similarity, respectively. TEs themselves are highly methylated and it can be tempting to view them as a single uniform group. However, the analysis of DNA methylation profiles in flanking regions provides evidence for distinct groups of chromatin properties at different TE families. These differences among TE families are reproducible in different tissues and different inbred lines. TE families with varying levels of DNA methylation in flanking regions also show distinct patterns of chromatin accessibility and modifications within the TEs. The differences in the patterns of DNA methylation flanking TE families arise from a combination of non-random insertion preferences of TE families, changes in DNA methylation triggered by the insertion of the TE and subsequent selection pressure. A set of nearly 70,000 TE polymorphisms among four assembled maize genomes were used to monitor the level of DNA methylation at haplotypes with and without the TE insertions. In many cases, TE families with high levels of DNA methylation in flanking sequence are enriched for insertions into highly methylated regions. The majority of the >2,500 TE insertions into unmethylated regions result in changes in DNA methylation in haplotypes with the TE, suggesting the widespread potential for TE insertions to condition altered methylation in conserved regions of the genome. This study highlights the interplay between TEs and the methylome of a major crop species.

Klíčová slova:

Biology and life sciences – Cell biology – Chromosome biology – Chromatin – Chromatin modification – DNA methylation – Genetics – Epigenetics – DNA modification – Gene expression – DNA – Genomics – Plant genomics – Mobile genetic elements – Transposable elements – Genome analysis – Genome annotation – Plant genetics – Genetic elements – Heredity – Genetic mapping – Haplotypes – Biochemistry – Nucleic acids – Bioengineering – Biotechnology – Plant biotechnology – Plant science – Organisms – Eukaryota – Plants – Grasses – Maize – Computational biology – Physical sciences – Chemistry – Chemical reactions – Methylation – Engineering and technology – Research and analysis methods – Animal studies – Experimental organism systems – Model organisms – Plant and algal models


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