title: Stochastic and epigenetic changes of gene expression in Arabidopsis polyploids.
abstract: Polyploidization is an abrupt speciation mechanism for eukaryotes and is especially common in plants. However, little is known about patterns and mechanisms of gene regulation during early stages of polyploid formation. Here we analyzed differential expression patterns of the progenitors' genes among successive selfing generations and independent lineages. The synthetic Arabidopsis allotetraploid lines were produced by a genetic cross between A. thaliana and A. arenosa autotetraploids. We found that some progenitors' genes are differentially expressed in early generations, whereas other genes are silenced in late generations or among different siblings within a selfing generation, suggesting that the silencing of progenitors' genes is rapidly and/or stochastically established. Moreover, a subset of genes is affected in autotetraploid and multiple independent allotetraploid lines and in A. suecica, a natural allotetraploid derived from A. thaliana and A. arenosa, indicating locus-specific susceptibility to ploidy-dependent gene regulation. The role of DNA methylation in silencing progenitors' genes is tested in DNA-hypomethylation transgenic lines of A. suecica using RNA interference (RNAi). Two silenced genes are reactivated in both ddm1- and met1-RNAi lines, consistent with the demethylation of centromeric repeats and gene-specific regions in the genome. A rapid and stochastic process of differential gene expression is reinforced by epigenetic regulation during polyploid formation and evolution.
authors.affiliation: Genetics Program, Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843-2474, USA.
authors.forename: Jianlin
authors.initials: J
authors.lastname: Wang
authors.forename: Lu
authors.initials: L
authors.lastname: Tian
authors.forename: Andreas
authors.initials: A
authors.lastname: Madlung
authors.forename: Hyeon-Se
authors.initials: HS
authors.lastname: Lee
authors.forename: Meng
authors.initials: M
authors.lastname: Chen
authors.forename: Jinsuk J
authors.initials: JJ
authors.lastname: Lee
authors.forename: Brian
authors.initials: B
authors.lastname: Watson
authors.forename: Trevor
authors.initials: T
authors.lastname: Kagochi
authors.forename: Luca
authors.initials: L
authors.lastname: Comai
authors.forename: Z Jeffrey
authors.initials: ZJ
authors.lastname: Chen
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D001483:Base Sequence; D003001:Cloning, Molecular; D017931:DNA Primers; D018506:Gene Expression Regulation, Plant / Q000235:genetics*; D020868:Gene Silencing; D012150:Polymorphism, Restriction Fragment Length; D011123:Polyploidy; D018749:RNA, Plant / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics; D013269:Stochastic Processes
chemical_list: D029681:Arabidopsis Proteins; D017931:DNA Primers; D018749:RNA, Plant; D034741:RNA, Small Interfering