title: Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.
abstract: Detailed molecular profiling of Oryza sativa (rice) was carried out to uncover the features that are essential for germination and early seedling growth under anoxic conditions. Temporal analysis of the transcriptome and methylome from germination to young seedlings under aerobic and anaerobic conditions revealed 82% similarity in the transcriptome and no differences in the epigenome up to 24 h. Following germination, significant changes in the transcriptome and DNA methylation were observed between 4-day aerobically and anaerobically grown coleoptiles. A link between the epigenomic state and cell division versus cell elongation is suggested, as no differences in DNA methylation were observed between 24-h aerobically and anaerobically germinating embryos, when there is little cell division. After that, epigenetic changes appear to correlate with differences between cell elongation (anaerobic conditions) versus cell division (aerobic conditions) in the coleoptiles. Re-oxygenation of 3-day anaerobically grown seedlings resulted in rapid transcriptomic changes in DNA methylation in these coleoptiles. Unlike the transcriptome, changes in DNA methylation upon re-oxygenation did not reflect those seen in aerobic coleoptiles, but instead, reverted to a pattern similar to dry seeds. Reversion to the 'dry seed' state of DNA methylation upon re-oxygenation may act to 'reset the clock' for the rapid molecular changes and cell division that result upon re-oxygenation.
authors.affiliation: Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Vic, 3086, Australia.
authors.forename: Reena
authors.initials: R
authors.lastname: Narsai
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Secco
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
authors.forename: Matthew D
authors.initials: MD
authors.lastname: Schultz
authors.affiliation: Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.|Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
authors.forename: Joseph R
authors.initials: JR
authors.lastname: Ecker
authors.affiliation: ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia.
authors.forename: Ryan
authors.initials: R
authors.lastname: Lister
authors.affiliation: Department of Animal, Plant and Soil Science, ARC Centre of Excellence in Plant Energy Biology, School of Life Science, La Trobe University, Melbourne, Vic, 3086, Australia.
authors.forename: James
authors.initials: J
authors.lastname: Whelan
mesh_terms: D018548:Cotyledon / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D018506:Gene Expression Regulation, Plant / Q000235:genetics / Q000502:physiology; D018525:Germination / Q000235:genetics* / Q000502:physiology; D012275:Oryza / Q000235:genetics* / Q000378:metabolism / Q000502:physiology; D010100:Oxygen / Q000378:metabolism*; D010940:Plant Proteins / Q000235:genetics / Q000502:physiology; D036226:Seedlings / Q000235:genetics / Q000378:metabolism / Q000502:physiology; D059467:Transcriptome / Q000235:genetics*
chemical_list: D010940:Plant Proteins; D010100:Oxygen
keywords: DNA methylation; RNA-seq; low oxygen; rice