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Plant J. 2017 Feb;89(4):805-824. doi: 10.1111/tpj.13418. Epub 2017 Feb 11.

Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation.

Author information

1
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.
2
ARC Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, WA, 6009, Australia.
3
Genomic Analysis Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.
4
Howard Hughes Medical Institute, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA.

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.

KEYWORDS:

DNA methylation; RNA-seq; low oxygen; rice

PMID:
27859855
DOI:
10.1111/tpj.13418
[Indexed for MEDLINE]
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