title: Epigenomic consequences of immortalized plant cell suspension culture.
abstract: Plant cells grown in culture exhibit genetic and epigenetic instability. Using a combination of chromatin immunoprecipitation and DNA methylation profiling on tiling microarrays, we have mapped the location and abundance of histone and DNA modifications in a continuously proliferating, dedifferentiated cell suspension culture of Arabidopsis. We have found that euchromatin becomes hypermethylated in culture and that a small percentage of the hypermethylated genes become associated with heterochromatic marks. In contrast, the heterochromatin undergoes dramatic and very precise DNA hypomethylation with transcriptional activation of specific transposable elements (TEs) in culture. High throughput sequencing of small interfering RNA (siRNA) revealed that TEs activated in culture have increased levels of 21-nucleotide (nt) siRNA, sometimes at the expense of the 24-nt siRNA class. In contrast, TEs that remain silent, which match the predominant 24-nt siRNA class, do not change significantly in their siRNA profiles. These results implicate RNA interference and chromatin modification in epigenetic restructuring of the genome following the activation of TEs in immortalized cell culture.
authors.affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
authors.forename: Milos
authors.initials: M
authors.lastname: Tanurdzic
authors.forename: Matthew W
authors.initials: MW
authors.lastname: Vaughn
authors.forename: Hongmei
authors.initials: H
authors.lastname: Jiang
authors.forename: Tae-Jin
authors.initials: TJ
authors.lastname: Lee
authors.forename: R Keith
authors.initials: RK
authors.lastname: Slotkin
authors.forename: Bryon
authors.initials: B
authors.lastname: Sosinski
authors.forename: William F
authors.initials: WF
authors.lastname: Thompson
authors.forename: R W
authors.initials: RW
authors.lastname: Doerge
authors.forename: Robert A
authors.initials: RA
authors.lastname: Martienssen
mesh_terms: D017360:Arabidopsis / Q000166:cytology / Q000235:genetics* / Q000254:growth & development; D001483:Base Sequence; D002478:Cells, Cultured; D047369:Chromatin Immunoprecipitation; D032461:Chromosomes, Plant / Q000502:physiology*; D019175:DNA Methylation; D004251:DNA Transposable Elements / Q000235:genetics; D044127:Epigenesis, Genetic / Q000235:genetics*; D015870:Gene Expression; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant; D006657:Histones / Q000378:metabolism; D018515:Plant Leaves / Q000737:chemistry; D018749:RNA, Plant / Q000737:chemistry; D034741:RNA, Small Interfering / Q000378:metabolism
chemical_list: D004251:DNA Transposable Elements; D006657:Histones; D018749:RNA, Plant; D034741:RNA, Small Interfering