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Transcript profiling of the hypomethylated hog1 mutant of Arabidopsis

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Abstract

Transcript profiling was used to look for genes that differ in expression between the SAH hydrolase deficient and hypomethylated hog1-1 mutant and the parental (HOG1) line. This analysis identified a subset of gene transcripts that were up-regulated in hog1-1 plants. The majority of these transcripts were from genes located in the pericentromeric heterochromatin. About a third of the genes are annotated as transposons or having transposon homology. Subsequent experiments using Northern blots, RT-PCR and real-time RT-PCR confirmed the up-regulation of 19 of the genes and identified a set of molecular probes for genes that are up-regulated in the hog1-1 background. Six (of six genes tested) of the hog1-1 up-regulated genes are also up-regulated in the hypomethylated ddm1 mutant, three in the hypomethylated met1 mutant and three in the dcl3 mutant. The results suggest that the hypomethylation in the mutant lines may have a causal role in the up-regulation of these transcripts.

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Acknowledgements

We would like to thank Sean May and John Okyere for carrying out the Affymetrix genechip hybridization and for valuable discussions. We would also like to thank the following people and organisations for seeds of mutant lines and/or clones; Emma Wigmore (NASC), ABRC, Marjorie Matzke, Steve Jacobsen and Eric Richards. The IQ5 machine was purchased with a grant from the Isaac Newton Trust. The work was funded directly by a BBSRC grant to IJF and indirectly by BBSRC support for GARNet and NASC.

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  1. Nicholas David Jordan

    Present address: Ambion, Spitfire Close, Ermine Business Park, Huntingdon, Cambridgeshire, PE29 6XY, UK

  2. Jonathan Paul West

    Present address: The Art of Meat, West and Son, 45 Arbury Court, Cambridge, CB4 2JQ, UK

  3. Andrew Bottley

    Present address: Department of Crop Genetics, John Innes Centre, Norwich, NR4 7UH, UK

Authors and Affiliations

  1. Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK

    Nicholas David Jordan, Jonathan Paul West, Andrew Bottley, Mazhar Sheikh & Ian Furner

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Correspondence to Ian Furner.

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Jordan, N.D., West, J.P., Bottley, A. et al. Transcript profiling of the hypomethylated hog1 mutant of Arabidopsis . Plant Mol Biol 65, 571–586 (2007). https://doi.org/10.1007/s11103-007-9221-4

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